https://info.gersteinlab.org/api.php?action=feedcontributions&feedformat=atom&user=Public 2026-04-12T12:43:08Z User contributions MediaWiki 1.42.6 https://info.gersteinlab.org/index.php?title=Onboarding&diff=6476 2026-04-05T20:05:15Z

<p>Public: /* EVERYONE */</p> <hr /> <div>The following are information for new members of the lab. There is information that applies to '''EVERYONE''', information that applies only to '''REGULAR MEMBERS''', and information that applies only to '''MEMBERS WITH INITIALS'''. Privileges increase successively with each category.<br /> <br /> <br /> == EVERYONE ==<br /> ' ''you are affiliated with the lab'' '<br /> <br /> * &lt;B&gt;REGISTER&lt;/B&gt; New people need to register at the MBB business office -- e.g. so they get paid! Get your Yale Netid. <br /> <br /> * &lt;B&gt;GETTING CONNECTED&lt;/B&gt; Coordinate with the sysadmin ([http://info.gersteinlab.org/Staff Mihali Felipe]) to give you access to various Gersteinlab resources. You will need to provide your Yale Net ID. He will: <br /> ** Add you to the ALL list<br /> ** Grant you [http://meetings.gersteinlab.org Lab Meeting] access<br /> <br /> * &lt;B&gt;WIRELESS &amp; PRINTING&lt;/B&gt; Please contact MF, SKL or JL to get into MBGMesh. <br /> <br /> * &lt;B&gt;YCRC/HPC&lt;/B&gt; To get an account in the Yale clusters, fill and submit the following form ([http://research.computing.yale.edu/support/hpc/account-request YCRC/HPC]). <br /> <br /> * &lt;B&gt;INSERT YOUR INFORMATION ON WIKI PEOPLE PAGE&lt;/B&gt;<br /> For the [http://www.gersteinlab.org/people/ people] page part, use this [https://forms.gle/3qdnBKEcEhkV3nDx9 link] to submit your information (for the first time). Mentors are supposed to inform their mentees to fill the form when they start. Contact Yuhang Chen directly if you need to updated any info later. Notice the ERA commons ID should be a string similar to your name, not a string of numbers.<br /> <br /> * &lt;B&gt;WEEKLY MEETINGS&lt;/B&gt;<br /> ** &lt;B&gt;Please check your email frequently&lt;/B&gt; New people should check their emails (from ALL@GERSTEINLAB.ORG) for P1-all, gpmtg, and jclub announcements.<br /> ** A reasonable expectation for most of the people of the group is to be available for meetings during normal working hours, Monday to Friday. Obviously, for some people this is not possible. For those people, you should be very attentive to meeting times and try the utmost to be able to make meetings and inform Mark Gerstein (MG) of your bad times.<br /> <br /> ** &lt;B&gt;Meeting abbreviation and participants&lt;/B&gt;<br /> P1 - orientation with everyone<br /> P2 - subgroups for presentations such as related to Human Genome Annotation (ENCODE)<br /> indiv - individual or small group meetings <br /> gpmtg - Group meeting where all attend for the presentation of lab research<br /> jclub - Journal Club for the presentation of research outside of the lab<br /> <br /> * &lt;B&gt;MEETING&lt;/B&gt; When you have the account that can access the private web page, you should be able to log in and see this 'cryptical' [http://wiki.gersteinlab.org/labinfo/Main_Page#Meetings.2C_Presentations meeting information]<br /> <br /> * &lt;B&gt;SOCIAL MEDIA&lt;/B&gt; Join our lab on social media. This list is in order of priority (and in reverse order of entertainment).<br /> ** [https://www.linkedin.com/groups/11900219/ LinkedIn]<br /> ** [https://twitter.com/GersteinLab Twitter]<br /> ** [https://www.facebook.com/groups/54856837624/ Facebook]<br /> <br /> * &lt;B&gt;ACCOUNTS TO RESOURCES&lt;/B&gt; are summarized here:<br /> ** [http://accounts.gersteinlab.org/summary Accounts] <br /> ** [https://docs.google.com/document/d/1vR7qyB2baLvXgEfgwvxXiXJtrGzut-eFugcorY3TkYQ/edit?usp=drive_link Guide to obtaining and using HPC accounts]<br /> <br /> ----<br /> <br /> == REGULAR MEMBERS ==<br /> ' ''you are not a temporary member of the lab'' '<br /> <br /> In addition to the above, you would need the following:<br /> <br /> * &lt;B&gt;DESK &amp; KEYS&lt;/B&gt; Coordinate with [http://info.gersteinlab.org/Staff Lisa Adams] to get a desk and have access to the building and rooms.<br /> <br /> * &lt;B&gt;COMPUTER &amp; MONITOR&lt;/B&gt; We are a computing lab and you would generally need a computer to be productive. You might even need a monitor. Contact JL (Jason Liu) to request a laptop or desktop, and a monitor.<br /> <br /> * &lt;B&gt;eRA commons ID&lt;/B&gt; New people need to apply for an eRA commons ID.<br /> <br /> * &lt;B&gt;MORE RESOURCES&lt;/B&gt; Coordinate with the sysadmin ([http://info.gersteinlab.org/Staff Mihali Felipe]). He will:<br /> ** Grant you [http://info.gersteinlab.org/Lab_Dropbox Lab Dropbox] access<br /> ** Grant you gw.gersteinlab.org SSH access<br /> ** Grant you [http://info.gersteinlab.org/Calendar Calendar] access (GLCAL)<br /> ** Add you to the lab Slack Workspace [gerstein-lab.slack.com]<br /> <br /> * &lt;B&gt;CLASS SCHEDULE&lt;/B&gt; <br /> If you are taking classes, you need to put the schedule for your classes in the groups calendar. To do so, first go to http://partnerpage.google.com/gersteinlab.org and login. <br /> You will need to use your @gersteinlab.org account to do so. You will also have to get a member of the lab to share the calendar with you and you would need to add the URL of the <br /> calendar explicitly:<br /> i.e. http://www.google.com/calendar/ical/gersteinlab.org_250u3al9jepssp14pk039tsnlg%40group.calendar.google.com/public/basic.ics <br /> This will allow you to view/edit it. After logging in, simply go to the calendar and add an event with the class for all the times and days in which it happens.<br /> <br /> ----<br /> <br /> == MEMBERS WITH INITIALS ==<br /> ' ''exactly as described'' '<br /> <br /> In addition to the above, you would need the following:<br /> <br /> * '''BIOS''' Add your [https://docs.google.com/document/d/1EkxjRHpMJRpL7jRCLHA2fk1Q0__WhWD1sI82cfbUPkc/edit Lab member bio].<br /> <br /> * &lt;B&gt;EVEN MORE RESOURCES&lt;/B&gt; Coordinate with the sysadmin ([http://info.gersteinlab.org/Staff Mihali Felipe]). He will: <br /> ** Grant you [http://bit.ly/mglab-folder Google Folder] access. If your mbglab folder access is restricted, please timely contract with [http://info.gersteinlab.org/Staff Mihali] and add you to all the shares in the mbglab folder files. You can get detailed information about the shared cloud through [[Documentation on Shared Google Folder &amp; Dropbox Folder]].<br /> <br /> ----<br /> <br /> == PAST MEMBERS ==<br /> <br /> * &lt;B&gt;ADDING/REMOVING PEOPLE TO RESOURCES&lt;/B&gt;<br /> [https://docs.google.com/spreadsheets/d/1PoArdIGHz7Vem1Vqll534_-ap2N3AU1dQ8aAm_WpZQY/edit?usp=sharing Includes/Exceptions Spreadsheet]<br /> <br /> ----<br /> <br /> == OLD ONBOARDING ==<br /> ' ''mostly all the information above but arranged differently'' '<br /> <br /> This is a summary of procedures for new people entering the laboratory. Current people might want to keep these in mind and help out new people with these.<br /> <br /> * &lt;B&gt;REGISTER&lt;/B&gt; New people need to register at the MBB business office -- e.g. so they get paid! Get your Yale Netid. <br /> <br /> * &lt;B&gt;DESK &amp; KEYS&lt;/B&gt; Coordinate with [http://info.gersteinlab.org/Staff Lisa Adams] to get a desk and have access to the building and rooms.<br /> <br /> * &lt;B&gt;COMPUTER&lt;/B&gt; We are a computing lab and you would generally need a computer to be productive. Contact JL (Jason Liu) to request a laptop or desktop.<br /> <br /> * &lt;B&gt;WIRELESS &amp; PRINTING&lt;/B&gt; Please contact MF to get into MBGMesh. <br /> <br /> * &lt;B&gt;YCRC/HPC&lt;/B&gt; To get an account in the Yale clusters ([http://research.computing.yale.edu/support/hpc/account-request YCRC/HPC]), fill and submit the following form. <br /> * &lt;B&gt;eRA commons ID&lt;/B&gt; New people need to apply for an eRA commons ID.<br /> <br /> * &lt;B&gt;MISC&lt;/B&gt; Coordinate with the sysadmin ([http://info.gersteinlab.org/Staff Mihali Felipe]) to give you access to various Gersteinlab resources. You will need to provide your Yale Net ID. He will: <br /> ** Add you to the ALL list<br /> ** Grant you [http://gw.gersteinlab.org gw.gersteinlab.org] access<br /> ** Grant you [http://info.gersteinlab.org/Calendar Calendar] access (GLCAL)<br /> ** Grant you [http://meetings.gersteinlab.org Lab Meeting] access<br /> ** Grant you [http://info.gersteinlab.org/Lab_Dropbox Lab Dropbox] access<br /> ** Grant you [http://bit.ly/mglab-folder Google Folder] access. If your mbglab folder access is restricted, please timely contract with [http://info.gersteinlab.org/Staff Mihali] and add you to all the shares in the mbglab folder files. You can get detailed information about the shared cloud through [[Documentation on Shared Google Folder &amp; Dropbox Folder]].<br /> <br /> * &lt;B&gt;MEETING&lt;/B&gt; When you have the account that can access the private web page, you should be able to log in and see this 'cryptical' [http://wiki.gersteinlab.org/labinfo/Main_Page#Meetings.2C_Presentations meeting information]<br /> <br /> <br /> * &lt;B&gt;INSERT YOUR INFORMATION ON WIKI PEOPLE PAGE&lt;/B&gt;<br /> For the [http://www.gersteinlab.org/people/ people] page part, use this [https://forms.gle/kZdZkjCk3G1gEXhw9 link] to update your information. And you need to contact JG(Jiahao Gao) to make sure all your information is correct on the roster (incl. cell phone number)<br /> Please notice that:<br /> [1] New people will fill the form through the link and then JG will edit the final google sheet.<br /> [2] If you have initials you have all, but if you don't have initials and you just on the all list &amp; dropbox, please add listed on the people page. <br /> The summary of the current state of email addresses is at: http://accounts.gersteinlab.org/summary/group_all.diff.txt<br /> (Username public &amp; public password)<br /> After this your names will appear on people page http://www.gersteinlab.org/people/<br /> [3] For further questions or if you want to update your information, please contact JG.<br /> <br /> * &lt;B&gt;WEEKLY MEETINGS&lt;/B&gt;<br /> ** &lt;B&gt;Please check your email frequently&lt;/B&gt; New people should check their emails (from ALL@GERSTEINLAB.ORG) for P1-all, gpmtg, and jclub announcements. <br /> <br /> ** &lt;B&gt;Meeting abbreviation and participants&lt;/B&gt;<br /> P1 - orientation with everyone<br /> P2 - subgroups for presentations such as related to Human Genome Annotation (ENCODE)<br /> indiv - individual or small group meetings <br /> gpmtg - Group meeting where all attend for the presentation of lab research<br /> jclub - Journal Club for the presentation of research outside of the lab<br /> <br /> * &lt;B&gt;CLASS SCHEDULE&lt;/B&gt; <br /> If you are taking classes, you need to put the schedule for your classes in the groups calendar. To do so, first go to http://partnerpage.google.com/gersteinlab.org and login. <br /> You will need to use your @gersteinlab.org account to do so. You will also have to get a member of the lab to share the calendar with you and you would need to add the URL of the <br /> calendar explicitly:<br /> i.e. http://www.google.com/calendar/ical/gersteinlab.org_250u3al9jepssp14pk039tsnlg%40group.calendar.google.com/public/basic.ics <br /> This will allow you to view/edit it. After logging in, simply go to the calendar and add an event with the class for all the times and days in which it happens.<br /> <br /> * &lt;B&gt;SOCIAL MEDIA&lt;/B&gt; Join our lab on social media. This list is in order of priority (and in reverse order of entertainment).<br /> ** [https://www.linkedin.com/groups/11900219/ LinkedIn]<br /> ** [https://twitter.com/GersteinLab Twitter]<br /> ** [https://www.facebook.com/groups/54856837624/ Facebook]</div>

Public https://info.gersteinlab.org/index.php?title=Lab_Address&diff=6475 2026-04-05T20:00:39Z

<p>Public: /* Admin Assistant */</p> <hr /> <div>==PI Contact Address==<br /> Mark Gerstein, '''[http://contact.gerstein.info contact.gerstein.info]'''<br /> <br /> <br /> __TOC__<br /> ==Admin Assistant==<br /> Carrie Nardella&lt;BR&gt;<br /> 266 Whitney Ave, Bass 432, New Haven, CT 06520&lt;BR&gt;<br /> Carrie.Nardella@yale.edu&lt;BR&gt;<br /> Ph: 203-432-8189<br /> Fax: 203-432-6946<br /> <br /> ==Main Room Numbers==<br /> *Lab Offices - Bass 426: 203-432-8972<br /> *Lab Offices - Bass 428: 203-432-5065<br /> *Conference Room - Bass 434: 203-436-4442<br /> *Lab Offices - Bass 437: 203-432-5405<br /> *Lab Offices - Bass 341<br /> *Lab Offices - YSB 350<br /> *Lab Offices - 100 College Street, 9th Floor, Section A9, Desk A920.40 to A920.66 and Office A952A<br /> ** Directions: From the elevator, enter through the 'A' section and proceed directly to [https://www.dropbox.com/scl/fi/w0k7dhgxhjcmnnyitlg5n/2024-02-02-09.14.49.Location-of-Gerstein-Lab-at-100-College.A9.Right-from-elevator-n-straight-through.jpg?rlkey=4x42d7wgtj20v0vwj8vli8brd&amp;e=1&amp;dl=0 section A9]<br /> * West Campus rooms (in Building 900): WW108, WW110, WW113A (Server Room)<br /> ** [[Mihali Felipe]] (sysadm) (Emergencies only: 203-623-8873)<br /> ** There are no phone numbers in the West campus offices<br /> *Bass 432A <br /> ** Analog Phone Line for Conference Calls (203-432-3923)<br /> <br /> ==100 College Office==<br /> * '''Lab Offices''' - 100 College Street, 9th Floor, Section A9<br /> ** Desks: A920.40 to A920.66 ([https://docs.google.com/spreadsheets/d/1aNwiQFXwg5unuo607vs9RhvI1PI2wi6k1W4qOPrVziE/edit#gid=1619217485 Desk Layout])<br /> ** Directions: From the elevator, enter through the 'A' section and proceed directly to [https://www.dropbox.com/scl/fi/w0k7dhgxhjcmnnyitlg5n/2024-02-02-09.14.49.Location-of-Gerstein-Lab-at-100-College.A9.Right-from-elevator-n-straight-through.jpg?rlkey=4x42d7wgtj20v0vwj8vli8brd&amp;e=1&amp;dl=0 section A9]<br /> <br /> * '''Shared Conference Room''' - 100 College Street, 9th Floor<br /> ** Rooms: A926, A927<br /> <br /> ==Other Useful Numbers and Locations==<br /> *Bass 424: Shared conference room on Bass 4th floor<br /> &lt;!-- *Bass 425: 203-432-5599 --&gt;<br /> *100 College A926, A927: Shared conference room on 100 College 9th floor<br /> <br /> == Laboratory Floor Plans &amp; Room Instructions ==<br /> *[[Bass Fourth Floor]]<br /> *West Campus: [http://archive.gersteinlab.org/docs/2016/09.28/WestCampus.pdf Room Plans] + [https://www.dropbox.com/s/7og7f9hycc70rus/2018-08-14%2016.21.56.jpg?dl=0 Pic of Closet] + [[West Campus - Room H110 Allocation Details]]<br /> *[[Square Footage of Assigned Rooms]]<br /> *[[Room Temperatures]]<br /> *Desk Layout: [https://docs.google.com/spreadsheets/d/1aNwiQFXwg5unuo607vs9RhvI1PI2wi6k1W4qOPrVziE/edit#gid=1619217485 New] (private), [https://docs.google.com/presentation/d/16eDPLAC76DcMaCcnMsRcqKV1ggm4sbJ0ikofTPsUaBo/pub?start=false&amp;loop=false&amp;delayms=3000 Old] (public)<br /> <br /> ==Directions and Maps==<br /> * Bass<br /> We're mostly located on the fourth floor of the [http://www.gersteinlab.org/people/bass.jpg Bass Building], which is located at 266 Whitney Avenue. It faces the Biology department in Klein Tower. Click [http://www.gersteinlab.org/people/gerstein-map.html here] for an interactive satellite image of the Science Hill area from Google maps. Follow the link for an interactive [http://www.facilities.yale.edu/campus/Imapnew.asp campus map] and information for the [http://www.facilities.yale.edu/Campus/building1.asp?lstbldg=1030&amp;sec=3 Bass Center] from buildings &amp; grounds.<br /> * Access to Bass During Gibbs Demolition and Subsequent Construction (Dec '16 to TBD):<br /> Please see following link for specific entrances/exits to be used during construction: [http://yalesciencebuilding.yale.edu/construction-impact/area-access-pedestrian-impact Area Access &amp; Pedestrian Impact]. One nice way to get to us is to go in via the chemistry main entrance at 225 Prospect &amp; then go up one flight. Go past the labs and take the first right and then the first left. A few steps further and you will be pleasantly surprised to find the sky-bridge to Bass on your right. Take aforementioned sky-bridge directly on to the 4th floor of Bass where all the group offices are located. For those dependent on visual cues to get through life, see highlighted route: [http://files.gersteinlab.org/public-docs/2017/05.05/SCL_route_to_Bass.pdf Access to Bass through SCL]<br /> * Getting to Yale<br /> General [http://www.yale.edu/directions.html Directions] to Yale University are posted on the University webserver. These include a detailed University [http://www.yale.edu/yaleinfo/maps/5.html map] locating the Bass building in the Science Hill area. Directions locating the Bass building on Science Hill is available [http://www.gersteinlab.org/people/directions.html here]. (Some of these maps are locally [http://bioinfo.mbb.yale.edu/~mbg/yale-maps mirrored]; in particular, a [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/ConnAndVicinityReliefMap.gif relief map] of Connecticut and a map of the [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/TownsOfGreaterNewHaven.gif towns] in the New Haven area).<br /> * Taxi<br /> Good locations to take a taxi to are either 225 Prospect St. or 350 Edwards St.<br /> <br /> ==Rail==<br /> [https://new.mta.info/agency/new-york-city-transit/ Metro-North] and [http://www.amtrak.com/ Amtrak] service to New Haven (Taxis available at station.)<br /> <br /> ==Driving and Parking==<br /> ===From Boston===<br /> #Take Mass Pike to Interstate 84. <br /> #Take Interstate 84 South to Hartford.<br /> #Take Interstate 91 South to New Haven.<br /> #Take Exit 3 off of Interstate 91.<br /> #Turn right at the stoplight at the end of the exit ramp onto Orange Street. <br /> #Turn left onto Humphrey Street at next stoplight. <br /> #Proceed through the next stoplight into the parking lot (Lot 16). <br /> <br /> ===From New York===<br /> #Take Interstate 95 North to Interstate 91 at New Haven<br /> #Take exit 3 off Interstate 91. <br /> #Turn right at the stoplight at the end of the exit ramp onto Orange Street.<br /> #Turn left onto Humphrey Street at next stoplight.<br /> #Proceed through the next stoplight into the parking lot (Lot 16). <br /> (Before getting on 95, it's nice to take the Merritt. You might want to follow this [http://www.gersteinlab.org/people/ny-to-ct.gif route].)<br /> <br /> ===Parking===<br /> *16V <br /> Right after entering on 266 Whitney there's a pay lot, called 16V. See [https://en.parkopedia.com/parking/lot/lot_16v/06511/new_haven/?arriving=201809171500&amp;leaving=201809171700 parkopedia] and [https://your.yale.edu/community/getting-around-yale/parking/parking-locations Yale parking] for info. After parking here, it's best to enter Bass via the &quot;loading dock&quot; entrance, which remains open during YSB construction. <br /> *Edwards St.<br /> There is a parking lot on Edwards St available for visitors. Parking &quot;lot 29&quot; is called [https://www.google.com/maps/place/Pierson-Sage+Garage Pierson-Sage Garage]. A code is required to enter.<br /> Please contact your host or &quot;Lisa&quot; for the possibility of getting a code. You must exit the same way you entered.<br /> *After hours<br /> NOTE: There is also free open-surface parking after 4PM which remains open until 7AM. The lots are located on 260-266 Whitney Avenue, anywhere you seen an open gate.<br /> <br /> ==Other Stuff==<br /> [https://www.tripadvisor.com/Restaurants-g33851-New_Haven_Connecticut.html Tripadvisor: Nearby Restaurants], [https://theshopsatyale.com/dine/ Dining Near The Shops at Yale], [http://maps.yahoo.com/py/maps.py?Pyt=Tmap&amp;YY=28780&amp;addr=266%20Whitney%20Avenue&amp;city=New%20Haven&amp;state=CT&amp;slt=41.3180&amp;sln=-72.9199&amp;zip=06520&amp;mag=10&amp;cs=9&amp;newmag=9 Map of Bass Area], [http://yp.yahoo.com/py/ypMap.py?Pyt=Tmap&amp;YY=8688&amp;addr=266%20Whitney%20Avenue&amp;city=NEW%20HAVEN&amp;state=CT&amp;country=US&amp;slt=41.3180&amp;sln=-72.9199&amp;zip=06520&amp;mag=9&amp;cs=9&amp;stx=7737307&amp;stp=y&amp;ycat=7737307&amp;l=11&amp;tuid=566518&amp;tq=8&amp;btype=default Colony Inn] (nearby hotel), [http://yp.yahoo.com/py/ypResults.py?Pyt=Tmap&amp;YY=32031&amp;addr=266%20Whitney%20Avenue&amp;city=NEW%20HAVEN&amp;state=CT&amp;zip=06520&amp;slt=&amp;sln=&amp;cs=9&amp;stp=y&amp;stx=8014796&amp;btype=default Taxi] services.<br /> <br /> ==List of addresses==<br /> *ars &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - to ARS + MG <br /> *pi &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - MG for manuscripts &amp; conf.<br /> *piaa &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - MG &amp; his asst. <br /> *subs &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - magazine subscriptions <br /> *Mark &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - for google docs &amp; main address &amp; for gcal invites<br /> <br /> ==Old Stuff==<br /> *[http://archive.gersteinlab.org/docs/2017/04.04/PastedGraphic-1.png Chemical and Biophysical Instrumentation Center] (Has floorplan of SCL pertinent to Gerstein Lab space)</div>

Public https://info.gersteinlab.org/index.php?title=Lab_Address&diff=6474 2026-04-05T20:00:26Z

<p>Public: /* Admin Assistant */</p> <hr /> <div>==PI Contact Address==<br /> Mark Gerstein, '''[http://contact.gerstein.info contact.gerstein.info]'''<br /> <br /> <br /> __TOC__<br /> ==Admin Assistant==<br /> Carrie.Nardella&lt;BR&gt;<br /> 266 Whitney Ave, Bass 432, New Haven, CT 06520&lt;BR&gt;<br /> Carrie.Nardella@yale.edu&lt;BR&gt;<br /> Ph: 203-432-8189<br /> Fax: 203-432-6946<br /> <br /> ==Main Room Numbers==<br /> *Lab Offices - Bass 426: 203-432-8972<br /> *Lab Offices - Bass 428: 203-432-5065<br /> *Conference Room - Bass 434: 203-436-4442<br /> *Lab Offices - Bass 437: 203-432-5405<br /> *Lab Offices - Bass 341<br /> *Lab Offices - YSB 350<br /> *Lab Offices - 100 College Street, 9th Floor, Section A9, Desk A920.40 to A920.66 and Office A952A<br /> ** Directions: From the elevator, enter through the 'A' section and proceed directly to [https://www.dropbox.com/scl/fi/w0k7dhgxhjcmnnyitlg5n/2024-02-02-09.14.49.Location-of-Gerstein-Lab-at-100-College.A9.Right-from-elevator-n-straight-through.jpg?rlkey=4x42d7wgtj20v0vwj8vli8brd&amp;e=1&amp;dl=0 section A9]<br /> * West Campus rooms (in Building 900): WW108, WW110, WW113A (Server Room)<br /> ** [[Mihali Felipe]] (sysadm) (Emergencies only: 203-623-8873)<br /> ** There are no phone numbers in the West campus offices<br /> *Bass 432A <br /> ** Analog Phone Line for Conference Calls (203-432-3923)<br /> <br /> ==100 College Office==<br /> * '''Lab Offices''' - 100 College Street, 9th Floor, Section A9<br /> ** Desks: A920.40 to A920.66 ([https://docs.google.com/spreadsheets/d/1aNwiQFXwg5unuo607vs9RhvI1PI2wi6k1W4qOPrVziE/edit#gid=1619217485 Desk Layout])<br /> ** Directions: From the elevator, enter through the 'A' section and proceed directly to [https://www.dropbox.com/scl/fi/w0k7dhgxhjcmnnyitlg5n/2024-02-02-09.14.49.Location-of-Gerstein-Lab-at-100-College.A9.Right-from-elevator-n-straight-through.jpg?rlkey=4x42d7wgtj20v0vwj8vli8brd&amp;e=1&amp;dl=0 section A9]<br /> <br /> * '''Shared Conference Room''' - 100 College Street, 9th Floor<br /> ** Rooms: A926, A927<br /> <br /> ==Other Useful Numbers and Locations==<br /> *Bass 424: Shared conference room on Bass 4th floor<br /> &lt;!-- *Bass 425: 203-432-5599 --&gt;<br /> *100 College A926, A927: Shared conference room on 100 College 9th floor<br /> <br /> == Laboratory Floor Plans &amp; Room Instructions ==<br /> *[[Bass Fourth Floor]]<br /> *West Campus: [http://archive.gersteinlab.org/docs/2016/09.28/WestCampus.pdf Room Plans] + [https://www.dropbox.com/s/7og7f9hycc70rus/2018-08-14%2016.21.56.jpg?dl=0 Pic of Closet] + [[West Campus - Room H110 Allocation Details]]<br /> *[[Square Footage of Assigned Rooms]]<br /> *[[Room Temperatures]]<br /> *Desk Layout: [https://docs.google.com/spreadsheets/d/1aNwiQFXwg5unuo607vs9RhvI1PI2wi6k1W4qOPrVziE/edit#gid=1619217485 New] (private), [https://docs.google.com/presentation/d/16eDPLAC76DcMaCcnMsRcqKV1ggm4sbJ0ikofTPsUaBo/pub?start=false&amp;loop=false&amp;delayms=3000 Old] (public)<br /> <br /> ==Directions and Maps==<br /> * Bass<br /> We're mostly located on the fourth floor of the [http://www.gersteinlab.org/people/bass.jpg Bass Building], which is located at 266 Whitney Avenue. It faces the Biology department in Klein Tower. Click [http://www.gersteinlab.org/people/gerstein-map.html here] for an interactive satellite image of the Science Hill area from Google maps. Follow the link for an interactive [http://www.facilities.yale.edu/campus/Imapnew.asp campus map] and information for the [http://www.facilities.yale.edu/Campus/building1.asp?lstbldg=1030&amp;sec=3 Bass Center] from buildings &amp; grounds.<br /> * Access to Bass During Gibbs Demolition and Subsequent Construction (Dec '16 to TBD):<br /> Please see following link for specific entrances/exits to be used during construction: [http://yalesciencebuilding.yale.edu/construction-impact/area-access-pedestrian-impact Area Access &amp; Pedestrian Impact]. One nice way to get to us is to go in via the chemistry main entrance at 225 Prospect &amp; then go up one flight. Go past the labs and take the first right and then the first left. A few steps further and you will be pleasantly surprised to find the sky-bridge to Bass on your right. Take aforementioned sky-bridge directly on to the 4th floor of Bass where all the group offices are located. For those dependent on visual cues to get through life, see highlighted route: [http://files.gersteinlab.org/public-docs/2017/05.05/SCL_route_to_Bass.pdf Access to Bass through SCL]<br /> * Getting to Yale<br /> General [http://www.yale.edu/directions.html Directions] to Yale University are posted on the University webserver. These include a detailed University [http://www.yale.edu/yaleinfo/maps/5.html map] locating the Bass building in the Science Hill area. Directions locating the Bass building on Science Hill is available [http://www.gersteinlab.org/people/directions.html here]. (Some of these maps are locally [http://bioinfo.mbb.yale.edu/~mbg/yale-maps mirrored]; in particular, a [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/ConnAndVicinityReliefMap.gif relief map] of Connecticut and a map of the [http://bioinfo.mbb.yale.edu/~mbg/yale-maps/TownsOfGreaterNewHaven.gif towns] in the New Haven area).<br /> * Taxi<br /> Good locations to take a taxi to are either 225 Prospect St. or 350 Edwards St.<br /> <br /> ==Rail==<br /> [https://new.mta.info/agency/new-york-city-transit/ Metro-North] and [http://www.amtrak.com/ Amtrak] service to New Haven (Taxis available at station.)<br /> <br /> ==Driving and Parking==<br /> ===From Boston===<br /> #Take Mass Pike to Interstate 84. <br /> #Take Interstate 84 South to Hartford.<br /> #Take Interstate 91 South to New Haven.<br /> #Take Exit 3 off of Interstate 91.<br /> #Turn right at the stoplight at the end of the exit ramp onto Orange Street. <br /> #Turn left onto Humphrey Street at next stoplight. <br /> #Proceed through the next stoplight into the parking lot (Lot 16). <br /> <br /> ===From New York===<br /> #Take Interstate 95 North to Interstate 91 at New Haven<br /> #Take exit 3 off Interstate 91. <br /> #Turn right at the stoplight at the end of the exit ramp onto Orange Street.<br /> #Turn left onto Humphrey Street at next stoplight.<br /> #Proceed through the next stoplight into the parking lot (Lot 16). <br /> (Before getting on 95, it's nice to take the Merritt. You might want to follow this [http://www.gersteinlab.org/people/ny-to-ct.gif route].)<br /> <br /> ===Parking===<br /> *16V <br /> Right after entering on 266 Whitney there's a pay lot, called 16V. See [https://en.parkopedia.com/parking/lot/lot_16v/06511/new_haven/?arriving=201809171500&amp;leaving=201809171700 parkopedia] and [https://your.yale.edu/community/getting-around-yale/parking/parking-locations Yale parking] for info. After parking here, it's best to enter Bass via the &quot;loading dock&quot; entrance, which remains open during YSB construction. <br /> *Edwards St.<br /> There is a parking lot on Edwards St available for visitors. Parking &quot;lot 29&quot; is called [https://www.google.com/maps/place/Pierson-Sage+Garage Pierson-Sage Garage]. A code is required to enter.<br /> Please contact your host or &quot;Lisa&quot; for the possibility of getting a code. You must exit the same way you entered.<br /> *After hours<br /> NOTE: There is also free open-surface parking after 4PM which remains open until 7AM. The lots are located on 260-266 Whitney Avenue, anywhere you seen an open gate.<br /> <br /> ==Other Stuff==<br /> [https://www.tripadvisor.com/Restaurants-g33851-New_Haven_Connecticut.html Tripadvisor: Nearby Restaurants], [https://theshopsatyale.com/dine/ Dining Near The Shops at Yale], [http://maps.yahoo.com/py/maps.py?Pyt=Tmap&amp;YY=28780&amp;addr=266%20Whitney%20Avenue&amp;city=New%20Haven&amp;state=CT&amp;slt=41.3180&amp;sln=-72.9199&amp;zip=06520&amp;mag=10&amp;cs=9&amp;newmag=9 Map of Bass Area], [http://yp.yahoo.com/py/ypMap.py?Pyt=Tmap&amp;YY=8688&amp;addr=266%20Whitney%20Avenue&amp;city=NEW%20HAVEN&amp;state=CT&amp;country=US&amp;slt=41.3180&amp;sln=-72.9199&amp;zip=06520&amp;mag=9&amp;cs=9&amp;stx=7737307&amp;stp=y&amp;ycat=7737307&amp;l=11&amp;tuid=566518&amp;tq=8&amp;btype=default Colony Inn] (nearby hotel), [http://yp.yahoo.com/py/ypResults.py?Pyt=Tmap&amp;YY=32031&amp;addr=266%20Whitney%20Avenue&amp;city=NEW%20HAVEN&amp;state=CT&amp;zip=06520&amp;slt=&amp;sln=&amp;cs=9&amp;stp=y&amp;stx=8014796&amp;btype=default Taxi] services.<br /> <br /> ==List of addresses==<br /> *ars &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - to ARS + MG <br /> *pi &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - MG for manuscripts &amp; conf.<br /> *piaa &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - MG &amp; his asst. <br /> *subs &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - magazine subscriptions <br /> *Mark &lt;&lt;[[a]][[t]]&gt;&gt; gersteinlab &lt;&lt;[[dot]]&gt;&gt; org - for google docs &amp; main address &amp; for gcal invites<br /> <br /> ==Old Stuff==<br /> *[http://archive.gersteinlab.org/docs/2017/04.04/PastedGraphic-1.png Chemical and Biophysical Instrumentation Center] (Has floorplan of SCL pertinent to Gerstein Lab space)</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6470 2026-02-27T10:56:21Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2026/02.27/g0screenrt--summary.docx Gerstein lab experience with predicting allosteric residues and protein-ligand binding affinities] uploaded by DC on Feb 27 2026 (g0screenrt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/12.17/summary_mc-01.docx Gerstein lab experience with eQTLs, sequence variation, protein disorder, and 3D docking] uploaded by DC on Dec 17 2025 (g0sanofi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/12.17/summary_mc-01.docx Gerstein lab experience with eQTLs, sequence variation, and 3D docking] uploaded by DC on Dec 17 2025 (g0mcknight)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/10.27/g0biomedx_Summary.pdf Gerstein lab experience with construction of cell-type specific gene regulatory networks (GRNs)] uploaded by Mor on Oct 27 2025 (g0biomedx)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/09.09/g0sony2_summary.docx Gerstein lab experience with molecular mechanisms underlying diseases using large language models (LLMs)] uploaded by MOR on Sep 9 2025 (g0sony2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0laadsi--summary.docx Gerstein lab experience in building a tools for (a) predicting protein-compound interaction strengths and (b) building gene regulatory networks] uploaded by DC on Jun 30 2025 (g0laadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Pubmed_query&diff=6464 2026-01-08T16:37:17Z

<p>Public: /* Notes on Publication List */</p> <hr /> <div>==Other Views==<br /> <br /> There are a number of simplified views of the papers page available, with no extra links, viz:<br /> [http://papers.gersteinlab.org/simple.html '''title-first listing'''] and [http://papers.gersteinlab.org/papers/papers-simple.html traditional author-first listing]<br /> (These are suitable for copying into Word.) Also, here's a simple [http://papers.gersteinlab.org/papers directory listing] with all the paper IDs.<br /> <br /> ==Notes on Publication List==<br /> <br /> <br /> [https://files.gersteinlab.org/public-docs/2026/01.08/Notes_on_publications_20251216.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2025/02.17/Notes-on-publications--FROM--MG-truncate-CV-public-FAR24-end24bld-no-pgnum.cv57.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> <br /> [https://www.dropbox.com/scl/fi/g7ll9amhfnn90a23tgt2i/Notes-on-publications-FROM-M-Gerstein-CV-bld6Jan24-Public-CV-Jan-2024.cv57.pdf?rlkey=3xvtph03hkpm3ca6x461pmw6g&amp;dl=0 Information on Corresponding Author and Citation Stats of Gerstein Lab Papers]<br /> --&gt;<br /> <br /> ==PubMed Queries==<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D+NOT+preprint%5Bpt%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 12/1/2025)'''] to build papers page into PubMed without Preprints<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 7/21/2020)'''] to build papers page into PubMed<br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Query'''] to build papers page into PubMed<br /> <br /> * ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+10787728%5BUID%5D+NOT+11744447%5BUID%5D+NOT+14663468%5BUID%5D+NOT+14730174%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+17270657%5BUID%5D+NOT+21243890%5BUID%5D+NOT+21406498%5BUID%5D+NOT+21945273%5BUID%5D+NOT+28562279%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Old Query'''])<br /> <br /> * [http://linkstream2.gerstein.info/2013/11/30/pubmed-help-searching-for-specific-last-and-first-authors-3 Useful stuff in searching for specific last or first authors], which can result in some [[Useful Stats on Gerstein Lab Papers]]<br /> <br /> * [[Papers published with individuals who have left]] Yale <br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/myncbi/mark.gerstein.1/bibliography/44005333/public My NCBI] link of 445 M Gerstein papers as of Feb 2015 with PMIDs (via mark at gersteinlab user)<br /> <br /> ==Publication Analysis Services==<br /> <br /> * Google Scholar: '''http://scholar.google.ca/scholar?q=author:gerstein-m''' ([https://scholar.google.com/citations?hl=en&amp;view_op=search_authors&amp;mauthors=yale Ranking] of Yale researchers according to Scholar - we do well.) <br /> <br /> * [http://orcid.org/0000-0002-9746-3719 ORCID.org/0000-0002-9746-3719] for M Gerstein (very incomplete)<br /> <br /> * Highly Cited Researchers lists<br /> ** [https://linkstream2.gerstein.info/2016/11/21/archives-hcr-clarivate-analytics Thomson Reuters HIGHLY CITED RESEARCHERS (HCR) List] (on this '14, '15, '16)<br /> ** [https://hcr.clarivate.com Clarivate List] (supersedes above, on this in '17 &amp; '18)<br /> <br /> ==Paper Search==<br /> <br /> Adopted from [[Paper_search]]<br /> <br /> ===Medline Queries:===<br /> <br /> [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=PureSearch&amp;db=PubMed&amp;details_term=%28%28Gerstein%20M%5BAuthor%5D%20NOT%20%281963%5Bdp%5D%20%3A%201990%5Bdp%5D%29%29%20NOT%2011744447%5BUID%5D%20NOT%2010787728%5BUID%5D%29&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] / [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&amp;db=m&amp;term=Gerstein+M&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] (unrestricted) /<br /> [http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gerstein:Mark.html DBLP] / [http://liinwww.ira.uka.de/searchbib/index?query=GersteinM CS Bibliographies] /<br /> [http://citeseer.nj.nec.com/cs?cs=1&amp;q=m+gerstein+or+mark+gerstein&amp;co=Expected+Citations&amp;cm=50&amp;cf=Any&amp;ao=Expected+Citations&amp;am=20&amp;af=Any CiteSeer]<br /> <br /> http://pubnet.gersteinlab.org/images/mainlogo.jpg<br /> <br /> PubNet Graph of Gerstein Lab Publications ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5bdp%5d))%20NOT%2011744447%5BUID%5d%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607170530 cached])<br /> <br /> PubNet Graph of Gerstein and Montelione papers [http://www.nesg.org/ NESG] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=Gaetano%20Montelione&amp;query2=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171018 cached])<br /> <br /> PubNet Graph of Gerstein and Snyder papers [http://bioinfo.mbb.yale.edu/array/ CEGS] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;query2=snyder%20m%20and%20yale&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171429 cached])<br /> <br /> ===Lists of Papers===<br /> <br /> [http://papers.gersteinlab.org/index.html Main]<br /> [http://papers.gersteinlab.org/papers/papers-simple.html Simple]<br /> [http://papers.gersteinlab.org/papers/papers-ids.htm Table]<br /> [http://papers.gersteinlab.org/papers/papers-tags.htm XML tags]<br /> [http://papers.gersteinlab.org/papers/before97.shtml Pre 1997]<br /> [[Other_Papers]]<br /> <br /> ===Pre-prints:===<br /> <br /> [http://papers.gersteinlab.org/e-print E-print &lt;sup&gt;&amp;dagger;&lt;/sup&gt;] with full-text of some papers in press ([http://papers.gersteinlab.org/papers/help.shtml help] on this)<br /> <br /> &lt;sup&gt;&amp;dagger;&lt;/sup&gt;[http://www.gersteinlab.org/misc/permissions.html Please see our copyright statement]<br /> <br /> ==Sortable Lists of Publication Metrics==<br /> <br /> ===Sortable spreadsheets of Google Scholar &amp; Web of Science &amp; Altmetric (Dec 4, 2019)===<br /> [https://drive.google.com/file/d/1p5_J7Y8nt0WvXE5V7J4XYZ6LEMuwOAUC/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1Kn8eEpLUzulOtDx_XBXVc1jzb0pJNL2w/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1TmN_e8Fm3Cy4kKD8ILHl7-CFQhsEbQJM/view?usp=sharing GScholar]<br /> <br /> &amp; that again w/ MG as last/first author<br /> <br /> [https://drive.google.com/file/d/1vAZbrivv_2yadY5YFyGvZYaz1o7CSkcz/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1lOHkuXbOZNY2k39NdtUm3lT3Xv0dP5pP/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1wttEpxxBJUM0Guq0P1zgfin-Tph9GNdc/view?usp=sharing GScholar]<br /> <br /> <br /> ===Overall citation stats (Dec 4, 2019)===<br /> 595 publications <br /> <br /> Cited 144003 times and h-index: 166 (GScholar)<br /> <br /> No. papers with over 1000 citations each ------ No. all papers - 22 (No. papers w MG last/first author - 4)<br /> <br /> No. papers with 501-1000 citations each ------ 30 (12)<br /> <br /> No. papers with 201-500 citations each ------ 78 (40)<br /> <br /> No. papers with 101-200 citations each ------ 112 (64)<br /> <br /> No. papers with 51-100 citations each ------ 93 (56)<br /> <br /> No. papers with 50 citations or less each ------ 295 (187) # doesn’t include papers that don’t have a GScholar citation count, i.e. are non-citable or haven't been cited yet<br /> <br /> <br /> [https://drive.google.com/file/d/1rKaLefE71LRvSfCkXoir_SeiNo9nYBnB/view?usp=sharing Number of publications by journal names]<br /> <br /> <br /> ==Misc==<br /> <br /> === dump up to the end of '19 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/12.27/cv57-30-bld31Dec19--papers-simple--reformatted2.pdf scientific papers]<br /> <br /> === dump up to the end of '18 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-30-bld1jan19--papers-simple--reformatted.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-26-bld1Jan19--addendum-Rest.pdf other writings]<br /> <br /> === dump up to the end of '17 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18--papers-simple-refmt.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18--addendum-Rest.JustOtherPubs.pdf other writings]<br /> <br /> === dump up to the end of '16 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-26-bld1dec16--addendum-Rest--Just-Other-Writings.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-30-bld1dec16--papers-simple--reformatted.pdf other writings]<br /> <br /> === dump up to the end of '15 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-30--papers-simple--reformatted--28Jan16--FAR.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-27-28Jan16--FAR--Rest--other-papers.pdf other writings]<br /> <br /> === dump up to the end of '14 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-pubs-CV-31Dec2014.pdf scientific papers]<br /> <br /> === dump up to the end of '13 ===<br /> <br /> [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-pubs-CV-31Dec2013.pdf scientific papers]<br /> <br /> == Broken &amp; Defunct ==<br /> <br /> &lt;SMALL&gt;<br /> <br /> * [http://papers.gersteinlab.org/update/NCBIData.xml Current NCBI XML File]<br /> <br /> * [http://oldpapers.gersteinlab.org/search/labquery.pl?query=default (Old) link to construct above]<br /> <br /> * [http://www.scholaruniverse.com/profiles/people/090B29F9AC1BD0111E322273EF928B1C Scholar Universe]<br /> <br /> * [http://papers.gersteinlab.org/papers/misc/google.html Google Citation Summary]<br /> <br /> * [http://academic.research.microsoft.com/author/984673 Microsoft Academic Search Profile for M Gerstein]<br /> <br /> &lt;/SMALL&gt;</div>

Public https://info.gersteinlab.org/index.php?title=Pubmed_query&diff=6463 2026-01-07T19:06:14Z

<p>Public: /* Notes on Publication List */</p> <hr /> <div>==Other Views==<br /> <br /> There are a number of simplified views of the papers page available, with no extra links, viz:<br /> [http://papers.gersteinlab.org/simple.html '''title-first listing'''] and [http://papers.gersteinlab.org/papers/papers-simple.html traditional author-first listing]<br /> (These are suitable for copying into Word.) Also, here's a simple [http://papers.gersteinlab.org/papers directory listing] with all the paper IDs.<br /> <br /> ==Notes on Publication List==<br /> <br /> <br /> [https://files.gersteinlab.org/public-docs/2026/01.07/Notes_on_publications_20251216.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2025/02.17/Notes-on-publications--FROM--MG-truncate-CV-public-FAR24-end24bld-no-pgnum.cv57.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> <br /> [https://www.dropbox.com/scl/fi/g7ll9amhfnn90a23tgt2i/Notes-on-publications-FROM-M-Gerstein-CV-bld6Jan24-Public-CV-Jan-2024.cv57.pdf?rlkey=3xvtph03hkpm3ca6x461pmw6g&amp;dl=0 Information on Corresponding Author and Citation Stats of Gerstein Lab Papers]<br /> --&gt;<br /> <br /> ==PubMed Queries==<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D+NOT+preprint%5Bpt%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 12/1/2025)'''] to build papers page into PubMed without Preprints<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 7/21/2020)'''] to build papers page into PubMed<br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Query'''] to build papers page into PubMed<br /> <br /> * ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+10787728%5BUID%5D+NOT+11744447%5BUID%5D+NOT+14663468%5BUID%5D+NOT+14730174%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+17270657%5BUID%5D+NOT+21243890%5BUID%5D+NOT+21406498%5BUID%5D+NOT+21945273%5BUID%5D+NOT+28562279%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Old Query'''])<br /> <br /> * [http://linkstream2.gerstein.info/2013/11/30/pubmed-help-searching-for-specific-last-and-first-authors-3 Useful stuff in searching for specific last or first authors], which can result in some [[Useful Stats on Gerstein Lab Papers]]<br /> <br /> * [[Papers published with individuals who have left]] Yale <br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/myncbi/mark.gerstein.1/bibliography/44005333/public My NCBI] link of 445 M Gerstein papers as of Feb 2015 with PMIDs (via mark at gersteinlab user)<br /> <br /> ==Publication Analysis Services==<br /> <br /> * Google Scholar: '''http://scholar.google.ca/scholar?q=author:gerstein-m''' ([https://scholar.google.com/citations?hl=en&amp;view_op=search_authors&amp;mauthors=yale Ranking] of Yale researchers according to Scholar - we do well.) <br /> <br /> * [http://orcid.org/0000-0002-9746-3719 ORCID.org/0000-0002-9746-3719] for M Gerstein (very incomplete)<br /> <br /> * Highly Cited Researchers lists<br /> ** [https://linkstream2.gerstein.info/2016/11/21/archives-hcr-clarivate-analytics Thomson Reuters HIGHLY CITED RESEARCHERS (HCR) List] (on this '14, '15, '16)<br /> ** [https://hcr.clarivate.com Clarivate List] (supersedes above, on this in '17 &amp; '18)<br /> <br /> ==Paper Search==<br /> <br /> Adopted from [[Paper_search]]<br /> <br /> ===Medline Queries:===<br /> <br /> [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=PureSearch&amp;db=PubMed&amp;details_term=%28%28Gerstein%20M%5BAuthor%5D%20NOT%20%281963%5Bdp%5D%20%3A%201990%5Bdp%5D%29%29%20NOT%2011744447%5BUID%5D%20NOT%2010787728%5BUID%5D%29&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] / [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&amp;db=m&amp;term=Gerstein+M&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] (unrestricted) /<br /> [http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gerstein:Mark.html DBLP] / [http://liinwww.ira.uka.de/searchbib/index?query=GersteinM CS Bibliographies] /<br /> [http://citeseer.nj.nec.com/cs?cs=1&amp;q=m+gerstein+or+mark+gerstein&amp;co=Expected+Citations&amp;cm=50&amp;cf=Any&amp;ao=Expected+Citations&amp;am=20&amp;af=Any CiteSeer]<br /> <br /> http://pubnet.gersteinlab.org/images/mainlogo.jpg<br /> <br /> PubNet Graph of Gerstein Lab Publications ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5bdp%5d))%20NOT%2011744447%5BUID%5d%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607170530 cached])<br /> <br /> PubNet Graph of Gerstein and Montelione papers [http://www.nesg.org/ NESG] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=Gaetano%20Montelione&amp;query2=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171018 cached])<br /> <br /> PubNet Graph of Gerstein and Snyder papers [http://bioinfo.mbb.yale.edu/array/ CEGS] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;query2=snyder%20m%20and%20yale&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171429 cached])<br /> <br /> ===Lists of Papers===<br /> <br /> [http://papers.gersteinlab.org/index.html Main]<br /> [http://papers.gersteinlab.org/papers/papers-simple.html Simple]<br /> [http://papers.gersteinlab.org/papers/papers-ids.htm Table]<br /> [http://papers.gersteinlab.org/papers/papers-tags.htm XML tags]<br /> [http://papers.gersteinlab.org/papers/before97.shtml Pre 1997]<br /> [[Other_Papers]]<br /> <br /> ===Pre-prints:===<br /> <br /> [http://papers.gersteinlab.org/e-print E-print &lt;sup&gt;&amp;dagger;&lt;/sup&gt;] with full-text of some papers in press ([http://papers.gersteinlab.org/papers/help.shtml help] on this)<br /> <br /> &lt;sup&gt;&amp;dagger;&lt;/sup&gt;[http://www.gersteinlab.org/misc/permissions.html Please see our copyright statement]<br /> <br /> ==Sortable Lists of Publication Metrics==<br /> <br /> ===Sortable spreadsheets of Google Scholar &amp; Web of Science &amp; Altmetric (Dec 4, 2019)===<br /> [https://drive.google.com/file/d/1p5_J7Y8nt0WvXE5V7J4XYZ6LEMuwOAUC/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1Kn8eEpLUzulOtDx_XBXVc1jzb0pJNL2w/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1TmN_e8Fm3Cy4kKD8ILHl7-CFQhsEbQJM/view?usp=sharing GScholar]<br /> <br /> &amp; that again w/ MG as last/first author<br /> <br /> [https://drive.google.com/file/d/1vAZbrivv_2yadY5YFyGvZYaz1o7CSkcz/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1lOHkuXbOZNY2k39NdtUm3lT3Xv0dP5pP/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1wttEpxxBJUM0Guq0P1zgfin-Tph9GNdc/view?usp=sharing GScholar]<br /> <br /> <br /> ===Overall citation stats (Dec 4, 2019)===<br /> 595 publications <br /> <br /> Cited 144003 times and h-index: 166 (GScholar)<br /> <br /> No. papers with over 1000 citations each ------ No. all papers - 22 (No. papers w MG last/first author - 4)<br /> <br /> No. papers with 501-1000 citations each ------ 30 (12)<br /> <br /> No. papers with 201-500 citations each ------ 78 (40)<br /> <br /> No. papers with 101-200 citations each ------ 112 (64)<br /> <br /> No. papers with 51-100 citations each ------ 93 (56)<br /> <br /> No. papers with 50 citations or less each ------ 295 (187) # doesn’t include papers that don’t have a GScholar citation count, i.e. are non-citable or haven't been cited yet<br /> <br /> <br /> [https://drive.google.com/file/d/1rKaLefE71LRvSfCkXoir_SeiNo9nYBnB/view?usp=sharing Number of publications by journal names]<br /> <br /> <br /> ==Misc==<br /> <br /> === dump up to the end of '19 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/12.27/cv57-30-bld31Dec19--papers-simple--reformatted2.pdf scientific papers]<br /> <br /> === dump up to the end of '18 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-30-bld1jan19--papers-simple--reformatted.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-26-bld1Jan19--addendum-Rest.pdf other writings]<br /> <br /> === dump up to the end of '17 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18--papers-simple-refmt.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18--addendum-Rest.JustOtherPubs.pdf other writings]<br /> <br /> === dump up to the end of '16 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-26-bld1dec16--addendum-Rest--Just-Other-Writings.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-30-bld1dec16--papers-simple--reformatted.pdf other writings]<br /> <br /> === dump up to the end of '15 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-30--papers-simple--reformatted--28Jan16--FAR.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-27-28Jan16--FAR--Rest--other-papers.pdf other writings]<br /> <br /> === dump up to the end of '14 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-pubs-CV-31Dec2014.pdf scientific papers]<br /> <br /> === dump up to the end of '13 ===<br /> <br /> [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-pubs-CV-31Dec2013.pdf scientific papers]<br /> <br /> == Broken &amp; Defunct ==<br /> <br /> &lt;SMALL&gt;<br /> <br /> * [http://papers.gersteinlab.org/update/NCBIData.xml Current NCBI XML File]<br /> <br /> * [http://oldpapers.gersteinlab.org/search/labquery.pl?query=default (Old) link to construct above]<br /> <br /> * [http://www.scholaruniverse.com/profiles/people/090B29F9AC1BD0111E322273EF928B1C Scholar Universe]<br /> <br /> * [http://papers.gersteinlab.org/papers/misc/google.html Google Citation Summary]<br /> <br /> * [http://academic.research.microsoft.com/author/984673 Microsoft Academic Search Profile for M Gerstein]<br /> <br /> &lt;/SMALL&gt;</div>

Public https://info.gersteinlab.org/index.php?title=Pubmed_query&diff=6462 2026-01-07T19:05:15Z

<p>Public: /* Notes on Publication List */</p> <hr /> <div>==Other Views==<br /> <br /> There are a number of simplified views of the papers page available, with no extra links, viz:<br /> [http://papers.gersteinlab.org/simple.html '''title-first listing'''] and [http://papers.gersteinlab.org/papers/papers-simple.html traditional author-first listing]<br /> (These are suitable for copying into Word.) Also, here's a simple [http://papers.gersteinlab.org/papers directory listing] with all the paper IDs.<br /> <br /> ==Notes on Publication List==<br /> <br /> <br /> [http://files.gersteinlab.org/public-docs/2026/01.07/Notes_on_publications_20251216.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2025/02.17/Notes-on-publications--FROM--MG-truncate-CV-public-FAR24-end24bld-no-pgnum.cv57.pdf Information on Corresponding Author and Citation Stats of Gerstein Lab Papers] <br /> <br /> [https://www.dropbox.com/scl/fi/g7ll9amhfnn90a23tgt2i/Notes-on-publications-FROM-M-Gerstein-CV-bld6Jan24-Public-CV-Jan-2024.cv57.pdf?rlkey=3xvtph03hkpm3ca6x461pmw6g&amp;dl=0 Information on Corresponding Author and Citation Stats of Gerstein Lab Papers]<br /> --&gt;<br /> <br /> ==PubMed Queries==<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D+NOT+preprint%5Bpt%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 12/1/2025)'''] to build papers page into PubMed without Preprints<br /> <br /> * [https://pubmed.ncbi.nlm.nih.gov/?term=%28%28Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+%281957%5Bdp%5D+%3A+1990%5Bdp%5D%29%29+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D%29&amp;sort=date&amp;size=50 '''New Query (updated 7/21/2020)'''] to build papers page into PubMed<br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+OR+Gerstein+MB%5BAuthor%5D+OR+Gerstein+Mark%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+Gerstein+Maya%5BAuthor%5D+NOT+Gerstein+ME%5BAuthor%5D+NOT+Gerstein+Matthew%5BAuthor%5D+NOT+Gerstein+MI%5BAuthor%5D+NOT+11744447%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+21243890%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Query'''] to build papers page into PubMed<br /> <br /> * ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&amp;db=pubmed&amp;dispmax=200&amp;relpubdate=No%20Limit&amp;term=((Gerstein+M%5BAuthor%5D+NOT+(1957%5Bdp%5D+%3A+1990%5Bdp%5D))+NOT+10787728%5BUID%5D+NOT+11744447%5BUID%5D+NOT+14663468%5BUID%5D+NOT+14730174%5BUID%5D+NOT+16081066%5BUID%5D+NOT+14663468%5BUID%5D+NOT+17270657%5BUID%5D+NOT+21243890%5BUID%5D+NOT+21406498%5BUID%5D+NOT+21945273%5BUID%5D+NOT+28562279%5BUID%5D+OR+15499007%5BUID%5D+OR+17571346%5BUID%5D+OR+17571346%5BUID%5D+OR+8877505%5BUID%5D+OR+8816770%5BUID%5D+OR+7540695%5BUID%5D+OR+7567918%5BUID%5D+OR+7567918%5BUID%5D+OR+7577841%5BUID%5D+OR+7567917%5BUID%5D+OR+7643385%5BUID%5D+OR+8749848%5BUID%5D+OR+8808580%5BUID%5D+OR+8120887%5BUID%5D+OR+8029203%5BUID%5D+OR+8204609%5BUID%5D+OR+7922041%5BUID%5D+OR+7584390%5BUID%5D+OR+8078776%5BUID%5D+OR+8428572%5BUID%5D+OR+8429559%5BUID%5D+OR+8464069%5BUID%5D+OR+8234227%5BUID%5D+OR+8230220%5BUID%5D+OR+1584800%5BUID%5D+OR+2067013%5BUID%5D+OR+20981092%5BUID%5D+OR+21526222%5BUID%5D) '''Old Query'''])<br /> <br /> * [http://linkstream2.gerstein.info/2013/11/30/pubmed-help-searching-for-specific-last-and-first-authors-3 Useful stuff in searching for specific last or first authors], which can result in some [[Useful Stats on Gerstein Lab Papers]]<br /> <br /> * [[Papers published with individuals who have left]] Yale <br /> <br /> * [http://www.ncbi.nlm.nih.gov/sites/myncbi/mark.gerstein.1/bibliography/44005333/public My NCBI] link of 445 M Gerstein papers as of Feb 2015 with PMIDs (via mark at gersteinlab user)<br /> <br /> ==Publication Analysis Services==<br /> <br /> * Google Scholar: '''http://scholar.google.ca/scholar?q=author:gerstein-m''' ([https://scholar.google.com/citations?hl=en&amp;view_op=search_authors&amp;mauthors=yale Ranking] of Yale researchers according to Scholar - we do well.) <br /> <br /> * [http://orcid.org/0000-0002-9746-3719 ORCID.org/0000-0002-9746-3719] for M Gerstein (very incomplete)<br /> <br /> * Highly Cited Researchers lists<br /> ** [https://linkstream2.gerstein.info/2016/11/21/archives-hcr-clarivate-analytics Thomson Reuters HIGHLY CITED RESEARCHERS (HCR) List] (on this '14, '15, '16)<br /> ** [https://hcr.clarivate.com Clarivate List] (supersedes above, on this in '17 &amp; '18)<br /> <br /> ==Paper Search==<br /> <br /> Adopted from [[Paper_search]]<br /> <br /> ===Medline Queries:===<br /> <br /> [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=PureSearch&amp;db=PubMed&amp;details_term=%28%28Gerstein%20M%5BAuthor%5D%20NOT%20%281963%5Bdp%5D%20%3A%201990%5Bdp%5D%29%29%20NOT%2011744447%5BUID%5D%20NOT%2010787728%5BUID%5D%29&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] / [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&amp;db=m&amp;term=Gerstein+M&amp;dispmax=200&amp;relpubdate=No+Limit Gerstein M] (unrestricted) /<br /> [http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gerstein:Mark.html DBLP] / [http://liinwww.ira.uka.de/searchbib/index?query=GersteinM CS Bibliographies] /<br /> [http://citeseer.nj.nec.com/cs?cs=1&amp;q=m+gerstein+or+mark+gerstein&amp;co=Expected+Citations&amp;cm=50&amp;cf=Any&amp;ao=Expected+Citations&amp;am=20&amp;af=Any CiteSeer]<br /> <br /> http://pubnet.gersteinlab.org/images/mainlogo.jpg<br /> <br /> PubNet Graph of Gerstein Lab Publications ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5bdp%5d))%20NOT%2011744447%5BUID%5d%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607170530 cached])<br /> <br /> PubNet Graph of Gerstein and Montelione papers [http://www.nesg.org/ NESG] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=Gaetano%20Montelione&amp;query2=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171018 cached])<br /> <br /> PubNet Graph of Gerstein and Snyder papers [http://bioinfo.mbb.yale.edu/array/ CEGS] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=((Gerstein%20M%5BAuthor%5D%20NOT%20(1957%5Bdp%5D%20:%201990%5Bdp%5D))%20NOT%2011744447%5BUID%5D%20NOT%2014663468%5BUID%5D%20NOT%2010787728%5BUID%5D%20NOT%2014730174%5BUID%5D%20NOT%2012140549%5BUID%5D%20NOT%2014704431%5BUID%5D%20)&amp;query2=snyder%20m%20and%20yale&amp;node=author&amp;edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171429 cached])<br /> <br /> ===Lists of Papers===<br /> <br /> [http://papers.gersteinlab.org/index.html Main]<br /> [http://papers.gersteinlab.org/papers/papers-simple.html Simple]<br /> [http://papers.gersteinlab.org/papers/papers-ids.htm Table]<br /> [http://papers.gersteinlab.org/papers/papers-tags.htm XML tags]<br /> [http://papers.gersteinlab.org/papers/before97.shtml Pre 1997]<br /> [[Other_Papers]]<br /> <br /> ===Pre-prints:===<br /> <br /> [http://papers.gersteinlab.org/e-print E-print &lt;sup&gt;&amp;dagger;&lt;/sup&gt;] with full-text of some papers in press ([http://papers.gersteinlab.org/papers/help.shtml help] on this)<br /> <br /> &lt;sup&gt;&amp;dagger;&lt;/sup&gt;[http://www.gersteinlab.org/misc/permissions.html Please see our copyright statement]<br /> <br /> ==Sortable Lists of Publication Metrics==<br /> <br /> ===Sortable spreadsheets of Google Scholar &amp; Web of Science &amp; Altmetric (Dec 4, 2019)===<br /> [https://drive.google.com/file/d/1p5_J7Y8nt0WvXE5V7J4XYZ6LEMuwOAUC/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1Kn8eEpLUzulOtDx_XBXVc1jzb0pJNL2w/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1TmN_e8Fm3Cy4kKD8ILHl7-CFQhsEbQJM/view?usp=sharing GScholar]<br /> <br /> &amp; that again w/ MG as last/first author<br /> <br /> [https://drive.google.com/file/d/1vAZbrivv_2yadY5YFyGvZYaz1o7CSkcz/view?usp=sharing Altmetric]<br /> [https://drive.google.com/file/d/1lOHkuXbOZNY2k39NdtUm3lT3Xv0dP5pP/view?usp=sharing WoS]<br /> [https://drive.google.com/file/d/1wttEpxxBJUM0Guq0P1zgfin-Tph9GNdc/view?usp=sharing GScholar]<br /> <br /> <br /> ===Overall citation stats (Dec 4, 2019)===<br /> 595 publications <br /> <br /> Cited 144003 times and h-index: 166 (GScholar)<br /> <br /> No. papers with over 1000 citations each ------ No. all papers - 22 (No. papers w MG last/first author - 4)<br /> <br /> No. papers with 501-1000 citations each ------ 30 (12)<br /> <br /> No. papers with 201-500 citations each ------ 78 (40)<br /> <br /> No. papers with 101-200 citations each ------ 112 (64)<br /> <br /> No. papers with 51-100 citations each ------ 93 (56)<br /> <br /> No. papers with 50 citations or less each ------ 295 (187) # doesn’t include papers that don’t have a GScholar citation count, i.e. are non-citable or haven't been cited yet<br /> <br /> <br /> [https://drive.google.com/file/d/1rKaLefE71LRvSfCkXoir_SeiNo9nYBnB/view?usp=sharing Number of publications by journal names]<br /> <br /> <br /> ==Misc==<br /> <br /> === dump up to the end of '19 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/12.27/cv57-30-bld31Dec19--papers-simple--reformatted2.pdf scientific papers]<br /> <br /> === dump up to the end of '18 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-30-bld1jan19--papers-simple--reformatted.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2019/02.14/cv57-26-bld1Jan19--addendum-Rest.pdf other writings]<br /> <br /> === dump up to the end of '17 ===<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18--papers-simple-refmt.pdf scientific papers]<br /> [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18--addendum-Rest.JustOtherPubs.pdf other writings]<br /> <br /> === dump up to the end of '16 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-26-bld1dec16--addendum-Rest--Just-Other-Writings.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-30-bld1dec16--papers-simple--reformatted.pdf other writings]<br /> <br /> === dump up to the end of '15 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-30--papers-simple--reformatted--28Jan16--FAR.pdf scientific papers]<br /> [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-27-28Jan16--FAR--Rest--other-papers.pdf other writings]<br /> <br /> === dump up to the end of '14 ===<br /> <br /> [http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-pubs-CV-31Dec2014.pdf scientific papers]<br /> <br /> === dump up to the end of '13 ===<br /> <br /> [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-pubs-CV-31Dec2013.pdf scientific papers]<br /> <br /> == Broken &amp; Defunct ==<br /> <br /> &lt;SMALL&gt;<br /> <br /> * [http://papers.gersteinlab.org/update/NCBIData.xml Current NCBI XML File]<br /> <br /> * [http://oldpapers.gersteinlab.org/search/labquery.pl?query=default (Old) link to construct above]<br /> <br /> * [http://www.scholaruniverse.com/profiles/people/090B29F9AC1BD0111E322273EF928B1C Scholar Universe]<br /> <br /> * [http://papers.gersteinlab.org/papers/misc/google.html Google Citation Summary]<br /> <br /> * [http://academic.research.microsoft.com/author/984673 Microsoft Academic Search Profile for M Gerstein]<br /> <br /> &lt;/SMALL&gt;</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6461 2026-01-04T21:09:34Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper. After the press release is issued, we will add it to the Gerstein Lab press release page.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW (Usually this is a 95/5 split)<br /> Example sentence (for publication fee reimbursement only; not for inclusion in the manuscript, sent to Lisa):<br /> &quot;The payment has been allocated with xxx% charged to the ALW grant and xxx% to the xxx grant, in accordance with the established funding contribution proportions. These allocation splits were determined based on the relative level of support, resources, and overall contribution provided by each funding source toward the work described.&quot;<br /> <br /> Example funding statement for the paper (You can use other paper published by the lab as example as well):<br /> &quot;This work was supported by the xxx funds and the National Institutes of Health (NIH) under Grant xxx.&quot;<br /> <br /> <br /> *Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** We might have to do a justification for this. Here is some sample text: , noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Funding is usually applicable when MG is the last author.<br /> ** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)<br /> *** For data deposition, we will follow a three-tier approach: (1) primary code and supplementary tables will be hosted on the Gerstein Lab GitHub and provided as journal supplements; (2) the same materials, along with larger files, will be deposited on Dryad (which supports larger file sizes than Zenodo); and (3) all datasets will also be mirrored on the Gerstein Lab data server (files.gersteinlab.org).<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * Preprints<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet &amp; Bluesky<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Main_Page&diff=6460 2025-12-19T18:53:34Z

<p>Public: /* Important Public Items */</p> <hr /> <div>== Important Public Items ==<br /> *Gerstein Lab '''[https://www.youtube.com/channel/UCVM3Kd2UWdJrAfQ1RqyajHw Youtube]''' , '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''<br /> *'''[[FAQ]]''' on tools and data<br /> *'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''<br /> *[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] &amp; [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )<br /> *[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab<br /> <br /> <br /> __TOC__<br /> <br /> In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki.gersteinlab.org/ private lab wiki] for lab-specific information (login as user &quot;public&quot;). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]<br /> <br /> &lt;HR&gt;<br /> <br /> == Other Stuff for the Public ==<br /> *Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)<br /> *[[Summaries]] of lab research<br /> *[[Posters]] showing lab research<br /> *Misc. Public [[Documents]] about the lab<br /> *Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])<br /> *[[Status of Lab Web Resources]]<br /> *Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]<br /> <br /> == Info for New People ==<br /> * Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.<br /> * [[Glossary]] of terms.<br /> * Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]<br /> <br /> == Info for Lab Signature ==<br /> *For all lab signatures this the procedure: ask LI &amp; CC. MG will reply w/ an email say &quot;sign0mg&quot; LI will sign.<br /> <br /> == Info for Lab Members and Collaborators ==<br /> * Working on drafts, papers, grants, presentations &amp;c<br /> ** Lab [[Resources Document]] (NIH form)<br /> ** Conventions for editing Google Docs - http://goo.gl/kSrS9<br /> ** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)<br /> *** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')<br /> ** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]<br /> ** [[CRAMTOOLS and common directory]]<br /> <br /> * Computing<br /> ** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page. <br /> ** [[Gerstein Lab Computing in HPC]]<br /> ** [[Gerstein Lab Computing in GersteinLab West Campus]]<br /> ** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]<br /> <br /> * Calls, meetings, &amp;c<br /> **A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])<br /> **[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.<br /> **[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.<br /> ** Information on [[Meeting Invites]]<br /> ** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&amp;on=downloads Other info])<br /> **[[Bass434]] introduction<br /> **Booking [[Meeting Room]]<br /> **Booking a [[Conference Room at 100 College]]<br /> <br /> * Some Useful University Policies<br /> ** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]<br /> ** Snippets from [[MB&amp;B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]<br /> ** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]<br /> ** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]<br /> ** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]<br /> <br /> * Documents<br /> ** [[Uploading_documents]]<br /> ** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates) <br /> <br /> * Misc<br /> **[[Getting Mark's signature for documents]]<br /> **[[Temperature in Bass 432a]], real time measurements (see how cold it gets)<br /> **Prominent [[public wiki pages linked from elsewhere]]<br /> **[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.<br /> **[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]<br /> **[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)<br /> ** [[Recommendation Letters]]<br /> **[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&amp;single=true&amp;gid=2&amp;output=html Magazine Subscriptions]<br /> ** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]<br /> ** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]<br /> ** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)<br /> **[[OpenStack]]<br /> **[[IDP report]]<br /> **[[PEC package preprints]]<br /> **[[Summary of undergraduate involvement]]<br /> **Lab [http://bit.ly/mglab-folder google folder]<br /> **List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]</div>

Public https://info.gersteinlab.org/index.php?title=Main_Page&diff=6459 2025-12-19T15:48:59Z

<p>Public: </p> <hr /> <div>== Important Public Items ==<br /> *Gerstein Lab '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''<br /> *'''[[FAQ]]''' on tools and data<br /> *'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''<br /> *[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] &amp; [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )<br /> *[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab<br /> <br /> <br /> __TOC__<br /> <br /> In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki.gersteinlab.org/ private lab wiki] for lab-specific information (login as user &quot;public&quot;). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]<br /> <br /> &lt;HR&gt;<br /> <br /> == Other Stuff for the Public ==<br /> *Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)<br /> *[[Summaries]] of lab research<br /> *[[Posters]] showing lab research<br /> *Misc. Public [[Documents]] about the lab<br /> *Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])<br /> *[[Status of Lab Web Resources]]<br /> *Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]<br /> <br /> == Info for New People ==<br /> * Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.<br /> * [[Glossary]] of terms.<br /> * Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]<br /> <br /> == Info for Lab Signature ==<br /> *For all lab signatures this the procedure: ask LI &amp; CC. MG will reply w/ an email say &quot;sign0mg&quot; LI will sign.<br /> <br /> == Info for Lab Members and Collaborators ==<br /> * Working on drafts, papers, grants, presentations &amp;c<br /> ** Lab [[Resources Document]] (NIH form)<br /> ** Conventions for editing Google Docs - http://goo.gl/kSrS9<br /> ** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)<br /> *** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')<br /> ** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]<br /> ** [[CRAMTOOLS and common directory]]<br /> <br /> * Computing<br /> ** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page. <br /> ** [[Gerstein Lab Computing in HPC]]<br /> ** [[Gerstein Lab Computing in GersteinLab West Campus]]<br /> ** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]<br /> <br /> * Calls, meetings, &amp;c<br /> **A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])<br /> **[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.<br /> **[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.<br /> ** Information on [[Meeting Invites]]<br /> ** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&amp;on=downloads Other info])<br /> **[[Bass434]] introduction<br /> **Booking [[Meeting Room]]<br /> **Booking a [[Conference Room at 100 College]]<br /> <br /> * Some Useful University Policies<br /> ** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]<br /> ** Snippets from [[MB&amp;B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]<br /> ** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]<br /> ** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]<br /> ** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]<br /> <br /> * Documents<br /> ** [[Uploading_documents]]<br /> ** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates) <br /> <br /> * Misc<br /> **[[Getting Mark's signature for documents]]<br /> **[[Temperature in Bass 432a]], real time measurements (see how cold it gets)<br /> **Prominent [[public wiki pages linked from elsewhere]]<br /> **[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.<br /> **[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]<br /> **[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)<br /> ** [[Recommendation Letters]]<br /> **[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&amp;single=true&amp;gid=2&amp;output=html Magazine Subscriptions]<br /> ** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]<br /> ** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]<br /> ** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)<br /> **[[OpenStack]]<br /> **[[IDP report]]<br /> **[[PEC package preprints]]<br /> **[[Summary of undergraduate involvement]]<br /> **Lab [http://bit.ly/mglab-folder google folder]<br /> **List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]</div>

Public https://info.gersteinlab.org/index.php?title=Main_Page&diff=6458 2025-12-19T15:22:17Z

<p>Public: </p> <hr /> <div>== Important Public Items ==<br /> *Gerstein Lab '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''<br /> *'''[[FAQ]]''' on tools and data<br /> *'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''<br /> *[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] &amp; [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )<br /> *[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab<br /> <br /> <br /> __TOC__<br /> <br /> In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki1.gersteinlab.org/ private lab wiki] for lab-specific information (login as user &quot;public&quot;). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]<br /> <br /> &lt;HR&gt;<br /> <br /> == Other Stuff for the Public ==<br /> *Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)<br /> *[[Summaries]] of lab research<br /> *[[Posters]] showing lab research<br /> *Misc. Public [[Documents]] about the lab<br /> *Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])<br /> *[[Status of Lab Web Resources]]<br /> *Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]<br /> <br /> == Info for New People ==<br /> * Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.<br /> * [[Glossary]] of terms.<br /> * Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]<br /> <br /> == Info for Lab Signature ==<br /> *For all lab signatures this the procedure: ask LI &amp; CC. MG will reply w/ an email say &quot;sign0mg&quot; LI will sign.<br /> <br /> == Info for Lab Members and Collaborators ==<br /> * Working on drafts, papers, grants, presentations &amp;c<br /> ** Lab [[Resources Document]] (NIH form)<br /> ** Conventions for editing Google Docs - http://goo.gl/kSrS9<br /> ** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)<br /> *** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')<br /> ** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]<br /> ** [[CRAMTOOLS and common directory]]<br /> <br /> * Computing<br /> ** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page. <br /> ** [[Gerstein Lab Computing in HPC]]<br /> ** [[Gerstein Lab Computing in GersteinLab West Campus]]<br /> ** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]<br /> <br /> * Calls, meetings, &amp;c<br /> **A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])<br /> **[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.<br /> **[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.<br /> ** Information on [[Meeting Invites]]<br /> ** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&amp;on=downloads Other info])<br /> **[[Bass434]] introduction<br /> **Booking [[Meeting Room]]<br /> **Booking a [[Conference Room at 100 College]]<br /> <br /> * Some Useful University Policies<br /> ** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]<br /> ** Snippets from [[MB&amp;B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]<br /> ** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]<br /> ** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]<br /> ** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]<br /> <br /> * Documents<br /> ** [[Uploading_documents]]<br /> ** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates) <br /> <br /> * Misc<br /> **[[Getting Mark's signature for documents]]<br /> **[[Temperature in Bass 432a]], real time measurements (see how cold it gets)<br /> **Prominent [[public wiki pages linked from elsewhere]]<br /> **[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.<br /> **[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]<br /> **[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)<br /> ** [[Recommendation Letters]]<br /> **[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&amp;single=true&amp;gid=2&amp;output=html Magazine Subscriptions]<br /> ** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]<br /> ** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]<br /> ** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)<br /> **[[OpenStack]]<br /> **[[IDP report]]<br /> **[[PEC package preprints]]<br /> **[[Summary of undergraduate involvement]]<br /> **Lab [http://bit.ly/mglab-folder google folder]<br /> **List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]</div>

Public https://info.gersteinlab.org/index.php?title=Main_Page&diff=6457 2025-12-19T14:02:41Z

<p>Public: </p> <hr /> <div>== Important Public Items ==<br /> *Gerstein Lab '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''<br /> *'''[[FAQ]]''' on tools and data<br /> *'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''<br /> *[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] &amp; [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )<br /> *[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab<br /> <br /> <br /> __TOC__<br /> <br /> In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki1.gersteinlab.org/ private lab wiki] for lab-specific information (login as user &quot;public&quot;). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user &quot;public&quot;). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]<br /> <br /> &lt;HR&gt;<br /> <br /> == Other Stuff for the Public ==<br /> *Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)<br /> *[[Summaries]] of lab research<br /> *[[Posters]] showing lab research<br /> *Misc. Public [[Documents]] about the lab<br /> *Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])<br /> *[[Status of Lab Web Resources]]<br /> *Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]<br /> <br /> == Info for New People ==<br /> * Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.<br /> * [[Glossary]] of terms.<br /> * Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]<br /> <br /> == Info for Lab Signature ==<br /> *For all lab signatures this the procedure: ask LI &amp; CC. MG will reply w/ an email say &quot;sign0mg&quot; LI will sign.<br /> <br /> == Info for Lab Members and Collaborators ==<br /> * Working on drafts, papers, grants, presentations &amp;c<br /> ** Lab [[Resources Document]] (NIH form)<br /> ** Conventions for editing Google Docs - http://goo.gl/kSrS9<br /> ** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)<br /> *** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')<br /> ** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]<br /> ** [[CRAMTOOLS and common directory]]<br /> <br /> * Computing<br /> ** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page. <br /> ** [[Gerstein Lab Computing in HPC]]<br /> ** [[Gerstein Lab Computing in GersteinLab West Campus]]<br /> ** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]<br /> <br /> * Calls, meetings, &amp;c<br /> **A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])<br /> **[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.<br /> **[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.<br /> ** Information on [[Meeting Invites]]<br /> ** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&amp;on=downloads Other info])<br /> **[[Bass434]] introduction<br /> **Booking [[Meeting Room]]<br /> **Booking a [[Conference Room at 100 College]]<br /> <br /> * Some Useful University Policies<br /> ** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]<br /> ** Snippets from [[MB&amp;B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]<br /> ** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]<br /> ** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]<br /> ** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]<br /> <br /> * Documents<br /> ** [[Uploading_documents]]<br /> ** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates) <br /> <br /> * Misc<br /> **[[Getting Mark's signature for documents]]<br /> **[[Temperature in Bass 432a]], real time measurements (see how cold it gets)<br /> **Prominent [[public wiki pages linked from elsewhere]]<br /> **[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.<br /> **[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]<br /> **[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)<br /> ** [[Recommendation Letters]]<br /> **[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&amp;single=true&amp;gid=2&amp;output=html Magazine Subscriptions]<br /> ** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]<br /> ** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]<br /> ** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)<br /> **[[OpenStack]]<br /> **[[IDP report]]<br /> **[[PEC package preprints]]<br /> **[[Summary of undergraduate involvement]]<br /> **Lab [http://bit.ly/mglab-folder google folder]<br /> **List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]</div>

Public https://info.gersteinlab.org/index.php?title=Main_Page&diff=6456 2025-12-19T14:02:02Z

<p>Public: </p> <hr /> <div>== Important Public Items ==<br /> *Gerstein Lab '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''<br /> *'''[[FAQ]]''' on tools and data<br /> *'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''<br /> *[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] &amp; [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )<br /> *[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab<br /> <br /> <br /> __TOC__<br /> <br /> In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [https://privatewiki.gersteinlab.org/ private lab wiki] for lab-specific information (login as user &quot;public&quot;). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user &quot;public&quot;). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]<br /> <br /> &lt;HR&gt;<br /> <br /> == Other Stuff for the Public ==<br /> *Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)<br /> *[[Summaries]] of lab research<br /> *[[Posters]] showing lab research<br /> *Misc. Public [[Documents]] about the lab<br /> *Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]], [http://linkstream.gersteinlab.org/tag/seminars Just seminars])<br /> *[[Status of Lab Web Resources]]<br /> *Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]<br /> <br /> == Info for New People ==<br /> * Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.<br /> * [[Glossary]] of terms.<br /> * Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]<br /> <br /> == Info for Lab Signature ==<br /> *For all lab signatures this the procedure: ask LI &amp; CC. MG will reply w/ an email say &quot;sign0mg&quot; LI will sign.<br /> <br /> == Info for Lab Members and Collaborators ==<br /> * Working on drafts, papers, grants, presentations &amp;c<br /> ** Lab [[Resources Document]] (NIH form)<br /> ** Conventions for editing Google Docs - http://goo.gl/kSrS9<br /> ** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)<br /> *** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')<br /> ** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]<br /> ** [[CRAMTOOLS and common directory]]<br /> <br /> * Computing<br /> ** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page. <br /> ** [[Gerstein Lab Computing in HPC]]<br /> ** [[Gerstein Lab Computing in GersteinLab West Campus]]<br /> ** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]<br /> <br /> * Calls, meetings, &amp;c<br /> **A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])<br /> **[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.<br /> **[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.<br /> ** Information on [[Meeting Invites]]<br /> ** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&amp;on=downloads Other info])<br /> **[[Bass434]] introduction<br /> **Booking [[Meeting Room]]<br /> **Booking a [[Conference Room at 100 College]]<br /> <br /> * Some Useful University Policies<br /> ** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]<br /> ** Snippets from [[MB&amp;B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]<br /> ** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]<br /> ** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]<br /> ** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]<br /> <br /> * Documents<br /> ** [[Uploading_documents]]<br /> ** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates) <br /> <br /> * Misc<br /> **[[Getting Mark's signature for documents]]<br /> **[[Temperature in Bass 432a]], real time measurements (see how cold it gets)<br /> **Prominent [[public wiki pages linked from elsewhere]]<br /> **[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.<br /> **[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]<br /> **[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)<br /> ** [[Recommendation Letters]]<br /> **[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&amp;single=true&amp;gid=2&amp;output=html Magazine Subscriptions]<br /> ** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]<br /> ** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]<br /> ** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)<br /> **[[OpenStack]]<br /> **[[IDP report]]<br /> **[[PEC package preprints]]<br /> **[[Summary of undergraduate involvement]]<br /> **Lab [http://bit.ly/mglab-folder google folder]<br /> **List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6446 2025-12-17T15:57:15Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/12.17/summary_mc-01.docx Gerstein lab experience with eQTLs, sequence variation, protein disorder, and 3D docking] uploaded by DC on Dec 17 2025 (g0sanofi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/12.17/summary_mc-01.docx Gerstein lab experience with eQTLs, sequence variation, and 3D docking] uploaded by DC on Dec 17 2025 (g0mcknight)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/10.27/g0biomedx_Summary.pdf Gerstein lab experience with construction of cell-type specific gene regulatory networks (GRNs)] uploaded by Mor on Oct 27 2025 (g0biomedx)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/09.09/g0sony2_summary.docx Gerstein lab experience with molecular mechanisms underlying diseases using large language models (LLMs)] uploaded by MOR on Sep 9 2025 (g0sony2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0laadsi--summary.docx Gerstein lab experience in building a tools for (a) predicting protein-compound interaction strengths and (b) building gene regulatory networks] uploaded by DC on Jun 30 2025 (g0laadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Additional_Information_about_Personnel&diff=6445 2025-12-17T15:53:15Z

<p>Public: /* Most Current Snapshot of Lab People */</p> <hr /> <div>==Most Current Snapshot of Lab People==<br /> <br /> Current lab people (as of 16 Dec 2025) [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_curr_20251216.pdf PDF] [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_curr_20251216.docx DOCX]<br /> <br /> Past lab people (as of 16 Dec 2025) [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_alum_20251216.pdf PDF] [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_alum_20251216.docx DOCX]<br /> <br /> Google sheet for all undergrad information [https://docs.google.com/spreadsheets/d/10GR54kpytt8qFmrdLpwe6mtl2Jfc0Iv9qfdAY_9YWsY/edit?usp=sharing]<br /> <br /> Public view of the undergrad information [https://docs.google.com/spreadsheets/d/1RGBGWd_-_u5K4UblhYg6f7_SM09Qc6JyY9UXpqQ-a-U/edit?usp=sharing]<br /> <br /> [http://www.gersteinlab.org/people/initial.html List]of people with initials<br /> <br /> ==Justification Bios==<br /> Gerstein Lab Bios for Use in Justifications ([https://docs.google.com/document/d/1EkxjRHpMJRpL7jRCLHA2fk1Q0__WhWD1sI82cfbUPkc/edit MBGLab--Short-Bios-for-Use-in-Justifications--a1iHf5] or [http://goo.gl/a1iHf5 http://goo.gl/a1iHf5])<br /> <br /> <br /> ==Other Listings of Lab People==<br /> *[https://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia page]<br /> *[https://www.linkedin.com/groups/11900219/ Linked In Group] (You need to login to LinkedIn to see this page. Everyone in the lab and lab alumni should join our LinkedIn group.)<br /> *[http://academictree.org/compbio/tree.php?pid=31611 Academic Tree]<br /> *[http://genealogy.math.ndsu.nodak.edu/id.php?id=69445 Math Genealogy Project]<br /> <br /> ==Older Snapshots==<br /> <br /> === as of 12 Dec '24 ===<br /> Current Lab People [http://info.gersteinlab.org/images/b/ba/MBG_curr_20241209.pdf pdf] and [http://info.gersteinlab.org/images/6/67/MBG_curr_20241209.docx docx]<br /> <br /> Past Lab People [https://info.gersteinlab.org/images/f/fe/MBG_Alum_20241215.pdf pdf] and [https://info.gersteinlab.org/images/4/47/MBG_Alum_20241215.docx docx]<br /> <br /> === as of 29 June '23 ===<br /> Current Lab People [http://info.gersteinlab.org/images/8/83/MBG_curr_20230629.pdf pdf] and [http://info.gersteinlab.org/images/0/01/MBG_curr_20230629.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/8/8a/MBG_Alum_20230629.pdf pdf] and [http://info.gersteinlab.org/images/7/71/MBG_Alum_20230629.docx docx]<br /> <br /> === as of 27 Dec '22 ===<br /> Current Lab People [http://info.gersteinlab.org/images/e/e1/MBG_curr_20221227.pdf pdf] and [http://info.gersteinlab.org/images/0/0b/MBG_curr_20221227.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/5/5d/MBG_Alum_20221227.pdf pdf] and [http://info.gersteinlab.org/images/b/b8/MBG_Alum_20221227.docx docx]<br /> <br /> === as of 20 Dec '21 ===<br /> Current Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_curr_20211220.pdf pdf]<br /> <br /> Past Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_alum_20211220.pdf pdf]<br /> <br /> === as of 25 Apr '21 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_curr_20210425.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_alum_20210425.pdf pdf]<br /> <br /> === as of 21 Nov '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/11.21/gerstein_lab_curr_20201121.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/11.06/gerstein_lab_alum_20201106.pdf pdf]<br /> <br /> === as of 07 June '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_curr_20200607.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_alum_20200607.pdf pdf]<br /> <br /> === as of 12 Sept '19 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20190912.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_alum_20190912.pdf pdf]<br /> <br /> === as of 16 Oct '18 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181016.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181005.pdf pdf]<br /> <br /> === as of 8 Jan '18 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-22-bld8Jan18--AdaptedFrom--gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-23-bld27dec17--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as of 7 Dec '17 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_alum.pdf pdf]<br /> <br /> === as of 1 Dec '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-22-bld1dec16-AdaptedFrom--Gerstein_Lab_Personnel_112016.pdf pdf]<br /> <br /> Past Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-23-bld1dec16--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as 28 Jan '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/people-page-dump-28Jan16 dump dir]<br /> <br /> === as of 31 Sep. '14 ===<br /> <br /> Past Lab People [http://labmisc.gersteinlab.org/archive/Past_Postdoctoral_Associates_and_Fellows_Sep_14.pdf pdf]<br /> <br /> === as of 31 Dec. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-alums-CV-31Dec2013.pdf pdf]<br /> <br /> === as of 1 Jan. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2013/07.22/M-Gerstein-lab-people-n-alumni-1jan13-extract-from-pub-cv.pdf pdf]<br /> <br /> === as of 15 August '12 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/07.28/Past-Lab-People-as-of-15aug2012.pdf pdf]<br /> <br /> === as of 1 Dec. '11 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Lab-Personnel-and-Alumni-1Dec2011.pdf pdf]<br /> <br /> ==Misc==<br /> Lab [https://sites.gersteinlab.org/lab-reunion/ reunion] in 2019 <br /> <br /> Space usage by people affiliated with Gerstein lab from 7/1/2012 to 6/30/2013 [https://docs.google.com/spreadsheet/ccc?key=0AnSCkRiRBZ5KdGlfbGVKTmxNNTdTSlJINTU3eFFBdmc&amp;usp=sharing gsheet]<br /> <br /> Lab member [http://www.gersteinlab.org/people/map.html map]<br /> <br /> [http://www.gersteinlab.org/people/contact.html Personal Contact Information]<br /> <br /> [http://www.gersteinlab.org/people/files/acknowledgements.pdf Acknowledgements]<br /> <br /> A statistical [[summary of undergraduate involvement]] in the lab<br /> <br /> Previous Years' Personnel List<br /> <br /> [http://www.gersteinlab.org/people/files/people2005.html 2005]<br /> [http://www.gersteinlab.org/people/files/people2004.html 2004]<br /> [http://www.gersteinlab.org/people/files/people2003.html 2003]<br /> [http://www.gersteinlab.org/people/files/people2002.htm 2002]<br /> [http://www.gersteinlab.org/people/files/people2001.htm 2001]<br /> [http://www.gersteinlab.org/people/files/people2000.htm 2000]<br /> [http://www.gersteinlab.org/people/files/people1999.htm 1999]<br /> [http://www.gersteinlab.org/people/files/people1998.htm 1998]<br /> [http://www.gersteinlab.org/people/files/people1997.htm 1997]<br /> <br /> [https://docs.google.com/document/d/1zGmv764chmcFLhDg0G_caykJIB2ll0OX4eNSCeQnJQw/edit?usp=sharing Private Wiki for people page (Google doc)]<br /> [http://wiki.gersteinlab.org/labinfo/People_Page Private Wiki for people page (deprecated)]</div>

Public https://info.gersteinlab.org/index.php?title=Additional_Information_about_Personnel&diff=6444 2025-12-17T15:50:38Z

<p>Public: /* Most Current Snapshot of Lab People */</p> <hr /> <div>==Most Current Snapshot of Lab People==<br /> <br /> Current lab people (as of 16 Dec 2025) [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_curr_20251216.pdf PDF] [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_curr_20251216.docx DOCX]<br /> <br /> Past lab people (as of 16 Dec 2025) [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_alum_20251216.pdf PDF] [https://files.gersteinlab.org/public-docs/2025/12.16/MGlab_alum_20251216.docx DOCX]<br /> <br /> Current lab people (as of 11 Dec 2025) [https://info.gersteinlab.org/images/c/cb/MBG_curr_20251211.pdf PDF] [https://info.gersteinlab.org/images/7/7c/MBG_curr_20251211.docx DOCX]<br /> <br /> Past lab people (as of 15 Dec 2024) [https://info.gersteinlab.org/images/f/fe/MBG_Alum_20241215.pdf PDF] [https://info.gersteinlab.org/images/4/47/MBG_Alum_20241215.docx DOCX]<br /> <br /> Google sheet for all undergrad information [https://docs.google.com/spreadsheets/d/10GR54kpytt8qFmrdLpwe6mtl2Jfc0Iv9qfdAY_9YWsY/edit?usp=sharing]<br /> <br /> Public view of the undergrad information [https://docs.google.com/spreadsheets/d/1RGBGWd_-_u5K4UblhYg6f7_SM09Qc6JyY9UXpqQ-a-U/edit?usp=sharing]<br /> <br /> [http://www.gersteinlab.org/people/initial.html List]of people with initial<br /> <br /> ==Justification Bios==<br /> Gerstein Lab Bios for Use in Justifications ([https://docs.google.com/document/d/1EkxjRHpMJRpL7jRCLHA2fk1Q0__WhWD1sI82cfbUPkc/edit MBGLab--Short-Bios-for-Use-in-Justifications--a1iHf5] or [http://goo.gl/a1iHf5 http://goo.gl/a1iHf5])<br /> <br /> <br /> ==Other Listings of Lab People==<br /> *[https://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia page]<br /> *[https://www.linkedin.com/groups/11900219/ Linked In Group] (You need to login to LinkedIn to see this page. Everyone in the lab and lab alumni should join our LinkedIn group.)<br /> *[http://academictree.org/compbio/tree.php?pid=31611 Academic Tree]<br /> *[http://genealogy.math.ndsu.nodak.edu/id.php?id=69445 Math Genealogy Project]<br /> <br /> ==Older Snapshots==<br /> <br /> === as of 12 Dec '24 ===<br /> Current Lab People [http://info.gersteinlab.org/images/b/ba/MBG_curr_20241209.pdf pdf] and [http://info.gersteinlab.org/images/6/67/MBG_curr_20241209.docx docx]<br /> <br /> Past Lab People [https://info.gersteinlab.org/images/f/fe/MBG_Alum_20241215.pdf pdf] and [https://info.gersteinlab.org/images/4/47/MBG_Alum_20241215.docx docx]<br /> <br /> === as of 29 June '23 ===<br /> Current Lab People [http://info.gersteinlab.org/images/8/83/MBG_curr_20230629.pdf pdf] and [http://info.gersteinlab.org/images/0/01/MBG_curr_20230629.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/8/8a/MBG_Alum_20230629.pdf pdf] and [http://info.gersteinlab.org/images/7/71/MBG_Alum_20230629.docx docx]<br /> <br /> === as of 27 Dec '22 ===<br /> Current Lab People [http://info.gersteinlab.org/images/e/e1/MBG_curr_20221227.pdf pdf] and [http://info.gersteinlab.org/images/0/0b/MBG_curr_20221227.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/5/5d/MBG_Alum_20221227.pdf pdf] and [http://info.gersteinlab.org/images/b/b8/MBG_Alum_20221227.docx docx]<br /> <br /> === as of 20 Dec '21 ===<br /> Current Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_curr_20211220.pdf pdf]<br /> <br /> Past Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_alum_20211220.pdf pdf]<br /> <br /> === as of 25 Apr '21 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_curr_20210425.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_alum_20210425.pdf pdf]<br /> <br /> === as of 21 Nov '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/11.21/gerstein_lab_curr_20201121.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/11.06/gerstein_lab_alum_20201106.pdf pdf]<br /> <br /> === as of 07 June '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_curr_20200607.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_alum_20200607.pdf pdf]<br /> <br /> === as of 12 Sept '19 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20190912.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_alum_20190912.pdf pdf]<br /> <br /> === as of 16 Oct '18 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181016.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181005.pdf pdf]<br /> <br /> === as of 8 Jan '18 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-22-bld8Jan18--AdaptedFrom--gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-23-bld27dec17--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as of 7 Dec '17 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_alum.pdf pdf]<br /> <br /> === as of 1 Dec '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-22-bld1dec16-AdaptedFrom--Gerstein_Lab_Personnel_112016.pdf pdf]<br /> <br /> Past Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-23-bld1dec16--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as 28 Jan '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/people-page-dump-28Jan16 dump dir]<br /> <br /> === as of 31 Sep. '14 ===<br /> <br /> Past Lab People [http://labmisc.gersteinlab.org/archive/Past_Postdoctoral_Associates_and_Fellows_Sep_14.pdf pdf]<br /> <br /> === as of 31 Dec. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-alums-CV-31Dec2013.pdf pdf]<br /> <br /> === as of 1 Jan. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2013/07.22/M-Gerstein-lab-people-n-alumni-1jan13-extract-from-pub-cv.pdf pdf]<br /> <br /> === as of 15 August '12 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/07.28/Past-Lab-People-as-of-15aug2012.pdf pdf]<br /> <br /> === as of 1 Dec. '11 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Lab-Personnel-and-Alumni-1Dec2011.pdf pdf]<br /> <br /> ==Misc==<br /> Lab [https://sites.gersteinlab.org/lab-reunion/ reunion] in 2019 <br /> <br /> Space usage by people affiliated with Gerstein lab from 7/1/2012 to 6/30/2013 [https://docs.google.com/spreadsheet/ccc?key=0AnSCkRiRBZ5KdGlfbGVKTmxNNTdTSlJINTU3eFFBdmc&amp;usp=sharing gsheet]<br /> <br /> Lab member [http://www.gersteinlab.org/people/map.html map]<br /> <br /> [http://www.gersteinlab.org/people/contact.html Personal Contact Information]<br /> <br /> [http://www.gersteinlab.org/people/files/acknowledgements.pdf Acknowledgements]<br /> <br /> A statistical [[summary of undergraduate involvement]] in the lab<br /> <br /> Previous Years' Personnel List<br /> <br /> [http://www.gersteinlab.org/people/files/people2005.html 2005]<br /> [http://www.gersteinlab.org/people/files/people2004.html 2004]<br /> [http://www.gersteinlab.org/people/files/people2003.html 2003]<br /> [http://www.gersteinlab.org/people/files/people2002.htm 2002]<br /> [http://www.gersteinlab.org/people/files/people2001.htm 2001]<br /> [http://www.gersteinlab.org/people/files/people2000.htm 2000]<br /> [http://www.gersteinlab.org/people/files/people1999.htm 1999]<br /> [http://www.gersteinlab.org/people/files/people1998.htm 1998]<br /> [http://www.gersteinlab.org/people/files/people1997.htm 1997]<br /> <br /> [https://docs.google.com/document/d/1zGmv764chmcFLhDg0G_caykJIB2ll0OX4eNSCeQnJQw/edit?usp=sharing Private Wiki for people page (Google doc)]<br /> [http://wiki.gersteinlab.org/labinfo/People_Page Private Wiki for people page (deprecated)]</div>

Public https://info.gersteinlab.org/index.php?title=Additional_Information_about_Personnel&diff=6349 2025-12-11T21:39:33Z

<p>Public: </p> <hr /> <div>==Most Current Snapshot of Lab People==<br /> <br /> Current lab people (as of 11 Dec 2025) [https://info.gersteinlab.org/images/c/cb/MBG_curr_20251211.pdf PDF] [https://info.gersteinlab.org/images/7/7c/MBG_curr_20251211.docx DOCX]<br /> <br /> Past lab people (as of 15 Dec 2024) [https://info.gersteinlab.org/images/f/fe/MBG_Alum_20241215.pdf PDF] [https://info.gersteinlab.org/images/4/47/MBG_Alum_20241215.docx DOCX]<br /> <br /> Google sheet for all undergrad information [https://docs.google.com/spreadsheets/d/10GR54kpytt8qFmrdLpwe6mtl2Jfc0Iv9qfdAY_9YWsY/edit?usp=sharing]<br /> <br /> Public view of the undergrad information [https://docs.google.com/spreadsheets/d/1RGBGWd_-_u5K4UblhYg6f7_SM09Qc6JyY9UXpqQ-a-U/edit?usp=sharing]<br /> <br /> [http://www.gersteinlab.org/people/initial.html List]of people with initial<br /> <br /> ==Justification Bios==<br /> Gerstein Lab Bios for Use in Justifications ([https://docs.google.com/document/d/1EkxjRHpMJRpL7jRCLHA2fk1Q0__WhWD1sI82cfbUPkc/edit MBGLab--Short-Bios-for-Use-in-Justifications--a1iHf5] or [http://goo.gl/a1iHf5 http://goo.gl/a1iHf5])<br /> <br /> <br /> ==Other Listings of Lab People==<br /> *[https://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia page]<br /> *[https://www.linkedin.com/groups/11900219/ Linked In Group] (You need to login to LinkedIn to see this page. Everyone in the lab and lab alumni should join our LinkedIn group.)<br /> *[http://academictree.org/compbio/tree.php?pid=31611 Academic Tree]<br /> *[http://genealogy.math.ndsu.nodak.edu/id.php?id=69445 Math Genealogy Project]<br /> <br /> ==Older Snapshots==<br /> <br /> === as of 12 Dec '24 ===<br /> Current Lab People [http://info.gersteinlab.org/images/b/ba/MBG_curr_20241209.pdf pdf] and [http://info.gersteinlab.org/images/6/67/MBG_curr_20241209.docx docx]<br /> <br /> Past Lab People [https://info.gersteinlab.org/images/f/fe/MBG_Alum_20241215.pdf pdf] and [https://info.gersteinlab.org/images/4/47/MBG_Alum_20241215.docx docx]<br /> <br /> === as of 29 June '23 ===<br /> Current Lab People [http://info.gersteinlab.org/images/8/83/MBG_curr_20230629.pdf pdf] and [http://info.gersteinlab.org/images/0/01/MBG_curr_20230629.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/8/8a/MBG_Alum_20230629.pdf pdf] and [http://info.gersteinlab.org/images/7/71/MBG_Alum_20230629.docx docx]<br /> <br /> === as of 27 Dec '22 ===<br /> Current Lab People [http://info.gersteinlab.org/images/e/e1/MBG_curr_20221227.pdf pdf] and [http://info.gersteinlab.org/images/0/0b/MBG_curr_20221227.docx docx]<br /> <br /> Past Lab People [http://info.gersteinlab.org/images/5/5d/MBG_Alum_20221227.pdf pdf] and [http://info.gersteinlab.org/images/b/b8/MBG_Alum_20221227.docx docx]<br /> <br /> === as of 20 Dec '21 ===<br /> Current Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_curr_20211220.pdf pdf]<br /> <br /> Past Lab People [http://files2.gersteinlab.org/public-docs/2021/12.20/gerstein_lab_alum_20211220.pdf pdf]<br /> <br /> === as of 25 Apr '21 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_curr_20210425.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2021/04.25/gerstein_lab_alum_20210425.pdf pdf]<br /> <br /> === as of 21 Nov '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/11.21/gerstein_lab_curr_20201121.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/11.06/gerstein_lab_alum_20201106.pdf pdf]<br /> <br /> === as of 07 June '20 ===<br /> Current Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_curr_20200607.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2020/06.07/gerstein_lab_alum_20200607.pdf pdf]<br /> <br /> === as of 12 Sept '19 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20190912.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_alum_20190912.pdf pdf]<br /> <br /> === as of 16 Oct '18 ===<br /> <br /> Current Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181016.pdf pdf]<br /> <br /> Past Lab People [http://www.gersteinlab.org/people/files/gerstein_lab_curr_20181005.pdf pdf]<br /> <br /> === as of 8 Jan '18 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-22-bld8Jan18--AdaptedFrom--gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2018/01.10/cv57-23-bld27dec17--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as of 7 Dec '17 ===<br /> <br /> Current Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_people_12_7_17.pdf pdf]<br /> <br /> Past Lab People [http://files.gersteinlab.org/public-docs/2017/12.14/gerstein_lab_alum.pdf pdf]<br /> <br /> === as of 1 Dec '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-22-bld1dec16-AdaptedFrom--Gerstein_Lab_Personnel_112016.pdf pdf]<br /> <br /> Past Lab People [http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-23-bld1dec16--EditOn--Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf pdf]<br /> <br /> === as 28 Jan '16 ===<br /> <br /> Current Lab People [http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/people-page-dump-28Jan16 dump dir]<br /> <br /> === as of 31 Sep. '14 ===<br /> <br /> Past Lab People [http://labmisc.gersteinlab.org/archive/Past_Postdoctoral_Associates_and_Fellows_Sep_14.pdf pdf]<br /> <br /> === as of 31 Dec. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-alums-CV-31Dec2013.pdf pdf]<br /> <br /> === as of 1 Jan. '13 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2013/07.22/M-Gerstein-lab-people-n-alumni-1jan13-extract-from-pub-cv.pdf pdf]<br /> <br /> === as of 15 August '12 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/07.28/Past-Lab-People-as-of-15aug2012.pdf pdf]<br /> <br /> === as of 1 Dec. '11 ===<br /> <br /> Past Lab People [http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Lab-Personnel-and-Alumni-1Dec2011.pdf pdf]<br /> <br /> ==Misc==<br /> Lab [https://sites.gersteinlab.org/lab-reunion/ reunion] in 2019 <br /> <br /> Space usage by people affiliated with Gerstein lab from 7/1/2012 to 6/30/2013 [https://docs.google.com/spreadsheet/ccc?key=0AnSCkRiRBZ5KdGlfbGVKTmxNNTdTSlJINTU3eFFBdmc&amp;usp=sharing gsheet]<br /> <br /> Lab member [http://www.gersteinlab.org/people/map.html map]<br /> <br /> [http://www.gersteinlab.org/people/contact.html Personal Contact Information]<br /> <br /> [http://www.gersteinlab.org/people/files/acknowledgements.pdf Acknowledgements]<br /> <br /> A statistical [[summary of undergraduate involvement]] in the lab<br /> <br /> Previous Years' Personnel List<br /> <br /> [http://www.gersteinlab.org/people/files/people2005.html 2005]<br /> [http://www.gersteinlab.org/people/files/people2004.html 2004]<br /> [http://www.gersteinlab.org/people/files/people2003.html 2003]<br /> [http://www.gersteinlab.org/people/files/people2002.htm 2002]<br /> [http://www.gersteinlab.org/people/files/people2001.htm 2001]<br /> [http://www.gersteinlab.org/people/files/people2000.htm 2000]<br /> [http://www.gersteinlab.org/people/files/people1999.htm 1999]<br /> [http://www.gersteinlab.org/people/files/people1998.htm 1998]<br /> [http://www.gersteinlab.org/people/files/people1997.htm 1997]<br /> <br /> [https://docs.google.com/document/d/1zGmv764chmcFLhDg0G_caykJIB2ll0OX4eNSCeQnJQw/edit?usp=sharing Private Wiki for people page (Google doc)]<br /> [http://wiki.gersteinlab.org/labinfo/People_Page Private Wiki for people page (deprecated)]</div>

Public https://info.gersteinlab.org/index.php?title=File:MBG_curr_20251211.docx&diff=6348 2025-12-11T21:39:14Z

<p>Public: </p> <hr /> <div></div>

Public https://info.gersteinlab.org/index.php?title=File:MBG_curr_20251211.pdf&diff=6347 2025-12-11T21:35:23Z

<p>Public: </p> <hr /> <div></div>

Public https://info.gersteinlab.org/index.php?title=Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work&diff=6309 2025-11-25T15:20:47Z

<p>Public: /* 2025 */</p> <hr /> <div>__NOTOC__<br /> === 2025 ===<br /> <br /> *[https://news.yale.edu/2025/11/18/uncovering-hidden-cellular-connections-bridge-aging-and-disease Uncovering the hidden cellular connections that bridge aging and disease (Yale News)]<br /> *[https://news.yale.edu/2025/08/19/timing-everything-finding-treatment-windows-genetic-brain-disease?utm_source=YaleToday&amp;utm_medium=email&amp;utm_campaign=YT_YaleToday-Staff_8-25-2025 Timing is everything: Finding treatment windows in genetic brain disease. (Yale News)]<br /> *[https://medicine.yale.edu/news/yale-medicine-magazine/article/can-ai-predict-the-future/ Can AI Predict the Future? (Yale Medicine Magazine)]<br /> *[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]<br /> <br /> === 2024 ===<br /> *'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''<br /> *[https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/ AI tool that predicts gene activity could open path for disease treatments (Washington Post)]<br /> *'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''<br /> *[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]<br /> *[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]<br /> <br /> === 2023 ===<br /> * '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''<br /> * [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]<br /> ** [https://news.yale.edu/2023/08/01/mark-gerstein-receives-iscb-accomplishments-senior-scientist-award ISCB Award (Yale Release)] [https://mbb.yale.edu/news/mark-gerstein-receives-iscbs-2023-accomplishments-senior-scientist-award (#2)]<br /> <br /> === 2022 ===<br /> *[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]<br /> *[https://www.nytimes.com/2022/08/12/nyregion/database-new-yorkers-dna.html Hospital and Drugmaker Move to Build Vast Database of New Yorkers’ DNA (NY Times)]<br /> *[https://news.yale.edu/2022/06/29/blockchain-not-just-bitcoin-it-can-secure-and-store-genomes-too Blockchain not just for bitcoin: It can secure and store genomes, too (Yale Release)]<br /> **[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]<br /> === 2021 ===<br /> *[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]<br /> *[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]<br /> === 2020 ===<br /> * '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''<br /> * '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''<br /> === 2019 ===<br /> * '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]''' <br /> === 2018 ===<br /> * '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''<br /> *[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]<br /> *[https://yaledailynews.com/blog/2018/06/14/long-awaited-stem-report-calls-for-new-research-institutes Long-awaited STEM report calls for new research institutes (YDN)]<br /> *[http://blogs.nature.com/naturejobs/2018/04/11/clean-your-email-inbox-with-a-low-spam-diet Put your email inbox on a low-spam diet (Nature)]<br /> === 2017 ===<br /> *[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]<br /> *[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]<br /> *[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]<br /> <br /> === 2016 ===<br /> * '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''<br /> * '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''<br /> * [http://news.yale.edu/2016/04/18/research-note-don-t-forget-parents-when-celebrating-personal-genome Don’t forget parents when celebrating a personal genome (Yale Press Release)]<br /> <br /> === 2014 ===<br /> <br /> * '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''<br /> *[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]<br /> <br /> === 2013 ===<br /> <br /> * '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''<br /> *[http://www.nytimes.com/2013/06/18/science/poking-holes-in-the-privacy-of-dna.html?_r=0 Poking Holes in Genetic Privacy (The New York Times)]<br /> *[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]<br /> <br /> === 2012 ===<br /> <br /> * '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''<br /> ** [http://news.yale.edu/2012/09/05/yale-team-finds-order-amidst-chaos-within-human-genome-mom-and-dad-s-contributions-counte Yale team finds order amidst the chaos within the human genome; Mom and Dad's contributions counted and fossil DNA not dead after all (Yale Press Release)]<br /> * [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]<br /> ** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]<br /> ** [http://www.washingtonpost.com/national/health-science/genome-news-flash-were-all-a-little-bit-broken/2012/02/15/gIQAyacKIR_story.html Genome news flash: We’re all a little bit broken (The Washington Post)]<br /> * [http://www.nytimes.com/2012/05/04/science/it-started-with-genome-omes-proliferate-in-science.html It Started With ‘Genome’ - ‘Omes’ Proliferate in Science (The New York Times)]<br /> <br /> === 2011 ===<br /> *[http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html DNA Sequencing Caught in Deluge of Data (The New York Times)]<br /> *[http://science.energy.gov/news/in-the-news/2011/07-07-11/ National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase (U.S. DOE Office of Science)]<br /> * [http://news.yale.edu/2011/12/06/11-million-grant-makes-yale-national-center-study-rare-diseases $11 Million grant makes Yale a national center for study of rare diseases (Yale Press Release)]<br /> <br /> === 2010 ===<br /> <br /> *[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]<br /> *[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]<br /> *[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]<br /> * [http://news.yale.edu/2010/01/15/aaas-honors-four-yale-faculty-their-scientific-research AAAS Honors Four Yale Faculty for Their Scientific Research (Yale Press Release)]<br /> * [http://news.yale.edu/2010/12/22/massive-molecular-study-roundworm-reveals-nature-s-complexity Massive Molecular Study of the Roundworm Reveals Nature's Complexity (Yale Press Release)]<br /> * [http://news.yale.edu/2010/05/03/yale-scientists-explain-why-computers-crash-we-don-t Yale Scientists Explain Why Computers Crash But We Don't (Yale Press Release)]<br /> ** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]<br /> * [http://news.yale.edu/2010/03/29/molecular-middle-managers-make-more-decisions-bosses Molecular Middle Managers Make More Decisions Than Bosses (Yale Press Release)]<br /> <br /> === 2009 ===<br /> <br /> * [http://news.yale.edu/2009/12/27/yale-researchers-create-new-way-locate-big-genetic-variants Yale Researchers Create New Way To Locate Big Genetic Variants (Yale Press Release)]<br /> * [http://news.yale.edu/2009/01/22/mixing-genomics-and-geography-yields-insights-life-and-environment Mixing Genomics and Geography Yields Insights into Life and Environment (Yale Press Release)]<br /> <br /> === 2008 ===<br /> <br /> * [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]<br /> <br /> === 2007 ===<br /> <br /> * [http://news.yale.edu/2007/02/28/genome-sequence-shows-what-makes-bacteria-dangerous-troops-iraq-0 Genome Sequence Shows What Makes Bacteria Dangerous for Troops in Iraq (Yale Press Release)]<br /> <br /> === 2003 ===<br /> <br /> * [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]<br /> <br /> === 2001 ===<br /> <br /> * [http://new.yale.edu/2001/09/12/yale-scientists-receive-15-million-grant-human-genome-research Yale Scientists Receive $15 Million Grant for Human Genome Research (Yale Press Release)]<br /> <br /> === 2000 ===<br /> <br /> * Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&amp;E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])<br /> <br /> === 1998 ===<br /> <br /> * [http://news.yale.edu/1998/11/12/donaghue-investigator-program-awards-new-grants-yale-research-spinal-cord-injuries-cancer Donaghue Investigator Program Awards New Grants to Yale For Research on Spinal Cord Injuries, Cancer Metastasis, Elderly (Yale Press Release)]<br /> <br /> == More Stuff ==<br /> * Recent microblog [http://linkstream2.gerstein.info/category/x78qt listing] mentions of the lab in the press, with [http://linkstream2.gerstein.info/category/x78qtcore key bits] highlighted . ([http://linkstream2.gerstein.info/tag/x78qt Other items], potentially redundant.)<br /> * A [https://news.google.com/search?q=mark%20gerstein%20yale&amp;hl=en-US&amp;gl=US&amp;ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6308 2025-11-23T17:33:52Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper. After the press release is issued, we will add it to the Gerstein Lab press release page.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> *** We might have to do a justification for this. Here is some sample text: , noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Funding is usually applicable when MG is the last author.<br /> <br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)<br /> *** For data deposition, we will follow a three-tier approach: (1) primary code and supplementary tables will be hosted on the Gerstein Lab GitHub and provided as journal supplements; (2) the same materials, along with larger files, will be deposited on Dryad (which supports larger file sizes than Zenodo); and (3) all datasets will also be mirrored on the Gerstein Lab data server (files.gersteinlab.org).<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * Preprints<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet &amp; Bluesky<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6307 2025-11-23T17:31:33Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> *** We might have to do a justification for this. Here is some sample text: , noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Funding is usually applicable when MG is the last author.<br /> <br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)<br /> *** For data deposition, we will follow a three-tier approach: (1) primary code and supplementary tables will be hosted on the Gerstein Lab GitHub and provided as journal supplements; (2) the same materials, along with larger files, will be deposited on Dryad (which supports larger file sizes than Zenodo); and (3) all datasets will also be mirrored on the Gerstein Lab data server (files.gersteinlab.org).<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * Preprints<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet &amp; Bluesky<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6305 2025-10-27T14:29:16Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> [https://files.gersteinlab.org/public-docs/2025/10.27/g0biomedx_Summary.pdf Gerstein lab experience with construction of cell-type specific gene regulatory networks (GRNs)] uploaded by Mor on Oct 27 2025 (g0biomedx)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/09.09/g0sony2_summary.docx Gerstein lab experience with molecular mechanisms underlying diseases using large language models (LLMs)] uploaded by MOR on Sep 9 2025 (g0sony2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0laadsi--summary.docx Gerstein lab experience in building a tools for (a) predicting protein-compound interaction strengths and (b) building gene regulatory networks] uploaded by DC on Jun 30 2025 (g0laadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6303 2025-09-09T20:56:26Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/09.09/g0sony2_summary.docx Gerstein lab experience with molecular mechanisms underlying diseases using large language models (LLMs)] uploaded by MOR on Sep 9 2025 (g0sony2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0laadsi--summary.docx Gerstein lab experience in building a tools for (a) predicting protein-compound interaction strengths and (b) building gene regulatory networks] uploaded by DC on Jun 30 2025 (g0laadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work&diff=6302 2025-09-08T12:47:01Z

<p>Public: /* 2025 */</p> <hr /> <div>__NOTOC__<br /> === 2025 ===<br /> <br /> *[https://news.yale.edu/2025/08/19/timing-everything-finding-treatment-windows-genetic-brain-disease?utm_source=YaleToday&amp;utm_medium=email&amp;utm_campaign=YT_YaleToday-Staff_8-25-2025 Timing is everything: Finding treatment windows in genetic brain disease. (Yale News)]<br /> *[https://medicine.yale.edu/news/yale-medicine-magazine/article/can-ai-predict-the-future/ Can AI Predict the Future? (Yale Medicine Magazine)]<br /> *[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]<br /> <br /> === 2024 ===<br /> *'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''<br /> *[https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/ AI tool that predicts gene activity could open path for disease treatments (Washington Post)]<br /> *'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''<br /> *[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]<br /> *[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]<br /> <br /> === 2023 ===<br /> * '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''<br /> * [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]<br /> ** [https://news.yale.edu/2023/08/01/mark-gerstein-receives-iscb-accomplishments-senior-scientist-award ISCB Award (Yale Release)] [https://mbb.yale.edu/news/mark-gerstein-receives-iscbs-2023-accomplishments-senior-scientist-award (#2)]<br /> <br /> === 2022 ===<br /> *[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]<br /> *[https://www.nytimes.com/2022/08/12/nyregion/database-new-yorkers-dna.html Hospital and Drugmaker Move to Build Vast Database of New Yorkers’ DNA (NY Times)]<br /> *[https://news.yale.edu/2022/06/29/blockchain-not-just-bitcoin-it-can-secure-and-store-genomes-too Blockchain not just for bitcoin: It can secure and store genomes, too (Yale Release)]<br /> **[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]<br /> === 2021 ===<br /> *[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]<br /> *[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]<br /> === 2020 ===<br /> * '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''<br /> * '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''<br /> === 2019 ===<br /> * '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]''' <br /> === 2018 ===<br /> * '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''<br /> *[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]<br /> *[https://yaledailynews.com/blog/2018/06/14/long-awaited-stem-report-calls-for-new-research-institutes Long-awaited STEM report calls for new research institutes (YDN)]<br /> *[http://blogs.nature.com/naturejobs/2018/04/11/clean-your-email-inbox-with-a-low-spam-diet Put your email inbox on a low-spam diet (Nature)]<br /> === 2017 ===<br /> *[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]<br /> *[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]<br /> *[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]<br /> <br /> === 2016 ===<br /> * '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''<br /> * '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''<br /> * [http://news.yale.edu/2016/04/18/research-note-don-t-forget-parents-when-celebrating-personal-genome Don’t forget parents when celebrating a personal genome (Yale Press Release)]<br /> <br /> === 2014 ===<br /> <br /> * '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''<br /> *[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]<br /> <br /> === 2013 ===<br /> <br /> * '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''<br /> *[http://www.nytimes.com/2013/06/18/science/poking-holes-in-the-privacy-of-dna.html?_r=0 Poking Holes in Genetic Privacy (The New York Times)]<br /> *[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]<br /> <br /> === 2012 ===<br /> <br /> * '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''<br /> ** [http://news.yale.edu/2012/09/05/yale-team-finds-order-amidst-chaos-within-human-genome-mom-and-dad-s-contributions-counte Yale team finds order amidst the chaos within the human genome; Mom and Dad's contributions counted and fossil DNA not dead after all (Yale Press Release)]<br /> * [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]<br /> ** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]<br /> ** [http://www.washingtonpost.com/national/health-science/genome-news-flash-were-all-a-little-bit-broken/2012/02/15/gIQAyacKIR_story.html Genome news flash: We’re all a little bit broken (The Washington Post)]<br /> * [http://www.nytimes.com/2012/05/04/science/it-started-with-genome-omes-proliferate-in-science.html It Started With ‘Genome’ - ‘Omes’ Proliferate in Science (The New York Times)]<br /> <br /> === 2011 ===<br /> *[http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html DNA Sequencing Caught in Deluge of Data (The New York Times)]<br /> *[http://science.energy.gov/news/in-the-news/2011/07-07-11/ National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase (U.S. DOE Office of Science)]<br /> * [http://news.yale.edu/2011/12/06/11-million-grant-makes-yale-national-center-study-rare-diseases $11 Million grant makes Yale a national center for study of rare diseases (Yale Press Release)]<br /> <br /> === 2010 ===<br /> <br /> *[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]<br /> *[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]<br /> *[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]<br /> * [http://news.yale.edu/2010/01/15/aaas-honors-four-yale-faculty-their-scientific-research AAAS Honors Four Yale Faculty for Their Scientific Research (Yale Press Release)]<br /> * [http://news.yale.edu/2010/12/22/massive-molecular-study-roundworm-reveals-nature-s-complexity Massive Molecular Study of the Roundworm Reveals Nature's Complexity (Yale Press Release)]<br /> * [http://news.yale.edu/2010/05/03/yale-scientists-explain-why-computers-crash-we-don-t Yale Scientists Explain Why Computers Crash But We Don't (Yale Press Release)]<br /> ** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]<br /> * [http://news.yale.edu/2010/03/29/molecular-middle-managers-make-more-decisions-bosses Molecular Middle Managers Make More Decisions Than Bosses (Yale Press Release)]<br /> <br /> === 2009 ===<br /> <br /> * [http://news.yale.edu/2009/12/27/yale-researchers-create-new-way-locate-big-genetic-variants Yale Researchers Create New Way To Locate Big Genetic Variants (Yale Press Release)]<br /> * [http://news.yale.edu/2009/01/22/mixing-genomics-and-geography-yields-insights-life-and-environment Mixing Genomics and Geography Yields Insights into Life and Environment (Yale Press Release)]<br /> <br /> === 2008 ===<br /> <br /> * [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]<br /> <br /> === 2007 ===<br /> <br /> * [http://news.yale.edu/2007/02/28/genome-sequence-shows-what-makes-bacteria-dangerous-troops-iraq-0 Genome Sequence Shows What Makes Bacteria Dangerous for Troops in Iraq (Yale Press Release)]<br /> <br /> === 2003 ===<br /> <br /> * [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]<br /> <br /> === 2001 ===<br /> <br /> * [http://new.yale.edu/2001/09/12/yale-scientists-receive-15-million-grant-human-genome-research Yale Scientists Receive $15 Million Grant for Human Genome Research (Yale Press Release)]<br /> <br /> === 2000 ===<br /> <br /> * Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&amp;E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])<br /> <br /> === 1998 ===<br /> <br /> * [http://news.yale.edu/1998/11/12/donaghue-investigator-program-awards-new-grants-yale-research-spinal-cord-injuries-cancer Donaghue Investigator Program Awards New Grants to Yale For Research on Spinal Cord Injuries, Cancer Metastasis, Elderly (Yale Press Release)]<br /> <br /> == More Stuff ==<br /> * Recent microblog [http://linkstream2.gerstein.info/category/x78qt listing] mentions of the lab in the press, with [http://linkstream2.gerstein.info/category/x78qtcore key bits] highlighted . ([http://linkstream2.gerstein.info/tag/x78qt Other items], potentially redundant.)<br /> * A [https://news.google.com/search?q=mark%20gerstein%20yale&amp;hl=en-US&amp;gl=US&amp;ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)</div>

Public https://info.gersteinlab.org/index.php?title=Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work&diff=6301 2025-09-08T12:46:30Z

<p>Public: /* 2025 */</p> <hr /> <div>__NOTOC__<br /> === 2025 ===<br /> <br /> *[https://medicine.yale.edu/news/yale-medicine-magazine/article/can-ai-predict-the-future/ Can AI Predict the Future? (Yale Medicine Magazine)]<br /> *[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]<br /> *[https://news.yale.edu/2025/08/19/timing-everything-finding-treatment-windows-genetic-brain-disease?utm_source=YaleToday&amp;utm_medium=email&amp;utm_campaign=YT_YaleToday-Staff_8-25-2025 Timing is everything: Finding treatment windows in genetic brain disease. (Yale News)]<br /> <br /> === 2024 ===<br /> *'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''<br /> *[https://www.washingtonpost.com/science/2025/01/09/ai-predicts-gene-activity/ AI tool that predicts gene activity could open path for disease treatments (Washington Post)]<br /> *'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''<br /> *[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]<br /> *[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]<br /> <br /> === 2023 ===<br /> * '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''<br /> * [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]<br /> ** [https://news.yale.edu/2023/08/01/mark-gerstein-receives-iscb-accomplishments-senior-scientist-award ISCB Award (Yale Release)] [https://mbb.yale.edu/news/mark-gerstein-receives-iscbs-2023-accomplishments-senior-scientist-award (#2)]<br /> <br /> === 2022 ===<br /> *[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]<br /> *[https://www.nytimes.com/2022/08/12/nyregion/database-new-yorkers-dna.html Hospital and Drugmaker Move to Build Vast Database of New Yorkers’ DNA (NY Times)]<br /> *[https://news.yale.edu/2022/06/29/blockchain-not-just-bitcoin-it-can-secure-and-store-genomes-too Blockchain not just for bitcoin: It can secure and store genomes, too (Yale Release)]<br /> **[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]<br /> === 2021 ===<br /> *[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]<br /> *[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]<br /> === 2020 ===<br /> * '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''<br /> * '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''<br /> === 2019 ===<br /> * '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]''' <br /> === 2018 ===<br /> * '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''<br /> *[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]<br /> *[https://yaledailynews.com/blog/2018/06/14/long-awaited-stem-report-calls-for-new-research-institutes Long-awaited STEM report calls for new research institutes (YDN)]<br /> *[http://blogs.nature.com/naturejobs/2018/04/11/clean-your-email-inbox-with-a-low-spam-diet Put your email inbox on a low-spam diet (Nature)]<br /> === 2017 ===<br /> *[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]<br /> *[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]<br /> *[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]<br /> <br /> === 2016 ===<br /> * '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''<br /> * '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''<br /> * [http://news.yale.edu/2016/04/18/research-note-don-t-forget-parents-when-celebrating-personal-genome Don’t forget parents when celebrating a personal genome (Yale Press Release)]<br /> <br /> === 2014 ===<br /> <br /> * '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''<br /> *[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]<br /> <br /> === 2013 ===<br /> <br /> * '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''<br /> *[http://www.nytimes.com/2013/06/18/science/poking-holes-in-the-privacy-of-dna.html?_r=0 Poking Holes in Genetic Privacy (The New York Times)]<br /> *[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]<br /> <br /> === 2012 ===<br /> <br /> * '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''<br /> ** [http://news.yale.edu/2012/09/05/yale-team-finds-order-amidst-chaos-within-human-genome-mom-and-dad-s-contributions-counte Yale team finds order amidst the chaos within the human genome; Mom and Dad's contributions counted and fossil DNA not dead after all (Yale Press Release)]<br /> * [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]<br /> ** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]<br /> ** [http://www.washingtonpost.com/national/health-science/genome-news-flash-were-all-a-little-bit-broken/2012/02/15/gIQAyacKIR_story.html Genome news flash: We’re all a little bit broken (The Washington Post)]<br /> * [http://www.nytimes.com/2012/05/04/science/it-started-with-genome-omes-proliferate-in-science.html It Started With ‘Genome’ - ‘Omes’ Proliferate in Science (The New York Times)]<br /> <br /> === 2011 ===<br /> *[http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html DNA Sequencing Caught in Deluge of Data (The New York Times)]<br /> *[http://science.energy.gov/news/in-the-news/2011/07-07-11/ National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase (U.S. DOE Office of Science)]<br /> * [http://news.yale.edu/2011/12/06/11-million-grant-makes-yale-national-center-study-rare-diseases $11 Million grant makes Yale a national center for study of rare diseases (Yale Press Release)]<br /> <br /> === 2010 ===<br /> <br /> *[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]<br /> *[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]<br /> *[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]<br /> * [http://news.yale.edu/2010/01/15/aaas-honors-four-yale-faculty-their-scientific-research AAAS Honors Four Yale Faculty for Their Scientific Research (Yale Press Release)]<br /> * [http://news.yale.edu/2010/12/22/massive-molecular-study-roundworm-reveals-nature-s-complexity Massive Molecular Study of the Roundworm Reveals Nature's Complexity (Yale Press Release)]<br /> * [http://news.yale.edu/2010/05/03/yale-scientists-explain-why-computers-crash-we-don-t Yale Scientists Explain Why Computers Crash But We Don't (Yale Press Release)]<br /> ** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]<br /> * [http://news.yale.edu/2010/03/29/molecular-middle-managers-make-more-decisions-bosses Molecular Middle Managers Make More Decisions Than Bosses (Yale Press Release)]<br /> <br /> === 2009 ===<br /> <br /> * [http://news.yale.edu/2009/12/27/yale-researchers-create-new-way-locate-big-genetic-variants Yale Researchers Create New Way To Locate Big Genetic Variants (Yale Press Release)]<br /> * [http://news.yale.edu/2009/01/22/mixing-genomics-and-geography-yields-insights-life-and-environment Mixing Genomics and Geography Yields Insights into Life and Environment (Yale Press Release)]<br /> <br /> === 2008 ===<br /> <br /> * [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]<br /> <br /> === 2007 ===<br /> <br /> * [http://news.yale.edu/2007/02/28/genome-sequence-shows-what-makes-bacteria-dangerous-troops-iraq-0 Genome Sequence Shows What Makes Bacteria Dangerous for Troops in Iraq (Yale Press Release)]<br /> <br /> === 2003 ===<br /> <br /> * [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]<br /> <br /> === 2001 ===<br /> <br /> * [http://new.yale.edu/2001/09/12/yale-scientists-receive-15-million-grant-human-genome-research Yale Scientists Receive $15 Million Grant for Human Genome Research (Yale Press Release)]<br /> <br /> === 2000 ===<br /> <br /> * Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&amp;E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])<br /> <br /> === 1998 ===<br /> <br /> * [http://news.yale.edu/1998/11/12/donaghue-investigator-program-awards-new-grants-yale-research-spinal-cord-injuries-cancer Donaghue Investigator Program Awards New Grants to Yale For Research on Spinal Cord Injuries, Cancer Metastasis, Elderly (Yale Press Release)]<br /> <br /> == More Stuff ==<br /> * Recent microblog [http://linkstream2.gerstein.info/category/x78qt listing] mentions of the lab in the press, with [http://linkstream2.gerstein.info/category/x78qtcore key bits] highlighted . ([http://linkstream2.gerstein.info/tag/x78qt Other items], potentially redundant.)<br /> * A [https://news.google.com/search?q=mark%20gerstein%20yale&amp;hl=en-US&amp;gl=US&amp;ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6235 2025-09-08T01:48:38Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * Preprints<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6234 2025-09-08T01:47:20Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * Preprints<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6233 2025-09-08T01:46:09Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Website <br /> *** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE<br /> *** Best is where the paper ID is what, eg, ABCDE<br /> *** Try to use the GitHub standard for code data <br /> *** Ask MF about the lab GitHub<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6231 2025-09-08T01:41:23Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.<br /> *** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint. <br /> ** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers. <br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6228 2025-09-08T01:23:34Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC &amp; License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]<br /> ** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/<br /> ** If there are problems, don't write to the editor. Write to the publishing people. &quot;production people&quot;<br /> ** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg, lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6227 2025-09-08T01:17:27Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC&amp;License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply.<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6226 2025-09-08T01:16:44Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> *PMC&amp;License<br /> ** For license, go for open access for non-commercial use unless prohibitively expensive.<br /> ** Need to make sure paper comes out in PMC when paper comes out [https://guides.library.yale.edu/nihpolicy/how-to-comply].<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6224 2025-09-08T01:06:32Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** For license, go for open access for non-commercial use unless prohibitively expensive <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6222 2025-09-08T01:06:15Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> <br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** For license, go for open access for non-commercial use unless prohibitively expensive <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6221 2025-09-08T01:05:12Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> ***We should usually acknowledge grant XXX and ALW, noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)<br /> <br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** For license, go for open access for non-commercial use unless prohibitively expensive <br /> ** Funding is usually applicable when MG is the last author.<br /> *** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &amp;lab in the middle -someone else handles.<br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6219 2025-09-08T00:55:44Z

<p>Public: /* Long version of checklist */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> * MG affiliation and Corresponding author<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding + License<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioxriv. <br /> *** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries . For additional ones work with the lab asst. on the correct abbreviation. <br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** For license, go for open access for non-commercial use unless prohibitively expensive <br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Press &amp; PR<br /> ** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Proof_Stage_Checklist&diff=6160 2025-08-18T20:22:30Z

<p>Public: /* Short version */</p> <hr /> <div>==Short version==<br /> * Get grant right! <br /> * correct MG email + ORCID<br /> * papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github <br /> * github should have a license/permissions <br /> * lab homepage image<br /> * tweet <br /> * slide deck<br /> <br /> (see '''&lt;code&gt;Proofsx57m&lt;/code&gt;''' tag on correspondence)<br /> <br /> ==Long version of checklist==<br /> * MG affiliation and Corresponding author<br /> ** CHANGE corresponding email to mark ((at)) gersteinlab.org from pi ((at)) gersteinlab.org<br /> ** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719<br /> ** Check that MG's [[Affiliation]] is accurate <br /> <br /> * Funding + License<br /> ** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)<br /> *** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioxriv. <br /> *** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries . For additional ones work with the lab asst. on the correct abbreviation. <br /> ** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this. <br /> ** For license, go for open access for non-commercial use unless prohibitively expensive <br /> <br /> * Papers Page (papers.gersteinlab.org)<br /> ** Get a lab ID for the paper from Mark (eg lab &quot;ID=cmptxn&quot;). Occasionally, we can use the PubMed ID here, but normally this is the ID that has been used internally during the project pre-publication.<br /> ** Do a papers page rebuild, requires lab ID &amp; website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code<br /> *** Send the following information to whoever is in charge of rebuilding the papers page:<br /> **** PubMed ID or doi of the preprint<br /> **** A link to the paper<br /> **** A link to the tools or resources (see &quot;Tools &amp; Resources&quot; section below)<br /> **** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.<br /> **** Any additional information such as co-first authorship<br /> *** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources<br /> *** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv<br /> ** Co-first and co-corresponding authors can be indicated with the footnote field<br /> ** Use the link field to directly link the journal site (particularly if there is no pubmed)<br /> <br /> * Tools &amp; Resources<br /> ** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) &amp; in the lab github (https://github.gersteinlab.org)<br /> ** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball <br /> ** Make sure you software links the permissions statement &amp; has a license (MIT)<br /> ** Make sure you have a final URL for website/github materials from above and enter it into the papers page <br /> ** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ<br /> ** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)<br /> ** You can use the &quot;website&quot; field on the papers page to link your github site. <br /> <br /> * PMC &amp; preprints<br /> ** make sure journal publishes in PubMed Central (send email to editor to confirm this)<br /> ** Do a biorxiv submission (or another equiv. preprint server) <br /> ** use pi at gersteinlab.org for bioxriv submission<br /> *** Link this from the papers page<br /> *** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ). <br /> <br /> * Slides &amp; Images<br /> ** Make sure Mark has &quot;slide packs&quot; for the paper<br /> *** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org<br /> ** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .<br /> <br /> * Tweet<br /> **Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.<br /> **You can use the lab twitter (@GersteinLab)<br /> **Some recent examples:<br /> https://twitter.com/markgerstein/status/789117961843900417 <br /> https://twitter.com/markgerstein/status/851125314264715267<br /> https://twitter.com/markgerstein/status/813772503063609344<br /> <br /> * Wikipedia<br /> ** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate<br /> <br /> * Tag for this page<br /> ** [[Proofsx57m]]<br /> ** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6157 2025-06-30T23:41:49Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0laadsi--summary.docx Gerstein lab experience in building a tools for (a) predicting protein-compound interaction strengths and (b) building gene regulatory networks] uploaded by DC on Jun 30 2025 (g0laadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6156 2025-06-30T23:19:16Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/g0uncadsi--summary.docx Gerstein lab experience in building a machine learning model for neurogenomics (LNCTP), working with consortia, and disseminating software tools] uploaded by DC on Jun 30 2025 (g0uncadsi)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6155 2025-06-30T17:58:01Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.30/x57gbig_rppr_final_summary.docx Gerstein Lab's Experience in Integrative Deep-Learning Models for Brain Traits Using Genomics and Imaging (Final RPPR)] uploaded by XZ on Jun 30 2025 (x57gbig)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6151 2025-06-24T19:42:35Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.24/g0cgc--summary.docx Gerstein lab experience in cancer genomics and minor splicing] uploaded by DC on Jun 24 2025 (g0cgc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6150 2025-06-10T12:26:05Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.10/g0taxonomy--summary.docx Gerstein lab experience in GENCODE, annotating pseudogenes throughout the genome, and minor introns splicing analysis] uploaded by DC on Jun 10 2025 (g0taxonomy)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6149 2025-06-09T22:14:48Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and leveraging protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0u6c)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6148 2025-06-09T21:56:43Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool in neurodegenerative disease contexts] uploaded by DC on Jun 9 2025 (g0yaleai2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6147 2025-06-09T21:27:58Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/06.09/g0tactical--summary.docx Gerstein lab experience in cancer genomics, minor splicing, and using protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs] uploaded by DC on Jun 9 2025 (g0tactical)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

Public https://info.gersteinlab.org/index.php?title=Old_Resources&diff=6137 2025-04-07T16:39:15Z

<p>Public: </p> <hr /> <div>This is the old tools page. <br /> <br /> See [https://info.gersteinlab.org/Resources '''here'''] for the current up-to-date tools page. <br /> <br /> <br /> =Portals=<br /> <br /> ===Networks===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 10px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:Network.jpg|center|x75px]] &lt;br&gt; [http://networks.gersteinlab.org/ Networks] ||<br /> The Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments. To this end, we have developed a portal for our network research.<br /> |}<br /> <br /> ===Structural Variants (SV)===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:SVpage logo.png‎|center|x85px]] &lt;br&gt; [http://sv.gersteinlab.org/ Structural Variants]||<br /> Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).<br /> |}<br /> <br /> =Data Sets=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style=&quot;width:7%; text-align:center;&quot;|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://resource.psychencode.org/ '''PsychENCODE resource''']||style=&quot;width:7%; text-align:center;&quot;|2018||This website is a comprehensive functional genomic resource for the human brain from PsychENCODE Phase I, including all derived data, integrative models and links to raw data.<br /> |}<br /> <br /> =Evolution=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style=&quot;width:7%; text-align:center;&quot;|2008||An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including statistical coupling analysis (SCA), explicit likelihood of subset variation (ELSC), mutual information and correlation-based methods.<br /> |}<br /> <br /> =Genome Technology=<br /> <br /> ===Gene Regulation===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/Loregic '''Loregic''']||style=&quot;width:7%; text-align:center;&quot;|2015||Loregic is a computational method integrating gene expression and regulatory network data, to characterize the logical cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target, and finds the gate that best matches each triplet’s observed gene expression pattern across many conditions. Using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs.<br /> |}<br /> <br /> ===Allele-Specific Effects===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://alleledb.gersteinlab.org '''AlleleDB''']||style=&quot;width:7%; text-align:center;&quot;|2016||AlleleDB is an online resource for storing and visualizing allele-specific binding (ASB) and gene expression (ASE). Using variants from the 1000-Genomes Project and RNA-seq and ChIP-seq data from related projects, this resource serves as a repository for the catalog of ASB and ASE variants, associated genomic elements and personal genomes used in the study. AlleleDB also interfaces with the UCSC browser for visualization of results.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style=&quot;width:7%; text-align:center;&quot;|2011||AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then maps RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations in which there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified, thereby providing evidence for allele-specific events.<br /> |}<br /> <br /> ===ChIP-Seq ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://music.gersteinlab.org '''MUSIC'''] &lt;br&gt; [http://github.gersteinlab.org/MUSIC/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2014||<br /> MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] &lt;br&gt; [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2009|| A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as input DNA. PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances.<br /> |}<br /> <br /> ===Functional Annotation ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://funseq.gersteinlab.org/ '''FunSeq''']&lt;br&gt; - &amp; - &lt;br&gt;[http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style=&quot;width:7%; text-align:center;&quot;|2013&lt;br&gt;&amp;&lt;br&gt;2014||These tools can be used to automatically score and annotate the disease-causing potential of SNVs, particularly those which are non-coding. FunSeq can detect recurrent annotation elements in non-coding regions when running with multiple personal genomes. FunSeq2 is an extension of FunSeq that provides a means of prioritizing somatic variants from cancer whole genome sequencing.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://larva.gersteinlab.org/ '''LARVA'''] &lt;br&gt; [https://github.com/gersteinlab/LARVA Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2015||LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features (such as replication timing) to better estimate local mutation rates and mutational enrichments.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://vat.gersteinlab.org/ '''VAT'''] &lt;br&gt; [http://github.gersteinlab.org/vat/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://aloft.gersteinlab.org/ '''ALoFT'''] &lt;br&gt; [https://github.com/gersteinlab/aloft Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://moat.gersteinlab.org/ '''MOAT'''] &lt;br&gt; [https://github.com/gersteinlab/MOAT Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2017|| MOAT (Mutations Overburdening Annotations Tool) is a computational system for identifying significant mutation burdens in genomic elements with an empirical, nonparametric method. Taking a set of variant calls and a set of annotations, MOAT calculates which annotations have observed variant counts that are substantially elevated with respect to a distribution of expected variant counts determined by permutation of the input data.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://github.gersteinlab.org/uORFs/ '''uORFs'''] &lt;br&gt; [https://github.com/gersteinlab/uORFs Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2018|| A catalog of predicted functional upstream open reading frames (uORFs) in humans.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/GRAM '''GRAM'''] &lt;br&gt; [https://github.com/gersteinlab/GRAM Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2019|| A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner. GRAM combines a universal regulatory score defined by transcription factor binding with an easily obtainable modifier defined by transcription factor binding and expression to reflect the particular cell type. To use GRAM, you need to provide a non-coding variant file in BED format and the whole genome expression file (see github repo for details).<br /> <br /> |}<br /> <br /> ===Microarrays &amp; Proteomics===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://motips.gersteinlab.org/ '''MOTIPS''']||style=&quot;width:7%; text-align:center;&quot;|2010||MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://proteomics.gersteinlab.org '''PARE''']||style=&quot;width:7%; text-align:center;&quot;|2007||Protein Abundance and mRNA Expression (PARE) is a tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which may warrant further investigation.<br /> |}<br /> <br /> ===RNA-Seq===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://act.gersteinlab.org/ '''ACT''']||style=&quot;width:7%; text-align:center;&quot;|2011||The aggregation and correlation toolbox (ACT) is an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq''']&lt;br&gt;[http://github.gersteinlab.org/FusionSeq/ Github repo]||style=&quot;width:7%; text-align:center;&quot;|2010||FusionSeq may be used to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also includes a module to identify exact sequences at breakpoint junctions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq''']&lt;br&gt;[http://github.gersteinlab.org/IQSeq/ Github repo]||style=&quot;text-align:center;&quot;|2012||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools''']&lt;br&gt;[http://github.gersteinlab.org/RSEQtools/ Github repo]||style=&quot;text-align:center;&quot;|2011||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF is a compact data format that enables anonymization of confidential sequence information while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[https://github.com/gersteinlab/texp/blob/master/README.md '''TeXP''']&lt;br&gt;[https://github.com/gersteinlab/texp Github repo]||style=&quot;text-align:center;&quot;|2019||TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells.<br /> |}<br /> <br /> === Structural Variation ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/age/ '''AGE''']&lt;br&gt; [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style=&quot;width:7%; text-align:center;&quot;|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] &lt;br&gt;[http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style=&quot;width:7%; text-align:center;&quot;|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.<br /> |}<br /> <br /> =Networks=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style=&quot;width:7%; text-align:center;&quot;|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style=&quot;width:7%; text-align:center;&quot;|2014||A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://pubnet.gersteinlab.org/ '''PubNet''']||style=&quot;width:7%; text-align:center;&quot;|2005||A web-based tool that extracts several types of relationships returned by PubMed queries and maps them on to networks, allowing for graphical visualization, textual navigation, and topological analysis. <br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style=&quot;width:7%; text-align:center;&quot;|2004||TopNet is an automated web tool designed compare the topologies of sub-networks, looking for global differences associated with different types of proteins. This automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein network.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style=&quot;width:7%; text-align:center;&quot;|2006||(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.<br /> |}<br /> <br /> =Structure and Macromolecular Motions=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [http://3vee.molmovdb.org/ '''3V''']||style=&quot;width:7%; text-align:center;&quot;|2010||<br /> The 3V web server extracts and comprehensively analyzes the internal volumes of input RNA and protein structures. It identifies internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://helix.gersteinlab.org/ '''HIT''']||style=&quot;width:7%; text-align:center;&quot;|2006||The Helix Interaction Tool (HIT) is a comprehensive package for analyzing helix-helix packing in proteins. This enables the user to obtain quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style=&quot;width:7%; text-align:center;&quot;|1994-2009||A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution. Included is a library functions for analyzing structures, a convenient interactive command-line interpreter, and software for the calculation of geometrical quantities associated with macromolecular structures and their motions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style=&quot;width:7%; text-align:center;&quot;|2000||A web server for generating and viewing models of protein conformational change using interpolation with energy minimization. The user may opt to use either single- or multi-chain proteins as input.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://stress.molmovdb.org/ '''STRESS'''] &lt;br&gt; [https://github.com/gersteinlab/STRESS Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2016||STRucturally-identified ESSential residues (STRESS) is a web tool that enables users to submit PDB-formatted protein structures to predict both surface- and interior-allosteric residues. The software behind this tool employs 3D structures to build models of protein conformational change in order to perform allosteric site predictions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://intensification.gersteinlab.org// '''Intensification'''] &lt;br&gt; [https://github.com/gersteinlab/Intensification Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2016||Intensification is a database that contains the results for 12 repeat protein domains, from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). We make use of the modular structure of repeat motifs to amplify signals of selection from population genetics and traditional inter-species conservation.<br /> |-style=&quot;height: 100px;&quot;<br /> |}<br /> <br /> =more=<br /> [http://info.gersteinlab.org/More_tools more tools &amp; resources]</div>

Public https://info.gersteinlab.org/index.php?title=Resources&diff=6136 2025-04-07T16:38:44Z

<p>Public: </p> <hr /> <div>Source code for all software is available on our '''Github''' page: [http://github.gersteinlab.org/ Github.gersteinlab.org] (or, equivalently, [http://github.com/gersteinlab github.com/gersteinlab])<br /> &lt;HR&gt;<br /> The tools &amp; resources listed below have been '''published and are actively maintained''' by the Gerstein lab. You may view a list of the associated literature [http://papers.gersteinlab.org/subject/coretools/index.html '''here''']. <br /> <br /> In addition to the tools below, the lab has also published a number of [http://info.gersteinlab.org/More_tools '''tools that are not currently being actively maintained''']. <br /> <br /> You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']<br /> <br /> See [https://info.gersteinlab.org/Old_Resources '''the old tools page here'''].<br /> <br /> <br /> =Portals=<br /> <br /> === MolMovDB ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:Morph-icon.jpg‎]] &lt;br&gt; [http://www.molmovdb.org/ MolMovDB] ||<br /> Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures. <br /> |}<br /> <br /> <br /> <br /> ===Pseudogene.org===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:pseudogene.png‎]] &lt;br&gt; [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, &quot;pseudo-fold&quot; usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.<br /> |}</div>

Public https://info.gersteinlab.org/index.php?title=Old_Resources&diff=6135 2025-04-07T16:36:58Z

<p>Public: this is the old tools page created on Apr 7, 2025</p> <hr /> <div>This is the old tools page. <br /> <br /> See here [https://info.gersteinlab.org/Resources] for the current up-to-date tools page. <br /> <br /> <br /> =Portals=<br /> <br /> ===Networks===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 10px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:Network.jpg|center|x75px]] &lt;br&gt; [http://networks.gersteinlab.org/ Networks] ||<br /> The Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments. To this end, we have developed a portal for our network research.<br /> |}<br /> <br /> ===Structural Variants (SV)===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [[File:SVpage logo.png‎|center|x85px]] &lt;br&gt; [http://sv.gersteinlab.org/ Structural Variants]||<br /> Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).<br /> |}<br /> <br /> =Data Sets=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style=&quot;width:7%; text-align:center;&quot;|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://resource.psychencode.org/ '''PsychENCODE resource''']||style=&quot;width:7%; text-align:center;&quot;|2018||This website is a comprehensive functional genomic resource for the human brain from PsychENCODE Phase I, including all derived data, integrative models and links to raw data.<br /> |}<br /> <br /> =Evolution=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style=&quot;width:7%; text-align:center;&quot;|2008||An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including statistical coupling analysis (SCA), explicit likelihood of subset variation (ELSC), mutual information and correlation-based methods.<br /> |}<br /> <br /> =Genome Technology=<br /> <br /> ===Gene Regulation===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/Loregic '''Loregic''']||style=&quot;width:7%; text-align:center;&quot;|2015||Loregic is a computational method integrating gene expression and regulatory network data, to characterize the logical cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target, and finds the gate that best matches each triplet’s observed gene expression pattern across many conditions. Using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs.<br /> |}<br /> <br /> ===Allele-Specific Effects===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://alleledb.gersteinlab.org '''AlleleDB''']||style=&quot;width:7%; text-align:center;&quot;|2016||AlleleDB is an online resource for storing and visualizing allele-specific binding (ASB) and gene expression (ASE). Using variants from the 1000-Genomes Project and RNA-seq and ChIP-seq data from related projects, this resource serves as a repository for the catalog of ASB and ASE variants, associated genomic elements and personal genomes used in the study. AlleleDB also interfaces with the UCSC browser for visualization of results.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style=&quot;width:7%; text-align:center;&quot;|2011||AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then maps RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations in which there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified, thereby providing evidence for allele-specific events.<br /> |}<br /> <br /> ===ChIP-Seq ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://music.gersteinlab.org '''MUSIC'''] &lt;br&gt; [http://github.gersteinlab.org/MUSIC/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2014||<br /> MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] &lt;br&gt; [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2009|| A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as input DNA. PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances.<br /> |}<br /> <br /> ===Functional Annotation ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://funseq.gersteinlab.org/ '''FunSeq''']&lt;br&gt; - &amp; - &lt;br&gt;[http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style=&quot;width:7%; text-align:center;&quot;|2013&lt;br&gt;&amp;&lt;br&gt;2014||These tools can be used to automatically score and annotate the disease-causing potential of SNVs, particularly those which are non-coding. FunSeq can detect recurrent annotation elements in non-coding regions when running with multiple personal genomes. FunSeq2 is an extension of FunSeq that provides a means of prioritizing somatic variants from cancer whole genome sequencing.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://larva.gersteinlab.org/ '''LARVA'''] &lt;br&gt; [https://github.com/gersteinlab/LARVA Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2015||LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features (such as replication timing) to better estimate local mutation rates and mutational enrichments.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://vat.gersteinlab.org/ '''VAT'''] &lt;br&gt; [http://github.gersteinlab.org/vat/ Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://aloft.gersteinlab.org/ '''ALoFT'''] &lt;br&gt; [https://github.com/gersteinlab/aloft Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[http://moat.gersteinlab.org/ '''MOAT'''] &lt;br&gt; [https://github.com/gersteinlab/MOAT Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2017|| MOAT (Mutations Overburdening Annotations Tool) is a computational system for identifying significant mutation burdens in genomic elements with an empirical, nonparametric method. Taking a set of variant calls and a set of annotations, MOAT calculates which annotations have observed variant counts that are substantially elevated with respect to a distribution of expected variant counts determined by permutation of the input data.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://github.gersteinlab.org/uORFs/ '''uORFs'''] &lt;br&gt; [https://github.com/gersteinlab/uORFs Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2018|| A catalog of predicted functional upstream open reading frames (uORFs) in humans.<br /> |-style=&quot;height: 100px;&quot;<br /> <br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/GRAM '''GRAM'''] &lt;br&gt; [https://github.com/gersteinlab/GRAM Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2019|| A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner. GRAM combines a universal regulatory score defined by transcription factor binding with an easily obtainable modifier defined by transcription factor binding and expression to reflect the particular cell type. To use GRAM, you need to provide a non-coding variant file in BED format and the whole genome expression file (see github repo for details).<br /> <br /> |}<br /> <br /> ===Microarrays &amp; Proteomics===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://motips.gersteinlab.org/ '''MOTIPS''']||style=&quot;width:7%; text-align:center;&quot;|2010||MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://proteomics.gersteinlab.org '''PARE''']||style=&quot;width:7%; text-align:center;&quot;|2007||Protein Abundance and mRNA Expression (PARE) is a tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which may warrant further investigation.<br /> |}<br /> <br /> ===RNA-Seq===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://act.gersteinlab.org/ '''ACT''']||style=&quot;width:7%; text-align:center;&quot;|2011||The aggregation and correlation toolbox (ACT) is an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq''']&lt;br&gt;[http://github.gersteinlab.org/FusionSeq/ Github repo]||style=&quot;width:7%; text-align:center;&quot;|2010||FusionSeq may be used to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also includes a module to identify exact sequences at breakpoint junctions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq''']&lt;br&gt;[http://github.gersteinlab.org/IQSeq/ Github repo]||style=&quot;text-align:center;&quot;|2012||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools''']&lt;br&gt;[http://github.gersteinlab.org/RSEQtools/ Github repo]||style=&quot;text-align:center;&quot;|2011||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF is a compact data format that enables anonymization of confidential sequence information while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;text-align: center;&quot;|[https://github.com/gersteinlab/texp/blob/master/README.md '''TeXP''']&lt;br&gt;[https://github.com/gersteinlab/texp Github repo]||style=&quot;text-align:center;&quot;|2019||TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells.<br /> |}<br /> <br /> === Structural Variation ===<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/age/ '''AGE''']&lt;br&gt; [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style=&quot;width:7%; text-align:center;&quot;|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] &lt;br&gt;[http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style=&quot;width:7%; text-align:center;&quot;|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.<br /> |}<br /> <br /> =Networks=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style=&quot;width:7%; text-align:center;&quot;|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style=&quot;width:7%; text-align:center;&quot;|2014||A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://pubnet.gersteinlab.org/ '''PubNet''']||style=&quot;width:7%; text-align:center;&quot;|2005||A web-based tool that extracts several types of relationships returned by PubMed queries and maps them on to networks, allowing for graphical visualization, textual navigation, and topological analysis. <br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style=&quot;width:7%; text-align:center;&quot;|2004||TopNet is an automated web tool designed compare the topologies of sub-networks, looking for global differences associated with different types of proteins. This automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein network.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style=&quot;width:7%; text-align:center;&quot;|2006||(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.<br /> |}<br /> <br /> =Structure and Macromolecular Motions=<br /> :{|class=&quot;wikitable sortable&quot; border=&quot;1&quot; cellspacing=&quot;0&quot; cellpadding=&quot;10&quot;<br /> |- bgcolor=&quot;lightsteelblue&quot;<br /> !Name!!Release Date!!class=&quot;unsortable&quot;|Description<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;| [http://3vee.molmovdb.org/ '''3V''']||style=&quot;width:7%; text-align:center;&quot;|2010||<br /> The 3V web server extracts and comprehensively analyzes the internal volumes of input RNA and protein structures. It identifies internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://helix.gersteinlab.org/ '''HIT''']||style=&quot;width:7%; text-align:center;&quot;|2006||The Helix Interaction Tool (HIT) is a comprehensive package for analyzing helix-helix packing in proteins. This enables the user to obtain quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style=&quot;width:7%; text-align:center;&quot;|1994-2009||A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution. Included is a library functions for analyzing structures, a convenient interactive command-line interpreter, and software for the calculation of geometrical quantities associated with macromolecular structures and their motions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style=&quot;width:7%; text-align:center;&quot;|2000||A web server for generating and viewing models of protein conformational change using interpolation with energy minimization. The user may opt to use either single- or multi-chain proteins as input.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://stress.molmovdb.org/ '''STRESS'''] &lt;br&gt; [https://github.com/gersteinlab/STRESS Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2016||STRucturally-identified ESSential residues (STRESS) is a web tool that enables users to submit PDB-formatted protein structures to predict both surface- and interior-allosteric residues. The software behind this tool employs 3D structures to build models of protein conformational change in order to perform allosteric site predictions.<br /> |-style=&quot;height: 100px;&quot;<br /> |style=&quot;width:15%; text-align:center;&quot;|[http://intensification.gersteinlab.org// '''Intensification'''] &lt;br&gt; [https://github.com/gersteinlab/Intensification Github repo] ||style=&quot;width:7%; text-align:center;&quot;|2016||Intensification is a database that contains the results for 12 repeat protein domains, from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). We make use of the modular structure of repeat motifs to amplify signals of selection from population genetics and traditional inter-species conservation.<br /> |-style=&quot;height: 100px;&quot;<br /> |}<br /> <br /> =more=<br /> [http://info.gersteinlab.org/More_tools more tools &amp; resources]</div>

Public https://info.gersteinlab.org/index.php?title=Summaries&diff=6134 2025-03-31T13:09:24Z

<p>Public: </p> <hr /> <div>Summaries of different research areas<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.20/g0screenqtl-summary.docx Gerstein lab experience in isoQTLs, cell-type specific eQTLs, ASE &amp; ASB] uploaded by DC on Mar 20 2025 (g0screenqtl)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/g0adgbm_summary.pdf Gerstein Lab experience in investigating links and impacts across lifespan in brain cancer, aging, and alzheimer's disease] uploaded by MH on Mar 617'25 (g0adgbm)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.17/vfmod4_summary.pdf Gerstein Lab experience in multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Mar 617'25 (vfmod4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangenb_noncoding_annotation_AS.docx Gerstein Lab experience in non-coding genome annotation and allele-specific analysis] uploaded by MJ on Mar 6 '25 (g0pangenb)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.06/g0pangen2b_transformer_models_annotation.docx Gerstein Lab experience in transformer models for genome annotation and ML/AI tool development] uploaded by MJ on Mar 6 '25 (g0pangen2b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/03.04/g0screenad-summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in the context of neurodegenerative disease] uploaded by DC on Mar 4 '25 (g0screenad)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.13/g0screen--summary.docx Gerstein Lab experience in protein disorder, dynamics, and evolutionary conservation to rank protein-ligand pairs in clinical contexts] uploaded by DC on Feb 13 '25 (g0screen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2025/02.10/adx57g4_Project_Summary.pdf Gerstein Lab's experience in Transcriptome, Epigenome and Proteome Analysis for Constructing Gene Regulatory Networks and Identifying Disease Variants] uploaded by Mor on Feb 10 '25 (adx57g4)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/12.04/g0oslnctp--summary.docx Gerstein lab experience with developing the LNCTP tool for neurogenomic analysis and prediction] uploaded by DC on Dec 4 '24 (g0oslnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/g0stc_summary.pdf Gerstein Lab Experience in programmable salutogenesis] uploaded by MH on Nov 25 '24 (g0stc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0yccteam.pdf Gerstein Lab Experience in Brain Cancer, Germline Mutations, Aging, and Alzheimer's Disease: Investigating Links and Impacts Across Lifespan] uploaded by MH on Nov 25 '24 (g0yccteam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0ycc.pdf Gerstein Lab Experience in Dissecting the Cellular Origins, Gene Regulatory Network and Intercellular Crosstalk in Glioblastoma Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0ycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/11.25/summary_g0lion.pdf Gerstein Lab Experience in Dissecting the Differentially Expressed Genes, Gene Regulatory Network and Intercellular Crosstalk in Breast Cancer Pathogenesis through Single-Cell Genomics] uploaded by MH on Nov 25 '24 (g0lion)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Nov 9 '24 (g0u6b)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/09.15/Gerstein-lab-exp-prioritizing-cancer-variants.docx Gerstein lab experience in prioritizing genomic variants in cancer contexts] uploaded by DC Sep 15 '24 (g0nrdispycc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.26/gerstein-lab-experience-ngenomics.docx Gerstein lab experience in single-cell analyses for neurogenomics] uploaded by DC Aug 26 '24 (g0yscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/08.14/g0uciscorch_summary.docx Gerstein's lab experience in large-scale single-cell analysis and GRNs] uploaded by PN Aug 14 '24 (g0uciscorch) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.29/magen-prev-gerstein-lab-exp.docx Gerstein's lab experience in working with large consortia and with prioritizing genomic variants] uploaded by DC Jul 29 '24 (g0magen) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/adx57g3_Summary.pdf Gerstein's lab experience in analyzing transcriptome and epigenome datasets to build gene regulatory networks and models for identifying disease variants] uploaded by MOR Jul 8 '24 (adx57g3) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.08/g0exrnanci2_summary.pdf Gerstein's lab experience in exRNA research] uploaded by SZ Jul 8 '24 (g0exrnanci2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/07.01/g0cegs_summary_BB.pdf Gerstein’s lab experience in Center of Excellence in Genomic Science for Multi-Dimensional Perturbomics] uploaded by BB on Jul 1 '24 (g0cegs)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0biregnet_summary.pdf Gerstein Lab Experience in Integrative Gene Regulatory Network Construction and Analysis] uploaded by XZ on Jun 18 '24 (g0biregnet)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/g0bilnctp_summary.pdf Gerstein Lab Experience in Leveraging AI and Biosensors for Personalized Medicine and Predictive Health Analytics] uploaded by XZ on Jun 18 '24 (g0bilnctp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.18/vfmod3_summary.pdf Gerstein’s lab experience in Multi-modal modeling of cell-specific and time-dynamic features of Alzheimer’s disease] uploaded by BB on Jun 18 '24 (vfmod3)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.13/Gerstein_g0pangen2_transformer_model_experience.pdf Gerstein Lab Experience in transformer models for genomic datasets] uploaded by MJ on Jun 13 '24 (g0pangen2) <br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.10/g0brf24_summary.pdf Gerstein Lab Experience in single cell brain genomics] uploaded by ZC on Jun 10 '24 (g0brf24)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/06.03/x57gbig_rppr_summary.pdf Gerstein Lab Experience in Genomic and Computational Models] uploaded by XZ on Jun 3 '24 (x57gbig rppr)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.23/g0sysbio_summary.pdf Gerstein Lab Experience in Computational Tools and Databases] uploaded by MH on May 23 '24 (g0sysbio)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0sony_summary.docx Gerstein Lab Experience in Interpretable AI Frameworks for Predicting Individual-Level Health and Disease Status from Biosensors] uploaded by JL on May 15 '24 (g0sony)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/g0r01wear_summary.docx Gerstein Lab Experience in Leveraging Wearable Biosensors to Predict Clinical Health Events in Real Time] uploaded by JL on May 15 '24 (g0r01wear)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.14/BB_g0ddisam_summary.docx Gerstein Lab Experience in Time-series Methods for the Analysis of Multimodal Data] uploaded by BB on May 14 '24 (g0ddisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.17/g0nrdod-summary.docx Gerstein Lab Experience with developing machine learning and analytic approaches to identify variant effects in cancer contexts] uploaded by DC on Jan 19 '24 (g0nrdod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/12.09/G0hdisam_summary.docx Gerstein Lab Experience in eQTLs, isoQTLs, and allele-specific expression] uploaded by DC on Dec 9 '23 (G0hdisam)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/11.14/g0pangen_summary.docx Gerstein Lab Experience in personal genome construction] uploaded by MJ on Nov 14 '23 (g0pangen)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/10.23/g0udn_summary.docx Gerstein Lab Experience in variants impacts and genomic privacy] uploaded by PN on Oct 23 '23 (g0udn)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.21/summary_Gerstein_lab_g0adexpt.docx Gerstein Lab Experience in Interpretable Models for the Alzheimer's disease in the context of aging] uploaded by MOR on Sep 21 '23 (g0adexpt)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/09.15/summary_GersteinLab_g0bbnet.docx Gerstein Lab Experience in Biological Networks] uploaded by CD on Sep 15 '23 (g0bbnet)<br /> <br /> &lt;!-- waiting for new grant summary --&gt; <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/08.29/Summary_PsychENCODE_DACC.pdf Gerstein Lab Experience in PsychENCODE Data Analysis and Coordination Center] uploaded by MFE on Aug 29 '23 (psychdac2) <br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2023/08.17/nrdisp-summary-exp.docx Gerstein Lab Experience in prioritizing genomic variants in cancer contexts] uploaded by DC on Aug 14 '23 (nrdisp)<br /> <br /> [https://files.gersteinlab.org/public-docs/2023/02.25/summary__g0u6.docx Gerstein Lab Experience in pseudogenes &amp; cancer genomics of splicing] uploaded by DC on Feb 25 '23 (g0u6)<br /> <br /> &lt;!--<br /> [https://files.gersteinlab.org/public-docs/2023/01.30/plantpg2023.ProjectSummaryv3.docx Gerstein Lab Experience in plant pseudogenes] uploaded by CSDS on January 30 '23 (plantpg)<br /> --&gt;<br /> [https://files.gersteinlab.org/public-docs/2022/12.19/summary_GersteinLab_MutationFunction.docx Gerstein Lab Experience in mutation-function] uploaded by GW on December 19 '22 (g0morphic)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/05.15/priara_summary.pdf Gerstein Lab Experience in Privacy-Preserving] uploaded by XR on December 14 '22 (priara)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/g0pcf-skl.docx Gerstein Lab Experience in Prostate Cancer Research] uploaded by SKL on December 13 '22 (g0pcf)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.13/summary_gersteinLab_DiseaseOmics.docx Gerstein Lab Experience in disease omics] uploaded by GW on December 13 '22 (g0modacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.08/g0psygene.docx Gerstein Lab Experience in single cell analysis, pseudogenes, allelic analysis, variant prioritization and privacy] uploaded by TC on December 8 '22 (g0psygene)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.06/BB_vfmod_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research pt2] uploaded by BB on December 6 '22 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/12.01/Project_Summary_g0aiel.docx Gerstein Lab Experience in Interpretable Models Integrating Genomics and Epigenomics Features related to Aging] uploaded by MOR on December 1 '22 (g0aiel)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/06.28/Project_Summary_adx57g.docx Gerstein Lab Experience in Interpretable Deep Learning Models to Characterize Cell-type-specific Variant Impact] uploaded by PN on June 5 '22 (adx57g)<br /> <br /> [https://files.gersteinlab.org/public-docs/2022/05.18/Gerstein_Lab_Experience_in_Long_Tail_Variation_and_Regulatory_Genomics_in_Cancer.doc Gerstein Lab Experience in Long Tail Variation and Regulatory Genomics in Cancer] uploaded by HM on May 18 '22 (dodbrca)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.30/igvfregnets_summary.docx Gerstein Lab Experience in Network Reconstruction, Variant Prioritization in Networks, and Analyzing scATAC-seq &amp; scRNA-seq Data] uploaded by DC on Nov 30 '20 (igvf-regnets)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.23/dGTEx_lab_summaries.pdf Gerstein Lab Experience in integrating large-scale datasets, allele-specific expression, and deconvolution] uploaded by DC on Nov 23 '20 (dgtex)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.20/vfmap2_summary.docx Gerstein Lab Experience in Allele-Specific Expression Analysis] uploaded by AB on Nov 20 '20 (vfmap2)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.16/gdan_public_share.docx Gerstein Lab Experience in Noncoding variants and Single-cell analysis] uploaded by XL on Nov 16 '20 (gdan)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.12/vfmod_grant_summary.docx Gerstein Lab Experience in Integrative Models and Consortium Research] uploaded by AB on Nov 12 '20 (vfmod)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/11.04/PrivacyFileFormats-GeneNetworks-Research-Summary-GG-04Nov20.docx Gerstein Lab Experience in Privacy Preserving File Formats focused on Functional Genomics and Gene Network Representations] uploaded by GG on Nov 4 '20 (vfdacc)<br /> <br /> [https://files.gersteinlab.org/public-docs/2020/10.02/gencode_grant_summary_2020.docx Gerstein Lab Experience in GENCODE pseudogene] uploaded by YY on Oct 2 '20 (gencode)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/Summary_cge02_wbluma.docx Gerstein Lab Experience in methylation in sperms] uploaded by JX on Sep 29 '20 (cgen02)<br /> <br /> [http://org.gersteinlab.files.public-docs.s3.amazonaws.com/public-docs/2020/09.29/jxr03_summary.docx Gerstein Lab Experience in improving eQTLs detection] uploaded by JX on Sep 29 '20 (jxr03)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/09.14/viral_evolution_summary.docx Gerstein Lab Experience in viral evolution] uploaded by CJC on Sep 14 '20 (virevr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/CMG3_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG3] uploaded by SK on Aug 3 '21 (cmg3)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/08.03/JAXCEG_GersteinLab_text.docx Gerstein Lab Experience related to SV analysis and priortization] uploaded by SK on Aug 3 '21 (jaxceg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.05/hic_haplotype_summary.docx Gerstein Lab Experience with Hi-C data processing, haplotype phasing, and integrating haplotype-specific genomic data] uploaded by CJC on March 5 '20 (dis4dn)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/03.02/mbr03_summary.docx Gerstein Lab Experience in Interrelating GTEX and HMP: developing a method for connecting microorganisms to human genes and tissues] uploaded by JX on Mar 2 '20 (mbr03)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/pdacsup_summary.docx Gerstein Lab Experience in Identifying QTLs of Various Types and Associating Non-Coding Variants to Functional Activities at Cellular Resolution] uploaded by DC on Jan 27 '20 (pdacsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2020/01.27/scorchdc_summary.pdf Gerstein Lab Experience in RNA-seq &amp; ChIP-Seq Data Analyses, Bulk Tissue Deconvolution, Regulatory Nets, and the PsychENCODE Brain Cell Atlas] uploaded by DC on Jan 27 '20 (scorchdc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2020/01.20/psg_experience.docx Gerstein Lab Experience in Pseudogene Identification and Function Analysis] uploaded by KX on Jan 20 '20 (bbsrcpg)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/11.18/QCsupp_Summary.docx Gerstein Lab Experience in Quantum Computing] uploaded by PE on Nov 18 '19 (qcsup)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/10.27/scorchum1_lab_summary.docx Gerstein Lab Experience in Data Analysis and Tool Development in the context of Functional Genomic Consortia] uploaded by DC on Oct 24 '19 (scorchum1)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/09.04/scbr_summary_prior_contributions.docx Gerstein Lab Experience in Deconvolving Bulk Data to Estimate Cell Fractions, Analyzing Regulatory Nets &amp; Changes, and Predicting Phenotype w/a Deep-Learning Model] uploaded by DC on Sept 4 '19 (scbr)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/08.01/PrivacyFileFormats-Research-Summary-GG-01Aug18.docx Gerstein Lab Experience with Privacy Preserving File Formats for Functional Genomics Data] uploaded by GG on Aug 1 '19 (czioss)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/07.23/Gerstein-lab-experience-in-brain-and-cancer-genomics.docx Gerstein Lab Experience with Brain and Cancer Genomics] uploaded by MRS on July 23 '19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/04.07/GersteinLab_experience_with_personal_genome_and_annotation.docx Gerstein Lab Experience with Personal Genomes] uploaded by TG on April 7 '19 (x57gref/e)<br /> <br /> [http://files2.gersteinlab.org/public-docs/2019/03.17/CMG_accomplishmets_GersteinLab.docx Gerstein Lab Accomplishments for CMG2] uploaded by SK on March 17' 19 (cmg2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.20/x57gchina.docx Gerstein Lab Experience in exRNA-seq data] uploaded by YY on Feb 20' 19 (x57gchina)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/02.11/comp3D.docx Gerstein Lab Experience in Comparative analysis of 3D genomic data] uploaded by JX on Feb 11' 19 (cGen01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2019/01.03/summary4wiki.docx Gerstein Lab Experience in Data funsion and mutation effect on cancer invasiveness] uploaded by SKL on January 3' 19 (sbu01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.19/Gersteinlab_czi_grant.docx Gerstein Lab Experience in Single-cell Analysis] uploaded by XS on December 19 '18 (czi18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.11/DIRC_summary.docx Gerstein Lab Experience in Integrative Analysis of Multiple Omics Data] uploaded by TXL on December 19'18 (dirc)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/12.06/exRNA_summary.docx Gerstein Lab Experience in exRNA-Seq Data Analysis] uploaded by BL on December 06 '18 (exrna2)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/11.27/Privacy-Research-Summary-GG-26Nov18.docx Gerstein Lab Experience in Genome Privacy] uploaded by GG on November 27 '18 (prr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2018/01.31/Gerstein_Lab_Exprience_in_Variant_Prioritization.docx Gerstein Lab Experience in Variant Prioritization] uploaded by HM on January 31 '18 (sbr01)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/Keck18_summary.docx Gerstein Lab experience in cross-disciplinary network comparisons] uploaded by PM December '17 (Keck18)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.20/rm1nets_summary.docx Gerstein Lab experience in biological regulatory networks] uploaded by PM December '17 (rm1nets)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/12.06/Variant_Region_Call_Prioritization_Summary_Candisp3.docx Gerstein Lab experience in Variant Prioritization on Kidney Cancer] uploaded by LS December 6 '17 (candisp)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.03/Gerstein_textmining_experience.docx Gerstein Lab experience in text mining] uploaded by XK October 3 '17 (hubspoke) <br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/08.29/Retrotransposition.docx Gerstein Lab Experience in Retrotransposition] uploaded by FN August 29 '17 (pilot-cloud)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.08/Regulatorynetworks_summary.pdf Gerstein Lab Experience in Constructing Regulatory Networks] uploaded by PE on 7 August '17 (psychdac)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/08.03/GersteinLabTranscriptomeAnalysisCancerGenomics.docx Gerstein Lab Experience in Transcriptome Analysis and Cancer Genomics] uploaded by JW on 3 August '17 (cidc)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.19/GersteinLabNoncodingAnnotationAndVariantPrioritization.docx Gerstein Lab Experience in Noncoding Genome Annotation and Variant Prioritization] uploaded by HM on 19 July '17 (tmyale)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in July '17 (topmedfr01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/07.09/GersteinLabVarPrioritizationCancer.docx Gerstein Lab Experience in Variant Prioritization with Focus on Cancer] uploaded by HM on 9 July '17 (sbu01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/05.03/Gerstein_lab_eqtl.pdf Gerstein lab experience in RNA-seq, ChIP-seq, eQTL and integrative analysis] uploaded by SL on 3 May '17 (psychsup3)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN in May '17 (topmedir01)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.18/Gersteinlab_integrativeanalysis.pdf Gerstein lab experience in ChIP-seq, eQTL and integrative analysis ] uploaded by SL on 18 April '17 (Peccolab)<br /> <br /> [http://archive.gersteinlab.org/docs/2017/04.17/HL2nd_Research_Plans_For_Wiki.doc Gerstein lab experience in calling allele-specific variants and GWAS analysis and small (non-coding) RNA analysis] uploaded by JR on April '17 (HL2nd)<br /> <br /> [http://files.gersteinlab.org/public-docs/2017/10.09/Variant_Region_Call_Prioritization_Summary_Candisp.docx Gerstein lab experience in calling and prioritizing variants and regions] uploaded by LS on Dec '16 (candisp)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/10.11/Summary_functional_prioritization_TEs.docx Gerstein lab Experience in analyzing the functional impact of transposable elements] uploaded by FN on July '16 (te4c)<br /> <br /> [http://archive.gersteinlab.org/public-docs/2016/07.25/Summary_of_experience_in_analyzing_the_functional_impact_of_structural_variants.docx Gerstein lab Experience in analyzing the functional impact of structural variants] uploaded by FN on July '16 (topmed)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/07.19/Gerstein_lab_variant_characterization_experience_summary.docx Gerstein lab Experience in Computational techniques for the identification of genotypes responsible for diseases] uploaded by AH on May '16 (g0gwas)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/PseudogeneExperience.pdf Gerstein Lab Experience with Pseudogenes] uploaded by CSDS on 26 April '16 (u41pg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.26/4dac_summary.docx Summary of Previous Gerstein Lab Contributions in ENCODE ] uploaded by ANS on 26 April '16 (4dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Gersteinlab_RNAseqChipseq_experience_brainrelated2.pdf Gerstein Lab experience in RNA-Seq and Chip-Seq analysis in brain related projects] uploaded by SL on 13 April '16 (psychsup2)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.30/BrainRelatedRNAseqChipseqAlleleEnhancer_summary.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq, allelic analysis, enhancer analysis and integrative analysis] uploaded by SL on 30 March '16 (psychsup)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.28/MultiOmic_ProcessingPipelines_DataIntegration_DS.docx Gerstein Lab experience in the development of multi-omic processing pipelines and data integration] uploaded by DS on 28 March '16 (u24motr)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/04.13/Functional_Characterization_Summary.docx Gerstein lab Experience in Identification and Functional Characterization of Enhancers] uploaded by AH on March 22 '16 (um1fc)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/03.11/Research-summary-nlmtg16-MarkGerstein-11mar16mg.docx Gerstein Lab Experience in Several Major National Biomedical Data Science Initiatives, including 1KG, ENCODE, Brainspan, psychENCODE, Cancer Genomics, Genome Data Privacy, Proteomics and Networks] uploaded by LL on 11 March '16 (nlmtg16)<br /> <br /> [http://archive.gersteinlab.org/docs/2016/01.20/gtechR01_summary4wiki.pdf Gerstein Lab experience in noncoding genome annotation, allelic analysis and somatic variant prioritization] uploaded by SKL on 20 January '16 (gtechR01)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.15/calling-and-prioritizing.docx Gerstein Lab Experience in calling and prioritizing variants and regions ] uploaded by LS on 15 December '15 (CanDisp)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/4dnbod_2_summary.docx Gerstein Lab Experience in ChIP-Seq and RNA-Seq Analysis (brief) as of Dec. 2015] uploaded by MRS on 10 December '15 (4dnbod[take2])<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.03/IBC.public.pdf Gerstein Lab Experience in breast cancer genome analysis] uploaded by XL on 3 December '15 (SWOG)<br /> <br /> [https://files.gersteinlab.org/public-docs/2024/04.19/prvWrk_allost.pdf Gerstein Lab Experience in Predicting Allosteric Hotspots (mmls)] uploaded by DC on 3 December '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNASeqChipSeqintegrative_analysis.pdf Gerstein Lab experience in RNA-Seq, Chip-Seq and integrative analysis] uploaded by SL on 1 December '15 (pec2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/RNAseq_processing_pipelines_DS.docx Gerstein Lab experience creating RNAseq processing pipelines] uploaded by DS on 1 Dec '15 (u19asth)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.01/Privacy_Research_Summary_11.2015.docx Gerstein lab experience in genomic privacy] uploaded by AH on Nov 30 '15 (bd2kpr)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/NSF-BBSRC-grantSummaryNov2015toUSE.docx Gerstein lab experience in molecular characterisation of gene phenotypes] uploaded by CSDS on Nov 24 '15 (bbsrc)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_efforts_big_data.docx Gerstein lab experience in data science] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/12.10/Summary_networks_tools.docx Gerstein lab network related tools] uploaded by KKY on Nov 23 '15<br /> <br /> [http://archive.gersteinlab.org/docs/2015/09.18/Gerstein_Lab_Structural_Variation_and_Functional_Impact.pdf Gerstein Lab Structural Variation and Functional Impact (gspac)] uploaded by FN on 18 September '15<br /> <br /> [http://archive.gersteinlab.org/public-docs/2017/01.04/n/ncvarg_2015.docx Gerstein Lab exprience analyzing noncoding genomic variants as of Mar 2015] uploaded by SK on 1 June '15 (ncvarg15)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_analyzing_disease_implications_of_variants.pdf Gerstein Lab exprience analyzing disease implications of genetic variants as of Mar 2015] uploaded by TG on 1 June '15 (cmg2)<br /> <br /> [http://archive.gersteinlab.org/docs/2015/06.01/Gerstein_Lab_ChipSeq_RNASeq_Networks.pdf Gerstein Lab experience with Chip-Seq, RNA-Seq, and network analysis as of Feb 2015] uploaded by TG on 1 June '15 (4dnbod)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_genome_annotation&amp;variation_networks_comparative_genomics.pdf Gerstein Lab contributions to genome annotation and variation, networks, and comparative genomics] uploaded by TG on 16 December '14 (4dnuc)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/12.16/Gerstein_Lab_knowledgebase_design_and_analysis_of_sci_pubs.pdf Gerstein Lab expertise with knowledge-base design and analysis of scientific publications] uploaded by TG on 16 December '14 (4dnoh)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/06.13/gerstein-nsf-nrt_grant_v1.docx Yeast networks and Gerstein Lab expertise] uploaded by JC on 13 June '14 (nrt)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/03.06/YCC_report_2014.docx Gerstein Lab Cancer Research Accomplishments] uploaded by LL on 6 March '14 <br /> <br /> [http://archive.gersteinlab.org/docs/2014/02.24/1/Gerstein_Lab_network.htm Gerstein Lab contributions to statistical models of gene expression, network analysis, and mapping variation onto networks up to end of 2013] uploaded by DW on 24 February '14 (dddic)<br /> <br /> [http://archive.gersteinlab.org/docs/2014/01.24/Gerstein_lab_annotation_contributions.pdf Annotation related contributions by Gerstein lab up to end of 2013] uploaded by SK on 24 Jan '14 (ncvarg)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/12.02/Gerstein_lab_rna_seq_contributions_120213.pdf Gerstein Lab Contributions to RNA-Seq Analysis up to end of 2013] uploaded by MRS on 2 December '13 (exprofile)<br /> <br /> [http://archive.gersteinlab.org/docs/2013/11.25/GersteinLabContributions.docx Contributions to Networks &amp; Genomics by Gerstein lab up to end of 2013] uploaded by ANS on 25 November '13 (erggr)<br /> <br /> [http://archive.gersteinlab.org/docs/2012/03.13/Summary_of_Gersteinlab_Genomics_contributions_upto_2012.doc Summary of Gersteinlab Genomics contributions upto 2012] uploaded by DW on 13 March '12 (3dac)<br /> <br /> [http://archive.gersteinlab.org/docs/2011/01.16/Large-scale-collaborations-GersteinLab-involved-with.doc Writeup on large collaborations involving the Gerstein Lab] uploaded by mbg on 16 January '11 (3dac)<br /> <br /> * Progress on various projects <br /> <br /> [http://archive.gersteinlab.org/docs/2012/09.09/keck-2012-progress-report.doc Genome annotation, data integration, protein structure, sequencing costs, and privacy] uploaded by SB on 9 September '12 (keck)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/nih-CEGS-progress-report-2010Q1Q2-informatics-22May10mg.doc Informatics 2010Q1Q2; Gene Regulatory Networks] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/05.22/EXCERPTS-FROM--nih-CEGS-progress-report-14apr10mg.htm RNA-Seq, Chip-Seq, Human Variation, Informatics 14apr10mg] uploaded by MG on 22 May '10 (cegs)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.20/encode2-pgenes-progress-report-for-yr3-20Apr10-web-ver.doc Encode2 pseudogenes] uploaded by YHL on 20 April '10 (encode2pgenes)<br /> <br /> [http://archive.gersteinlab.org/docs/2010/04.16/EDITFORWEB--Update-for-Annual-Mtg--NIH-CEGS-2008-2009-informatics-progress-report.doc Informatics '08-'09; Structural Variation, Regulatory Networks] uploaded by mg on 16 April '10 (cegs)<br /> <br /> <br /> * Internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet ] listing contributions<br /> <br /> * Internal [http://wiki.gersteinlab.org/labinfo/Preparing_Research_Summaries instructions] to prepare research summaries</div>

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