GersteinInfo - User contributions [en]

Main Page

2026-04-27T19:55:12Z

Mbg: /* Other Stuff for the Public */

<div style="border: 1px solid black; padding: 10px;">[https://www.gersteinlab.org <big>'''Lab Home Page'''</big>]</div>

== Important Public Items ==
*Gerstein Lab '''[https://www.youtube.com/channel/UCVM3Kd2UWdJrAfQ1RqyajHw Youtube]''' , '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''
*'''[[FAQ]]''' on tools and data
*'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab

__TOC__

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 "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research (with shadow internal [https://docs.google.com/spreadsheets/d/1d4yWl-xCbvuJAY86JS5R1o91S_mQy2blyViusMTx54c/edit#gid=0 gsheet])
*[[Posters]] showing lab research
*Misc. Public [[Documents]] about the lab
*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])
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== Info for New People ==
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
* [[Glossary]] of terms.
* Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]

== Info for Lab Signature ==
*For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [[Gerstein Lab Computing in HPC]]
** [[Gerstein Lab Computing in GersteinLab West Campus]]
** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]

* Calls, meetings, &c
**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]])
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [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&on=downloads Other info])
**[[Bass434]] introduction
**Booking [[Meeting Room]]
**Booking a [[Conference Room at 100 College]]

* Some Useful University Policies
** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** 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]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]

* Documents
** [[Uploading_documents]]
** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates)

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** 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]
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
**[[OpenStack]]
**[[IDP report]]
**[[PEC package preprints]]
**[[Summary of undergraduate involvement]]
**Lab [http://bit.ly/mglab-folder google folder]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

Contact information

2026-04-21T01:57:09Z

Mbg: /* More Info on My Normal Email */

The main contact information for Mark Gerstein is at

{| style="color:white"
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="white"| [http://contact.gerstein.info '''contact.gerstein.info''']
| width="1" bgcolor="blue"|
|-
| width="1" bgcolor="blue"| || width="10" bgcolor="blue"|
| width="1" bgcolor="blue"|
|}
(More information is on this page, as it is easier to edit .)

===More Info on Zoom===

* Mark's personal Zoom Room: https://yale.zoom.us/my/mXXX.XXXXXXXX (where mXXX.XXXXXXXX is replaced by a string that's obvious.)
* Or Telephone 203-432-9666 with Meeting ID: 777 XXX XXXX (where I'll tell you the final 7 digits - think about Pi). Also, there's no extra passcode that you type in after the first code. So you just type in 777XXXXXXX## (after calling) and then you're in. This is made to be as simple as possible.

===More Info on Paper Mail and Physical Location===

* Note: Bass 432A is '''NOT''' at Bass library. It is in the Bass Center, located on Science Hill. (See https://map.yale.edu/place/building/BASS.)

* If we have a meeting at the medical school, it may be at 300 George.

* Address for FEDEX

Mark Gerstein
Bass 432A, MBB, Yale U.
266 Whitney Ave.
New Haven, CT 06511

* If you are trying to meet me in Bass, I often in Bass 434 in meetings. Also, check-in Bass 424.

* You sometimes need authorization to get in the building after 6 PM. If so, arrange to call me, so I can come down to meet you.

* Also, please make sure you announce yourself at my office. In particular, if you're waiting outside Bass 432, knock on the inner office (Bass 432A). Don't just sit on sofa outside in the corridor.

===More Info on Phone and Fax===
*If I give you my cell number (currently ending in x508), you can text it if you need me quickly.
*I have many other phone numbers cell and otherwise (i.e. 203-xxx-x559, xxx-xxx-x230, xxx-xxx-x836, xxx-xxx-x188 and xxx-xxx-x587‬). I may call from them but best not to use them to initiate calls or texts.
**The most likely numbers for me to call from are x508, x230, x836, and public cell (x858).
**[[Further Detail on Contact Info|Even more detail]] on this.
**Unfortunately, x508 doesn't work for international texts, so I'll probably give you x230 in this context.

===More Info on Email===
====More Info on My Normal Email====
* Philosophy
Found this quote on the web and thought it useful here: "Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues."
* Confidential information
** My email goes into a variety of fairly public servers (e.g. gmail). Consequently, I do not like sending personal information (such as important computer passwords and credit-card or social security numbers) over unencrypted email. I also do like sending scanned versions of my signature.
**If you want this information, you can get it via contacting my assistant. She can either tell it to you over the phone or fax it or mail it to you. You might want to refrain from sending me information like this to me over email.
** If you really want to send me confidential information I can use Signal or proton mail. (But please give me a heads up on this via regular email.)
* No Web forms
In general, please try to avoid subscribing my main addresses on contact.gerstein.info to any type of
web form - eg for a journal subscription or a rec. letter.
I am quite serious about this! It will really annoy me if you do this!
I am taking this step basically to try to alleviate the large amount of e-mail
congestion I suffer. Use my assistant address.
* Email addresses to avoid or to use selectively
**Do not use mark ((at)) gersteins.net, mbg ((at)) pobox.com, mark ((at)) gerstein.info, and mbg ((at)) csb.yale.edu (which are all defunct).
**Mark.Gerstein ((at)) Yale.edu works but has issues with spam filters.
**piaa ((at)) gersteinlab.org goes to me and my assistant so is not that confidential.
**pi ((at)) gersteinlab.org also goes to my assistant and is used for journal submissions.
* I am slow to respond to email.
** Text if you need a fast response.
**I read messages sent to me via lists and via CC (or BCC) much more slowly than those directly to one of my two canonical email addresses. Unfortunately, it is rather common for me to get overwhelmed with professional emails. I know I am sometimes slow in responding, so if you want to reach me quickly, try to use text route.
**In relation to my slowness, you might also want to reflect on an [http://www.newyorker.com/humor/2010/10/25/101025sh_shouts_marks email auto-response] I was considering using.

====Don't Use Skype, Linkedin, Twitter in Preference to Email====

Do not try to "email me" through linkedin, twitter direct message, Skype chat, etc. Best to send a traditional email. You are, of course, welcome to follow me on Twitter or link to me on LinkedIn but I don't check direct messages that often. Likewise, if we schedule a "phone chat" over skype, I may use the chat feature during the call, but please don't try to contact me using this afterwards. Use email.

====More Info on the PleasePageMark Email====

This is deprecated but still works: Email to the pleasepagemark address is fast but not instantaneous. Also, for the message to work, you need to have both the right to address (i.e. pleasepagemark) and correct subject line. If you just put blue in the subject and send to my normal email address, nothing happens. Likewise, if you just send to pleasepagemark without the right subject. The idea is here is to make sending these messages harder, to cut down on spam and abuse.

Affiliation

2026-04-21T01:15:55Z

Mbg:

* Way to List Affiliations for Mark Gerstein on papers :

Mark B. Gerstein 1,2,3,4,5

<PRE>
1 Program in Computational Biology & Bioinformatics,
2 Department of Molecular Biophysics & Biochemistry
3 Department of Statistics & Data Science
4 Department of Computer Science, and
5 Department of Biomedical Informatics & Data Science
Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
(mark {{AT}} gersteinlab.org OR pi {{AT}} gersteinlab.org)
</PRE>
ORICID : 0000-0002-9746-3719

(The above affiliations are ranked, so if the list needs to be truncated. Keep those at the top.)

* This is distinct from Mark's title, which is

The Albert L Williams Professor of Biomedical Informatics

* Short email signature block
<PRE>
###
### Mark Gerstein
### Williams Prof. of Biomed. Informatics
### Yale U.
### GersteinLab.org
###
</PRE>
* Long ("pretentious, but useful") signature block
<PRE>
###
### Mark Gerstein, PhD
### Albert L Williams Professor of Biomedical Informatics, Molecular Biophysics & Biochemistry, Computer Science, and Statistics & Data Science
### co-director of the Program in Computational Biology & Bioinformatics and the Center for Biomedical Data Science
### Yale University
### http://GersteinLab.org
###
</PRE>
* More on Lab [https://sites.gersteinlab.org/affiliations Affiliations]

Further Detail on Contact Info

2026-04-19T20:29:44Z

Mbg:

* <code>xxx-xxx-x508 - </code>Always use for text and voicemail; it is the best general-purpose number but has the slow gvoice prompt when calling.
* <code>xxx-xxx-x230 - </code>Often goes to watch and is best to call casually. Don't text here or leave a voicemail.
* <code>xxx-xxx-x836 - </code>Is best when I'm driving or out. Don't text here or leave a voicemail.
* <code>203-903-1858 - </code>My "public cell". Use for lower-priority text.
* <code>203-432-6105 - </code>Routes calls to the public cell above. Occasionally works for a callback, but I usually don't pick up.
* <code>203-718-6559 - </code>Defunct
* <code>203-xxx-x188 - </code>Might call from this number. Don't text here or leave a voicemail.

(back to [http://contact.gerstein.info top of contact info])

Further Detail on Contact Info

2026-04-19T20:27:18Z

Mbg:

* <code>xxx-xxx-x508 - </code>Always use for text and voicemail; it is the best general-purpose number but has the slow gvoice prompt when calling.
* <code>xxx-xxx-x230 - </code>Often goes to watch and is best to call casually. Don't text here or leave a voicemail.
* <code>xxx-xxx-x836 - </code>Is best when I'm driving or out. Don't text here or leave a voicemail.
* <code>203-903-1858 - </code>My "public cell". Use for lower-priority text.
* <code>203-432-6105 - </code>Routes calls to the public cell above. Occasionally works for a callback, but I usually don't pick up.
* <code>203-718-6559 - </code>Defunct

(back to [http://contact.gerstein.info top of contact info])

Selected Press Accounts Highlighting Gerstein Lab Work

2026-04-18T18:58:34Z

Mbg:

__NOTOC__
=== 2026 ===

*[https://www.nytimes.com/2026/01/28/science/alphagenome-ai-deepmind-genetics.html With AlphaGenome, Researchers Are Using A.I. to Decode the Human Blueprint (NY Times)]

=== 2025 ===
*[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)]
*[https://news.yale.edu/2025/08/19/timing-everything-finding-treatment-windows-genetic-brain-disease?utm_source=YaleToday&utm_medium=email&utm_campaign=YT_YaleToday-Staff_8-25-2025 Timing is everything: Finding treatment windows in genetic brain disease. (Yale News)]
*[https://medicine.yale.edu/news/yale-medicine-magazine/article/can-ai-predict-the-future/ Can AI Predict the Future? (Yale Medicine Magazine)]
*[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]

=== 2024 ===
*'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''
*[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)]
*'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''
*[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]
*[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]

=== 2023 ===
* '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''
* [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]
** [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)]

=== 2022 ===
*[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]
*[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)]
*[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)]
**[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]
=== 2021 ===
*[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]
*[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]
=== 2020 ===
* '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''
* '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''
=== 2019 ===
* '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]'''
=== 2018 ===
* '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''
*[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]
*[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)]
*[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)]
=== 2017 ===
*[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]
*[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]
*[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]

=== 2016 ===
* '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''
* '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''
* [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)]

=== 2014 ===

* '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''
*[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]

=== 2013 ===

* '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''
*[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)]
*[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]

=== 2012 ===

* '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''
** [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)]
* [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]
** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]
** [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)]
* [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)]

=== 2011 ===
*[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)]
*[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)]
* [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)]

=== 2010 ===

*[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]
*[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]
*[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]
* [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)]
* [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)]
* [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)]
** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]
* [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)]

=== 2009 ===

* [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)]
* [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)]

=== 2008 ===

* [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]

=== 2007 ===

* [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)]

=== 2003 ===

* [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]

=== 2001 ===

* [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)]

=== 2000 ===

* Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])

=== 1998 ===

* [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)]

== More Stuff ==
* 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.)
* A [https://news.google.com/search?q=mark%20gerstein%20yale&hl=en-US&gl=US&ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)

Proof Stage Checklist

2026-03-13T19:57:30Z

Mbg: /* Long version of checklist */

==Short version==
* Get grant right!
* correct MG email + ORCID
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
* github should have a license/permissions
* lab homepage image
* tweet
* slide deck
* perhaps do PR + patent
* ask RM for help

(see '''<code>Proofsx57m</code>''' tag on correspondence)

==Long version of checklist==

* Press & PR
** 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.

* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Check that MG's [[Affiliation]] is accurate

* Funding
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
*** We should usually acknowledge grant XXX and ALW (Usually this is a 95/5 split)
Example sentence (for publication fee reimbursement only; not for inclusion in the manuscript, sent to Lisa):
"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."

Example funding statement for the paper (You can use other paper published by the lab as example as well):
"This work was supported by the xxx funds and the National Institutes of Health (NIH) under Grant xxx."

*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.
** 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.)
** Funding is usually applicable when MG is the last author.
** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.

*PMC & License
** For license, go for open access for non-commercial use unless prohibitively expensive.
** 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]
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)

* Papers Page (papers.gersteinlab.org)
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
** 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.
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
*** Send the following information to whoever is in charge of rebuilding the papers page:
**** PubMed ID or doi of the preprint
**** A link to the paper
**** A link to the tools or resources (see "Tools & Resources" section below)
**** 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.
**** Any additional information such as co-first authorship
*** 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
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
** Co-first and co-corresponding authors can be indicated with the footnote field
** Use the link field to directly link the journal site (particularly if there is no pubmed)

* Tools & Resources
** Website
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
*** Best is where the paper ID is what, eg, ABCDE
*** Try to use the GitHub standard for code data
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
*** 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).
** You can use the "website" field on the papers page to link your github site.

* Preprints
** Do a biorxiv submission (or another equiv. preprint server)
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).

* Slides & Images
** Make sure Mark has "slide packs" for the paper
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .

* Tweet & Bluesky
**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.
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
https://twitter.com/markgerstein/status/789117961843900417
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344

* Patents
** discuss with MG before posting a preprint

* Wikipedia
** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate

* Tag for this page
** [[Proofsx57m]]
** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]

Proof Stage Checklist

2026-03-13T19:56:43Z

Mbg: /* Short version */

==Short version==
* Get grant right!
* correct MG email + ORCID
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
* github should have a license/permissions
* lab homepage image
* tweet
* slide deck
* perhaps do PR + patent
* ask RM for help

(see '''<code>Proofsx57m</code>''' tag on correspondence)

==Long version of checklist==

* Press & PR
** 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.

* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Check that MG's [[Affiliation]] is accurate

* Funding
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
*** We should usually acknowledge grant XXX and ALW (Usually this is a 95/5 split)
Example sentence (for publication fee reimbursement only; not for inclusion in the manuscript, sent to Lisa):
"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."

Example funding statement for the paper (You can use other paper published by the lab as example as well):
"This work was supported by the xxx funds and the National Institutes of Health (NIH) under Grant xxx."

*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.
** 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.)
** Funding is usually applicable when MG is the last author.
** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.

*PMC & License
** For license, go for open access for non-commercial use unless prohibitively expensive.
** 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]
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)

* Papers Page (papers.gersteinlab.org)
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
** 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.
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
*** Send the following information to whoever is in charge of rebuilding the papers page:
**** PubMed ID or doi of the preprint
**** A link to the paper
**** A link to the tools or resources (see "Tools & Resources" section below)
**** 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.
**** Any additional information such as co-first authorship
*** 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
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
** Co-first and co-corresponding authors can be indicated with the footnote field
** Use the link field to directly link the journal site (particularly if there is no pubmed)

* Tools & Resources
** Website
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
*** Best is where the paper ID is what, eg, ABCDE
*** Try to use the GitHub standard for code data
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
*** 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).
** You can use the "website" field on the papers page to link your github site.

* Preprints
** Do a biorxiv submission (or another equiv. preprint server)
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).

* Slides & Images
** Make sure Mark has "slide packs" for the paper
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .

* Tweet & Bluesky
**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.
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
https://twitter.com/markgerstein/status/789117961843900417
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344

* Wikipedia
** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate

* Tag for this page
** [[Proofsx57m]]
** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]

Proof Stage Checklist

2026-03-13T19:56:27Z

Mbg: /* Short version */

==Short version==
* Get grant right!
* correct MG email + ORCID
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
* github should have a license/permissions
* lab homepage image
* tweet
* slide deck
* perhaps do PR + patent

(see '''<code>Proofsx57m</code>''' tag on correspondence)

==Long version of checklist==

* Press & PR
** 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.

* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Check that MG's [[Affiliation]] is accurate

* Funding
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
*** We should usually acknowledge grant XXX and ALW (Usually this is a 95/5 split)
Example sentence (for publication fee reimbursement only; not for inclusion in the manuscript, sent to Lisa):
"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."

Example funding statement for the paper (You can use other paper published by the lab as example as well):
"This work was supported by the xxx funds and the National Institutes of Health (NIH) under Grant xxx."

*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.
** 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.)
** Funding is usually applicable when MG is the last author.
** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.

*PMC & License
** For license, go for open access for non-commercial use unless prohibitively expensive.
** 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]
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)

* Papers Page (papers.gersteinlab.org)
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
** 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.
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
*** Send the following information to whoever is in charge of rebuilding the papers page:
**** PubMed ID or doi of the preprint
**** A link to the paper
**** A link to the tools or resources (see "Tools & Resources" section below)
**** 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.
**** Any additional information such as co-first authorship
*** 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
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
** Co-first and co-corresponding authors can be indicated with the footnote field
** Use the link field to directly link the journal site (particularly if there is no pubmed)

* Tools & Resources
** Website
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
*** Best is where the paper ID is what, eg, ABCDE
*** Try to use the GitHub standard for code data
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
*** 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).
** You can use the "website" field on the papers page to link your github site.

* Preprints
** Do a biorxiv submission (or another equiv. preprint server)
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).

* Slides & Images
** Make sure Mark has "slide packs" for the paper
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .

* Tweet & Bluesky
**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.
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
https://twitter.com/markgerstein/status/789117961843900417
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344

* Wikipedia
** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate

* Tag for this page
** [[Proofsx57m]]
** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]

Old Profile Stuff

2026-02-22T19:44:25Z

Mbg: /* Recent OLD CVs */

== Old Research Descriptions ==

* [https://files.gersteinlab.org/public-docs/2025/02.17/sites-gersteinlab-org-research.pdf Gerstein Lab Research page prior to Feb 2025 update]

* Listing of Key Research Contributions (as of 30-Nov-2019) ([http://files.gersteinlab.org/public-docs/2019/12.28/Key-Research-Contributions--EXTRACT-FROM--mb0mg--Gerstein-final-30nov19.pdf PDF], [http://files.gersteinlab.org/public-docs/2019/12.28/Key-Research-Contributions--EXTRACT-FROM--mb0mg--Gerstein-final-30nov19.docx DOC])

* [http://www.gersteinlab.org/about/index.html.006 Older research description]

* [http://www.gersteinlab.org/about/short-bio.txt Micro-BIO]

* Here is a 50-word description of Mark Gerstein's research (31-Aug-2009)

Dr. Gerstein is the Albert Williams Professor of Biomedical Informatics, Molecular Biophysics &
Biochemistry and Computer Science at Yale University. His research involves applying quantitative
approaches such as data mining and simulation to problems in molecular biology. He is specifically
interested in human genome annotation, molecular networks, and macromolecular geometry.

* Longer Wiki Description of [[Mbg-research]] (out of date as of Aug-2009)

* [[Gerstein Lab Research - 22 Jul. 2013 | Long 1648 Word Research Description]] with References (current as of 22-July-2013)

* [[NIH grant justification text for MG]]

* Old Wiki description of research interests - http://info.gersteinlab.org/Current_Research_Interests_for_Mark_Gerstein

Research Program [http://papers.gersteinlab.org/about/sum2006 2006], [http://papers.gersteinlab.org/papers/papers-research.shtml 2002a],
[http://bioinfo.mbb.yale.edu/about/sum/res-sum-020128.htm 2002b], [http://papers.gersteinlab.org/about/sum2001 2001]

[http://bioinfo.mbb.yale.edu/about/nih-style-full-cv-apr-05.doc Complete CV, MS Word format] (pubs only up to 2005)

[http://archive.gersteinlab.org/mark/out/log/2011/08.08/cv/cv-nih-format.html NIH-style Old Short CV]

* Older Research Description (010108) with figures and many file formats:
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108.doc doc]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.pdf pdf]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.ppt ppt]
* [http://www.gersteinlab.org/about/long-descrip.pdf An even older (1999) version in pdf]

== Old CVs ==
=== Recent OLD CVs ===

https://www.dropbox.com/scl/fi/4gvr1r1wl4w6pgdf3pls4/MG-truncate-CV-public-FAR24-end24bld-no-pgnum.cv57.pdf?rlkey=om005q7izegpc6la3zl7bcj5i&dl=0

https://www.dropbox.com/scl/fi/7fanrd14hzrpp9e5b3uti/M-Gerstein-Full-public-CV-bld11may24.cv57.pdf?rlkey=9tbgrqco6odc17r9gl4vrcgy0&dl=0

https://www.dropbox.com/scl/fi/0pnka2ijlk3egdhyo9645/M-Gerstein-CV-bld6Jan24-Public-CV-Jan-2024.cv57.pdf?rlkey=08un1ufxhvc13mrpog1fwf1zs&dl=0

https://www.dropbox.com/s/hrmczyzq2zj1x93/M-Gerstein-Full-public-CV-bld12Jan23-FAR.onweb.pdf?dl=0

https://www.dropbox.com/s/5r8kwh4tfqcprqf/M-Gerstein-Full-public-CV-bld14Aug22-SS.onweb.pdf?dl=0

=== CV Build as of 31 Dec 2019 ===

http://files.gersteinlab.org/public-docs/2019/12.28/M-Gerstein-CV-bld31Dec19--public.pdf

=== CV Build as of 1 Jan 2019 ===

http://files.gersteinlab.org/public-docs/2019/01.03/M-Gerstein-full-public-CV--bld1Jan19-cv57.pdf

=== CV Build as of 8 Jan 2018 ===

http://files.gersteinlab.org/public-docs/2018/01.10/Full-CV-M-Gerstein--for-FAR-bld8Jan18-cv57.pdf

https://linkstream.gersteinlab.org/2018/01/10/highlights-of-2017/

Current as of 8 Jan. 2018 (w. some sections less current)

=== CV Build as of 28 Jan 2016 ===

http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/M-Gerstein-Full-CV-28Jan16-publ.pdf

=== CV Build as of 30 Sep 2015 ===

http://archive.gersteinlab.org/public-docs/2015/10.21/M-Gerstein-full-CV-30Sep2015-publ.pdf

=== CV Build as of 30 Jan 2015 ===

[http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-public-CV-31Dec2014.pdf Built CV with publications and people]

=== CV Build as of 28 Nov 2014 ===

[http://archive.gersteinlab.org/public-docs/2014/11.28/M-Gerstein-public-CV-28nov14.pdf Built CV with publications and people]

=== CV Build as of 31 Dec 2013 ===

[http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-public-CV-31Dec2013.pdf Built CV with publications and people]

=== CV Build as of Jan 2013 ===

[http://archive.gersteinlab.org/mark/out/log/2013/01.23/M-Gerstein-public-cv-1jan13.pdf Built CV with publications and people]

=== Old CV Build in Jan 2012 (obsolete but maybe useful)===

[http://archive.gersteinlab.org/mark/out/log/2012/01.30/cv/M-Gerstein-publ-CV-29jan2012.pdf Built CV with publications and people]

[http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Lab-Personnel-and-Alumni-1Dec2011.pdf Listing of Lab Personnel and Alumni]

[http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Scientific-Pubs-1Jan2012.pdf Scientific Publications up to Jan. '12]

[http://archive.gersteinlab.org/mark/out/log/2012/01.30/cv/M-Gerstein-Other-Writings-1jan2012.pdf Other Writings up to Jan. '12]


==Old overview lectures==

http://lectures.gersteinlab.org/summary/7-slide-overview-of-the-GersteinLab-20170203/

http://lectures.gersteinlab.org/summary/Talk-at-Levitt-alumni-gathering--20140911-i0levalum-final/

http://lectures.gersteinlab.org/summary/5-slide-overview-of-the-lab/

==Old Profile Pages==
* DEFUNCT profile links

** Yale Pantheon page (via eli.yale.edu), which can be used as an outbox: http://pantheon.yale.edu/~mg269
** [http://www.google.com/profiles/bluehat Google] (defunct Google profile page)
** [http://info.med.yale.edu/bbs/faculty/ger_ma.html BBS Page]
** [http://expertise.cos.com/cgi-bin/exp.cgi?id=414253 COS]
** [http://www.mbb.yale.edu/faculty/pages/gerstein.html MB&B]
** [http://bigthink.com/markgerstein Delphi Fellow]

Current M Gerstein CV

2026-02-22T19:43:51Z

Mbg:

Full public CV for Mark Gerstein

https://www.dropbox.com/scl/fi/rjg6qojb9drc9h8bia59x/M-Gerstein-Full-CV-public-15Jan26-FAR25.pdf?rlkey=bip52eb85q7umrauzeoxk4te1&dl=0

Current as of 15 Jan. 2026 (w. some sections less current)

Short CV for Mark Gerstein

http://files.gersteinlab.org/public-docs/2019/08.11/MBG-Short-CV--cv57-31Jul19.html

(Current as of 31 Jul. 19)

([[MBG-Profile|More stuff]])

Main Page

2026-01-25T19:02:03Z

Mbg:

<div style="border: 1px solid black; padding: 10px;">[https://www.gersteinlab.org <big>'''Lab Home Page'''</big>]</div>

== Important Public Items ==
*Gerstein Lab '''[https://www.youtube.com/channel/UCVM3Kd2UWdJrAfQ1RqyajHw Youtube]''' , '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''
*'''[[FAQ]]''' on tools and data
*'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab

__TOC__

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 "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*[[Posters]] showing lab research
*Misc. Public [[Documents]] about the lab
*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])
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== Info for New People ==
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
* [[Glossary]] of terms.
* Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]

== Info for Lab Signature ==
*For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [[Gerstein Lab Computing in HPC]]
** [[Gerstein Lab Computing in GersteinLab West Campus]]
** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]

* Calls, meetings, &c
**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]])
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [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&on=downloads Other info])
**[[Bass434]] introduction
**Booking [[Meeting Room]]
**Booking a [[Conference Room at 100 College]]

* Some Useful University Policies
** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** 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]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]

* Documents
** [[Uploading_documents]]
** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates)

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** 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]
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
**[[OpenStack]]
**[[IDP report]]
**[[PEC package preprints]]
**[[Summary of undergraduate involvement]]
**Lab [http://bit.ly/mglab-folder google folder]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

Main Page

2026-01-25T19:00:34Z

Mbg:

[https://www.gersteinlab.org <big>'''Lab Home Page'''</big>]

== Important Public Items ==
*Gerstein Lab '''[https://www.youtube.com/channel/UCVM3Kd2UWdJrAfQ1RqyajHw Youtube]''' , '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''
*'''[[FAQ]]''' on tools and data
*'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab

__TOC__

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 "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*[[Posters]] showing lab research
*Misc. Public [[Documents]] about the lab
*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])
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== Info for New People ==
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
* [[Glossary]] of terms.
* Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]

== Info for Lab Signature ==
*For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [[Gerstein Lab Computing in HPC]]
** [[Gerstein Lab Computing in GersteinLab West Campus]]
** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]

* Calls, meetings, &c
**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]])
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [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&on=downloads Other info])
**[[Bass434]] introduction
**Booking [[Meeting Room]]
**Booking a [[Conference Room at 100 College]]

* Some Useful University Policies
** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** 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]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]

* Documents
** [[Uploading_documents]]
** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates)

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** 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]
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
**[[OpenStack]]
**[[IDP report]]
**[[PEC package preprints]]
**[[Summary of undergraduate involvement]]
**Lab [http://bit.ly/mglab-folder google folder]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

USA Today Oped from Other Papers for M Gerstein

2025-12-11T01:17:18Z

Mbg: /* D Greenbaum & M Gerstein (2013). "Your DNA vulnerable to snooping, too?",USA Today, July 27, Opinion */

===D Greenbaum & M Gerstein (2013). "Your DNA vulnerable to snooping, too?",''USA Today'', July 27, Opinion===

Link to original article:
http://www.usatoday.com/story/opinion/2013/06/27/dov-greenbaum-and-mark-gerstein-on-nsa-and-genetics/2465589

==== Wiki Text of OPED ====

Your DNA vulnerable to snooping, too?

Dov Greenbaum, and Mark Gerstein 5:46 p.m. EDT June 27, 2013

The science-fiction imagery of 1984 or Minority Report comes to mind amid the unprecedented revelations describing the National Security Agency's sweeping surveillance programs to data mine personal information on people in the U.S. and snoop on our allies.

Imagine combining these dystopian realities with Gattaca, where in addition to trawling our personal communications, the government mines our genomes as well.

An international consortium of genomic researchers across 41 countries potentially moved us a step closer to such a reality when it announced this month a new data-sharing agreement for the expected deluge of human genomes to be sequenced in the near future as the cost falls to levels of an MRI.

In one sense, this agreement is highly beneficial. Large genomic databases are integral to mapping and shedding light on the genetic basis of disease and for developing drugs.

Science vs. social media

Moreover, it's worth noting that Big Brother and Big Genomics aren't the only ones collecting Big Data on you. Retailers analyze consumer shopping habits to the extent that they can often predict a pregnancy, and researchers have been able to determine probable gender, ethnicity, religion and other personal information from just your likes on Facebook.

Further, the younger generation has already made it socially acceptable to embrace information-sharing technology. With the torrent of real-time data gushing from our smartphones, the concept of privacy is still evolving and raises the question of whether the information available to researchers mining DNA databases will be any more personal, revealing or detrimental than what we already disclose unwittingly through social media.

Perhaps. Cables uncovered by WikiLeaks already suggest that Big Brother's intrusive interests extend past compiling electronic communications and include exploring DNA of foreign diplomats. Unchecked, a number of troubling scenarios could result from a government with access to vast genomic databases.

For example, just as spymasters now use the "data exhaust" from our cellphone and e-mail traffic to track targeted individuals, they could in the future use DNA from bits of shed hair and skin to follow someone's movements.

Moreover, analyzing a small segment of someone's DNA could be used to disclose medical conditions or to plant incriminating synthesized DNA at a crime scene ? both blackmail scenarios.

Finally, there is the future potential of a biological weapon designed to target a particular group or even an individual based on unique genetic variants.

DNA research benefits, too

These potential abuses notwithstanding, just as we acquiesce to the cataloging of our data by large corporations in exchange for fast Internet searches or grudgingly submit ourselves to being watched by the NSA in the hopes of preventing terrorism, we should promote vast collections of DNA as powerful tools to combat disease.

Mining large DNA databases has uncovered genes associated with numerous diseases, including macular degeneration and diabetes, and it has enabled targeted treatments for cancer patients.

Now, the public needs to be reassured not only that threats of government exploitation are held in check, but also that the more pedestrian concerns of leaks to employers, insurance providers, or even friends are prevented.

How? Technological solutions alone are unlikely to work, and private databases have become increasingly vulnerable to hackers. Better is a hybrid social-and-technological approach. Codes of conduct, regulatory oversight and punitive threats typically keep data-mining financial organizations in line.

Oversight by a non-governmental agency could similarly protect our genomic data. Additionally, professional licensing, and requiring continuing bioethical and computer security education, could function on a more individual level.

Science fiction movies were entertaining because of their futuristic imagery and seemingly implausible story lines. But as the NSA snooping scandal and the advances in genomics have shown, science is no longer just fiction.

==== Cached Copies & Related Info ====

Main:
[http://archive.gersteinlab.org/mark/out/log/2013/06.29/genomicprism-usa-today-oped/Your-DNA-vulnerable-to-snooping-too.genomicprism.simple.txt TEXT],
[http://archive.gersteinlab.org/mark/out/log/2013/06.29/genomicprism-usa-today-oped/Your-DNA-vulnerable-to-snooping-too.genomicprism.pdf PDF]

Other:
[http://archive.gersteinlab.org/mark/out/log/2013/06.29/genomicprism-usa-today-oped/Your-DNA-vulnerable-to-snooping-too.genomicprism.simple.html Local HTML],
[http://archive.gersteinlab.org/mark/out/log/2013/06.29/genomicprism-usa-today-oped Directory with more formats]

Related Contact based on Tag [https://linkstream2.gerstein.info/tag/genomicprism '''<code>genomicprism</code>''']

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

Proof Stage Checklist

2025-12-09T15:07:37Z

Mbg: /* Long version of checklist */

==Short version==
* Get grant right!
* correct MG email + ORCID
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
* github should have a license/permissions
* lab homepage image
* tweet
* slide deck

(see '''<code>Proofsx57m</code>''' tag on correspondence)

==Long version of checklist==

* Press & PR
** 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.

* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Check that MG's [[Affiliation]] is accurate

* Funding
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
*** We should usually acknowledge grant XXX and ALW (Usually this is a 95/5 split)
** 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.
*** 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.)
** Funding is usually applicable when MG is the last author.

*** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.

*PMC & License
** For license, go for open access for non-commercial use unless prohibitively expensive.
** 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]
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)

* Papers Page (papers.gersteinlab.org)
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
** 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.
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
*** Send the following information to whoever is in charge of rebuilding the papers page:
**** PubMed ID or doi of the preprint
**** A link to the paper
**** A link to the tools or resources (see "Tools & Resources" section below)
**** 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.
**** Any additional information such as co-first authorship
*** 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
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
** Co-first and co-corresponding authors can be indicated with the footnote field
** Use the link field to directly link the journal site (particularly if there is no pubmed)

* Tools & Resources
** Website
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
*** Best is where the paper ID is what, eg, ABCDE
*** Try to use the GitHub standard for code data
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
*** 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).
** You can use the "website" field on the papers page to link your github site.

* Preprints
** Do a biorxiv submission (or another equiv. preprint server)
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).

* Slides & Images
** Make sure Mark has "slide packs" for the paper
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .

* Tweet & Bluesky
**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.
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
https://twitter.com/markgerstein/status/789117961843900417
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344

* Wikipedia
** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate

* Tag for this page
** [[Proofsx57m]]
** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]

Pubmed query

2025-12-01T05:42:22Z

Mbg: /* PubMed Queries */

==Other Views==

There are a number of simplified views of the papers page available, with no extra links, viz:
[http://papers.gersteinlab.org/simple.html '''title-first listing'''] and [http://papers.gersteinlab.org/papers/papers-simple.html traditional author-first listing]
(These are suitable for copying into Word.) Also, here's a simple [http://papers.gersteinlab.org/papers directory listing] with all the paper IDs.

==Notes on Publication List==

[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]


==PubMed Queries==

* [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&sort=date&size=50 '''New Query (updated 12/1/2025)'''] to build papers page into PubMed without Preprints

* [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&sort=date&size=50 '''New Query (updated 7/21/2020)'''] to build papers page into PubMed

* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pubmed&dispmax=200&relpubdate=No%20Limit&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

* ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pubmed&dispmax=200&relpubdate=No%20Limit&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'''])

* [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]]

* [[Papers published with individuals who have left]] Yale

* [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)

==Publication Analysis Services==

* Google Scholar: '''http://scholar.google.ca/scholar?q=author:gerstein-m''' ([https://scholar.google.com/citations?hl=en&view_op=search_authors&mauthors=yale Ranking] of Yale researchers according to Scholar - we do well.)

* [http://orcid.org/0000-0002-9746-3719 ORCID.org/0000-0002-9746-3719] for M Gerstein (very incomplete)

* Highly Cited Researchers lists
** [https://linkstream2.gerstein.info/2016/11/21/archives-hcr-clarivate-analytics Thomson Reuters HIGHLY CITED RESEARCHERS (HCR) List] (on this '14, '15, '16)
** [https://hcr.clarivate.com Clarivate List] (supersedes above, on this in '17 & '18)

==Paper Search==

Adopted from [[Paper_search]]

===Medline Queries:===

[http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=PureSearch&db=PubMed&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&dispmax=200&relpubdate=No+Limit Gerstein M] / [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m&term=Gerstein+M&dispmax=200&relpubdate=No+Limit Gerstein M] (unrestricted) /
[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] /
[http://citeseer.nj.nec.com/cs?cs=1&q=m+gerstein+or+mark+gerstein&co=Expected+Citations&cm=50&cf=Any&ao=Expected+Citations&am=20&af=Any CiteSeer]

http://pubnet.gersteinlab.org/images/mainlogo.jpg

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)&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607170530 cached])

PubNet Graph of Gerstein and Montelione papers [http://www.nesg.org/ NESG] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=Gaetano%20Montelione&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)&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171018 cached])

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)&query2=snyder%20m%20and%20yale&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171429 cached])

===Lists of Papers===

[http://papers.gersteinlab.org/index.html Main]
[http://papers.gersteinlab.org/papers/papers-simple.html Simple]
[http://papers.gersteinlab.org/papers/papers-ids.htm Table]
[http://papers.gersteinlab.org/papers/papers-tags.htm XML tags]
[http://papers.gersteinlab.org/papers/before97.shtml Pre 1997]
[[Other_Papers]]

===Pre-prints:===

[http://papers.gersteinlab.org/e-print E-print &dagger;] with full-text of some papers in press ([http://papers.gersteinlab.org/papers/help.shtml help] on this)

&dagger;[http://www.gersteinlab.org/misc/permissions.html Please see our copyright statement]

==Sortable Lists of Publication Metrics==

===Sortable spreadsheets of Google Scholar & Web of Science & Altmetric (Dec 4, 2019)===
[https://drive.google.com/file/d/1p5_J7Y8nt0WvXE5V7J4XYZ6LEMuwOAUC/view?usp=sharing Altmetric]
[https://drive.google.com/file/d/1Kn8eEpLUzulOtDx_XBXVc1jzb0pJNL2w/view?usp=sharing WoS]
[https://drive.google.com/file/d/1TmN_e8Fm3Cy4kKD8ILHl7-CFQhsEbQJM/view?usp=sharing GScholar]

& that again w/ MG as last/first author

[https://drive.google.com/file/d/1vAZbrivv_2yadY5YFyGvZYaz1o7CSkcz/view?usp=sharing Altmetric]
[https://drive.google.com/file/d/1lOHkuXbOZNY2k39NdtUm3lT3Xv0dP5pP/view?usp=sharing WoS]
[https://drive.google.com/file/d/1wttEpxxBJUM0Guq0P1zgfin-Tph9GNdc/view?usp=sharing GScholar]

===Overall citation stats (Dec 4, 2019)===
595 publications

Cited 144003 times and h-index: 166 (GScholar)

No. papers with over 1000 citations each ------ No. all papers - 22 (No. papers w MG last/first author - 4)

No. papers with 501-1000 citations each ------ 30 (12)

No. papers with 201-500 citations each ------ 78 (40)

No. papers with 101-200 citations each ------ 112 (64)

No. papers with 51-100 citations each ------ 93 (56)

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

[https://drive.google.com/file/d/1rKaLefE71LRvSfCkXoir_SeiNo9nYBnB/view?usp=sharing Number of publications by journal names]

==Misc==

=== dump up to the end of '19 ===

[http://files.gersteinlab.org/public-docs/2019/12.27/cv57-30-bld31Dec19--papers-simple--reformatted2.pdf scientific papers]

=== dump up to the end of '18 ===

[http://files.gersteinlab.org/public-docs/2019/02.14/cv57-30-bld1jan19--papers-simple--reformatted.pdf scientific papers]
[http://files.gersteinlab.org/public-docs/2019/02.14/cv57-26-bld1Jan19--addendum-Rest.pdf other writings]

=== dump up to the end of '17 ===

[http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18--papers-simple-refmt.pdf scientific papers]
[http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18--addendum-Rest.JustOtherPubs.pdf other writings]

=== dump up to the end of '16 ===

[http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-26-bld1dec16--addendum-Rest--Just-Other-Writings.pdf scientific papers]
[http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-30-bld1dec16--papers-simple--reformatted.pdf other writings]

=== dump up to the end of '15 ===

[http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-30--papers-simple--reformatted--28Jan16--FAR.pdf scientific papers]
[http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-27-28Jan16--FAR--Rest--other-papers.pdf other writings]

=== dump up to the end of '14 ===

[http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-pubs-CV-31Dec2014.pdf scientific papers]

=== dump up to the end of '13 ===

[http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-pubs-CV-31Dec2013.pdf scientific papers]

== Broken & Defunct ==



* [http://papers.gersteinlab.org/update/NCBIData.xml Current NCBI XML File]

* [http://oldpapers.gersteinlab.org/search/labquery.pl?query=default (Old) link to construct above]

* [http://www.scholaruniverse.com/profiles/people/090B29F9AC1BD0111E322273EF928B1C Scholar Universe]

* [http://papers.gersteinlab.org/papers/misc/google.html Google Citation Summary]

* [http://academic.research.microsoft.com/author/984673 Microsoft Academic Search Profile for M Gerstein]

Pubmed query

2025-12-01T05:40:26Z

Mbg: /* PubMed Queries */

==Other Views==

There are a number of simplified views of the papers page available, with no extra links, viz:
[http://papers.gersteinlab.org/simple.html '''title-first listing'''] and [http://papers.gersteinlab.org/papers/papers-simple.html traditional author-first listing]
(These are suitable for copying into Word.) Also, here's a simple [http://papers.gersteinlab.org/papers directory listing] with all the paper IDs.

==Notes on Publication List==

[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]


==PubMed Queries==

* [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+NOT+preprint%5Bpt%5DBUID%5D%29&sort=date&size=50 '''New Query (updated 12/1/2025)'''] to build papers page into PubMed without Preprints

* [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&sort=date&size=50 '''New Query (updated 7/21/2020)'''] to build papers page into PubMed

* [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pubmed&dispmax=200&relpubdate=No%20Limit&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

* ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pubmed&dispmax=200&relpubdate=No%20Limit&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'''])

* [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]]

* [[Papers published with individuals who have left]] Yale

* [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)

==Publication Analysis Services==

* Google Scholar: '''http://scholar.google.ca/scholar?q=author:gerstein-m''' ([https://scholar.google.com/citations?hl=en&view_op=search_authors&mauthors=yale Ranking] of Yale researchers according to Scholar - we do well.)

* [http://orcid.org/0000-0002-9746-3719 ORCID.org/0000-0002-9746-3719] for M Gerstein (very incomplete)

* Highly Cited Researchers lists
** [https://linkstream2.gerstein.info/2016/11/21/archives-hcr-clarivate-analytics Thomson Reuters HIGHLY CITED RESEARCHERS (HCR) List] (on this '14, '15, '16)
** [https://hcr.clarivate.com Clarivate List] (supersedes above, on this in '17 & '18)

==Paper Search==

Adopted from [[Paper_search]]

===Medline Queries:===

[http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=PureSearch&db=PubMed&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&dispmax=200&relpubdate=No+Limit Gerstein M] / [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m&term=Gerstein+M&dispmax=200&relpubdate=No+Limit Gerstein M] (unrestricted) /
[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] /
[http://citeseer.nj.nec.com/cs?cs=1&q=m+gerstein+or+mark+gerstein&co=Expected+Citations&cm=50&cf=Any&ao=Expected+Citations&am=20&af=Any CiteSeer]

http://pubnet.gersteinlab.org/images/mainlogo.jpg

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)&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607170530 cached])

PubNet Graph of Gerstein and Montelione papers [http://www.nesg.org/ NESG] ([http://pubnet.gersteinlab.org/cgi-bin/graph.pl?query1=Gaetano%20Montelione&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)&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171018 cached])

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)&query2=snyder%20m%20and%20yale&node=author&edge=coauthor current]) ([http://pubnet.gersteinlab.org/cgi-bin/view.pl?id=050607171429 cached])

===Lists of Papers===

[http://papers.gersteinlab.org/index.html Main]
[http://papers.gersteinlab.org/papers/papers-simple.html Simple]
[http://papers.gersteinlab.org/papers/papers-ids.htm Table]
[http://papers.gersteinlab.org/papers/papers-tags.htm XML tags]
[http://papers.gersteinlab.org/papers/before97.shtml Pre 1997]
[[Other_Papers]]

===Pre-prints:===

[http://papers.gersteinlab.org/e-print E-print &dagger;] with full-text of some papers in press ([http://papers.gersteinlab.org/papers/help.shtml help] on this)

&dagger;[http://www.gersteinlab.org/misc/permissions.html Please see our copyright statement]

==Sortable Lists of Publication Metrics==

===Sortable spreadsheets of Google Scholar & Web of Science & Altmetric (Dec 4, 2019)===
[https://drive.google.com/file/d/1p5_J7Y8nt0WvXE5V7J4XYZ6LEMuwOAUC/view?usp=sharing Altmetric]
[https://drive.google.com/file/d/1Kn8eEpLUzulOtDx_XBXVc1jzb0pJNL2w/view?usp=sharing WoS]
[https://drive.google.com/file/d/1TmN_e8Fm3Cy4kKD8ILHl7-CFQhsEbQJM/view?usp=sharing GScholar]

& that again w/ MG as last/first author

[https://drive.google.com/file/d/1vAZbrivv_2yadY5YFyGvZYaz1o7CSkcz/view?usp=sharing Altmetric]
[https://drive.google.com/file/d/1lOHkuXbOZNY2k39NdtUm3lT3Xv0dP5pP/view?usp=sharing WoS]
[https://drive.google.com/file/d/1wttEpxxBJUM0Guq0P1zgfin-Tph9GNdc/view?usp=sharing GScholar]

===Overall citation stats (Dec 4, 2019)===
595 publications

Cited 144003 times and h-index: 166 (GScholar)

No. papers with over 1000 citations each ------ No. all papers - 22 (No. papers w MG last/first author - 4)

No. papers with 501-1000 citations each ------ 30 (12)

No. papers with 201-500 citations each ------ 78 (40)

No. papers with 101-200 citations each ------ 112 (64)

No. papers with 51-100 citations each ------ 93 (56)

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

[https://drive.google.com/file/d/1rKaLefE71LRvSfCkXoir_SeiNo9nYBnB/view?usp=sharing Number of publications by journal names]

==Misc==

=== dump up to the end of '19 ===

[http://files.gersteinlab.org/public-docs/2019/12.27/cv57-30-bld31Dec19--papers-simple--reformatted2.pdf scientific papers]

=== dump up to the end of '18 ===

[http://files.gersteinlab.org/public-docs/2019/02.14/cv57-30-bld1jan19--papers-simple--reformatted.pdf scientific papers]
[http://files.gersteinlab.org/public-docs/2019/02.14/cv57-26-bld1Jan19--addendum-Rest.pdf other writings]

=== dump up to the end of '17 ===

[http://files.gersteinlab.org/public-docs/2018/01.10/cv57-30-bld8Jan18--papers-simple-refmt.pdf scientific papers]
[http://files.gersteinlab.org/public-docs/2018/01.10/cv57-26-bld8Jan18--addendum-Rest.JustOtherPubs.pdf other writings]

=== dump up to the end of '16 ===

[http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-26-bld1dec16--addendum-Rest--Just-Other-Writings.pdf scientific papers]
[http://archive.gersteinlab.org/public-docs/2017/03.26/2016-summary--cv57/cv57-30-bld1dec16--papers-simple--reformatted.pdf other writings]

=== dump up to the end of '15 ===

[http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-30--papers-simple--reformatted--28Jan16--FAR.pdf scientific papers]
[http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/papers-page-dump-28Jan16/cv57-27-28Jan16--FAR--Rest--other-papers.pdf other writings]

=== dump up to the end of '14 ===

[http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-pubs-CV-31Dec2014.pdf scientific papers]

=== dump up to the end of '13 ===

[http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-pubs-CV-31Dec2013.pdf scientific papers]

== Broken & Defunct ==



* [http://papers.gersteinlab.org/update/NCBIData.xml Current NCBI XML File]

* [http://oldpapers.gersteinlab.org/search/labquery.pl?query=default (Old) link to construct above]

* [http://www.scholaruniverse.com/profiles/people/090B29F9AC1BD0111E322273EF928B1C Scholar Universe]

* [http://papers.gersteinlab.org/papers/misc/google.html Google Citation Summary]

* [http://academic.research.microsoft.com/author/984673 Microsoft Academic Search Profile for M Gerstein]

LA Times Oped on AI

2025-11-26T05:04:43Z

Mbg:

===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)===

'''Link to original article: https://www.latimes.com/opinion/story/2025-11-15/artificial-intelligence-frankenstein'''
----
==== Wiki Text of OPED ====
'''Can AI developers avoid Frankenstein’s fateful mistake?'''

By Dov Greenbaum and Mark Gerstein

Audiences already know the story of Frankenstein. The gothic novel — adapted dozens of times, most recently in director Guillermo del Toro’s haunting revival now available on Netflix — is embedded in our cultural DNA as the cautionary tale of science gone wrong. But popular culture misreads author Mary Shelley’s warning. The lesson isn’t “don’t create dangerous things.” It’s “don’t walk away from what you create.”

This distinction matters: The fork in the road comes after creation, not before. All powerful technologies can become destructive — the choice between outcomes lies in stewardship or abdication. Victor Frankenstein’s sin wasn’t simply bringing life to a grotesque creature. It was refusing to raise it, insisting that the consequences were someone else’s problem. Every generation produces its Victors. Ours work in artificial intelligence.

Recently, a California appeals court fined an attorney $10,000 after 21 of 23 case citations in their brief proved to be AI fabrications — nonexistent precedents. Hundreds of similar instances have been documented nationwide, growing from a few cases a month to a few cases a day. This summer, a Georgia appeals court vacated a divorce ruling after discovering that 11 of 15 citations were AI fabrications. How many more went undetected, ready to corrupt the legal record?

The problem runs deeper than irresponsible deployment. For decades, computer systems were provably correct — a pocket calculator can consistently offer users the mathematically correct answers every time. Engineers could demonstrate how an algorithm would behave. Failures meant implementation errors, not uncertainty about the system itself.

Modern AI changes that paradigm. A recent study reported in Science confirms what AI experts have long known: plausible falsehoods — what the industry calls “hallucinations” — are inevitable in these systems. They’re trained to predict what sounds plausible, not to verify what’s true. When confident answers aren’t justified, the systems guess anyway. Their training rewards confidence over uncertainty. As one AI researcher quoted in the report put it, fixing this would “kill the product.”

This creates a fundamental veracity problem. These systems work by extracting patterns from vast training datasets — patterns so numerous and interconnected that even their designers cannot reliably predict what they’ll produce. We can only observe how they actually behave in practice, sometimes not until well after damage is done.

This unpredictability creates cascading consequences. These failures don’t disappear, they become permanent. Every legal fabrication that slips in undetected enters databases as precedent. Fake medical advice spreads across health sites. AI-generated “news” circulates through social media. This synthetic content is even scraped back into training data for future models. Today’s hallucinations become tomorrow’s facts.

So how do we address this without stifling innovation? We already have a model in pharmaceuticals. Drug companies cannot be certain of all biological effects in advance, so they test extensively, with most drugs failing before reaching patients. Even approved drugs face unexpected real-world problems. That’s why continuous monitoring remains essential. AI needs a similar framework.

Responsible stewardship — the opposite of Victor Frankenstein’s abandonment — requires three interconnected pillars. First: prescribed training standards. Drug manufacturers must control ingredients, document production practices and conduct quality testing. AI companies should face parallel requirements: documented provenance for training data, with contamination monitoring to prevent reuse of problematic synthetic content, prohibited content categories and bias testing across demographics. Pharmaceutical regulators require transparency while current AI companies need to disclose little.

Second: pre-deployment testing. Drugs undergo extensive trials before reaching patients. Randomized controlled trials were a major achievement, developed to demonstrate safety and efficacy. Most fail. That’s the point. Testing catches subtle dangers before deployment. AI systems for high-stakes applications, including legal research, medical advice and financial management, need structured testing to document error rates and establish safety thresholds.

Third: continuous surveillance after deployment. Drug companies are obligated to track adverse events of their products and report them to regulators. In turn, the regulators can mandate warnings, restrictions or withdrawal when problems emerge. AI needs equivalent oversight.

Why does this need regulation rather than voluntary compliance? Because AI systems are fundamentally different from traditional tools. A hammer doesn’t pretend to be a carpenter. AI systems do, projecting authority through confident prose, whether retrieving or fabricating facts. Without regulatory requirements, companies optimizing for engagement will necessarily sacrifice accuracy for market share.

The trick is regulating without crushing innovation. The EU’s AI Act shows how hard that is. Under the Act, companies building high-risk AI systems must document how their systems work, assess risks and monitor them closely. A small startup might spend more on lawyers and paperwork than on building the actual product. Big companies with legal teams can handle this. Small teams can’t.

Pharmaceutical regulation shows the same pattern. Post-market surveillance prevented tens of thousands of deaths when the FDA discovered that Vioxx — an arthritis medication prescribed to more than 80 million patients worldwide — doubled the risk of heart attacks. Still, billion-dollar regulatory costs mean only large companies can compete, and beneficial treatments for rare diseases, perhaps best tackled by small biotechs, go undeveloped.

Graduated oversight addresses this problem, scaling requirements and costs with demonstrated harm. An AI assistant with low error rates gets extra monitoring. Higher rates trigger mandatory fixes. Persistent problems? Pull it from the market until it’s fixed. Companies either improve their systems to stay in business, or they exit. Innovation continues, but now there’s more accountability.

Responsible stewardship cannot be voluntary. Once you create something powerful, you’re responsible for it. The question isn’t whether to build advanced AI systems — we’re already building them. The question is whether we’ll require the careful stewardship those systems demand.

The pharmaceutical framework — prescribed training standards, structured testing, continuous surveillance — offers a proven model for critical technologies we cannot fully predict. Shelley’s lesson was never about the creation itself. It was about what happens when creators walk away. Two centuries later, as Del Toro’s adaptation reaches millions this month, the lesson remains urgent. This time, with synthetic intelligence rapidly spreading through our society, we might not get another chance to choose the other path.

Dov Greenbaum is professor of law and director of the Zvi Meitar Institute for Legal Implications of Emerging Technologies at Reichman University in Israel.

Mark Gerstein is the Albert L. Williams Professor of Biomedical Informatics at Yale University.

----
==== Cached Copies ====

Reprint (
[https://www.dropbox.com/scl/fi/woocw8alkg395kbli8phd/frankenstein.normal.pdf?rlkey=3gbuxsszcfpj881b4jpd1oiqz&dl=0 Full-PDF],
[https://www.dropbox.com/scl/fi/74cymotsxislbwhv6i8f5/frankenstein.simple.pdf?rlkey=c9noj432zn6z8hbnbv05afu8x&dl=0 Simple-PDF],
[https://www.dropbox.com/scl/fi/93uoc8e9edft21sbn3qop/frankenstein.normal.html?rlkey=bo6ot7q2ljvfojr0sissgrtn2&dl=0 Full-HTML],
[https://www.dropbox.com/scl/fi/w4dx2w33u8k2zcdbr1yk2/frankenstein.simple.html?rlkey=a3lee30t0rnf19dw1xb9jif71&dl=0 Simple-HTML]
)

Revisions tag: [https://linkstream2.gerstein.info/tag/frankenstein/ frankenstein] + https://mail.google.com/mail/u/0/#search/frankenstein (frankenstein)

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

LA Times Oped on AI

2025-11-26T04:56:36Z

Mbg: /* D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion) */

===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)===

'''Link to original article: https://www.latimes.com/opinion/story/2025-11-15/artificial-intelligence-frankenstein'''
----
==== Cached Copies ====

Reprint (
[https://www.dropbox.com/scl/fi/woocw8alkg395kbli8phd/frankenstein.normal.pdf?rlkey=3gbuxsszcfpj881b4jpd1oiqz&dl=0 Full-PDF],
[https://www.dropbox.com/scl/fi/74cymotsxislbwhv6i8f5/frankenstein.simple.pdf?rlkey=c9noj432zn6z8hbnbv05afu8x&dl=0 Simple-PDF],
[https://www.dropbox.com/scl/fi/93uoc8e9edft21sbn3qop/frankenstein.normal.html?rlkey=bo6ot7q2ljvfojr0sissgrtn2&dl=0 Full-HTML],
[https://www.dropbox.com/scl/fi/w4dx2w33u8k2zcdbr1yk2/frankenstein.simple.html?rlkey=a3lee30t0rnf19dw1xb9jif71&dl=0 Simple-HTML]
)

Revisions tag: [https://linkstream2.gerstein.info/tag/frankenstein/ frankenstein] + https://mail.google.com/mail/u/0/#search/frankenstein (frankenstein)

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

----
==== Wiki Text of OPED ====
'''Can AI developers avoid Frankenstein’s fateful mistake?'''

By Dov Greenbaum and Mark Gerstein

Audiences already know the story of Frankenstein. The gothic novel — adapted dozens of times, most recently in director Guillermo del Toro’s haunting revival now available on Netflix — is embedded in our cultural DNA as the cautionary tale of science gone wrong. But popular culture misreads author Mary Shelley’s warning. The lesson isn’t “don’t create dangerous things.” It’s “don’t walk away from what you create.”

This distinction matters: The fork in the road comes after creation, not before. All powerful technologies can become destructive — the choice between outcomes lies in stewardship or abdication. Victor Frankenstein’s sin wasn’t simply bringing life to a grotesque creature. It was refusing to raise it, insisting that the consequences were someone else’s problem. Every generation produces its Victors. Ours work in artificial intelligence.

Recently, a California appeals court fined an attorney $10,000 after 21 of 23 case citations in their brief proved to be AI fabrications — nonexistent precedents. Hundreds of similar instances have been documented nationwide, growing from a few cases a month to a few cases a day. This summer, a Georgia appeals court vacated a divorce ruling after discovering that 11 of 15 citations were AI fabrications. How many more went undetected, ready to corrupt the legal record?

The problem runs deeper than irresponsible deployment. For decades, computer systems were provably correct — a pocket calculator can consistently offer users the mathematically correct answers every time. Engineers could demonstrate how an algorithm would behave. Failures meant implementation errors, not uncertainty about the system itself.

Modern AI changes that paradigm. A recent study reported in Science confirms what AI experts have long known: plausible falsehoods — what the industry calls “hallucinations” — are inevitable in these systems. They’re trained to predict what sounds plausible, not to verify what’s true. When confident answers aren’t justified, the systems guess anyway. Their training rewards confidence over uncertainty. As one AI researcher quoted in the report put it, fixing this would “kill the product.”

This creates a fundamental veracity problem. These systems work by extracting patterns from vast training datasets — patterns so numerous and interconnected that even their designers cannot reliably predict what they’ll produce. We can only observe how they actually behave in practice, sometimes not until well after damage is done.

This unpredictability creates cascading consequences. These failures don’t disappear, they become permanent. Every legal fabrication that slips in undetected enters databases as precedent. Fake medical advice spreads across health sites. AI-generated “news” circulates through social media. This synthetic content is even scraped back into training data for future models. Today’s hallucinations become tomorrow’s facts.

So how do we address this without stifling innovation? We already have a model in pharmaceuticals. Drug companies cannot be certain of all biological effects in advance, so they test extensively, with most drugs failing before reaching patients. Even approved drugs face unexpected real-world problems. That’s why continuous monitoring remains essential. AI needs a similar framework.

Responsible stewardship — the opposite of Victor Frankenstein’s abandonment — requires three interconnected pillars. First: prescribed training standards. Drug manufacturers must control ingredients, document production practices and conduct quality testing. AI companies should face parallel requirements: documented provenance for training data, with contamination monitoring to prevent reuse of problematic synthetic content, prohibited content categories and bias testing across demographics. Pharmaceutical regulators require transparency while current AI companies need to disclose little.

Second: pre-deployment testing. Drugs undergo extensive trials before reaching patients. Randomized controlled trials were a major achievement, developed to demonstrate safety and efficacy. Most fail. That’s the point. Testing catches subtle dangers before deployment. AI systems for high-stakes applications, including legal research, medical advice and financial management, need structured testing to document error rates and establish safety thresholds.

Third: continuous surveillance after deployment. Drug companies are obligated to track adverse events of their products and report them to regulators. In turn, the regulators can mandate warnings, restrictions or withdrawal when problems emerge. AI needs equivalent oversight.

Why does this need regulation rather than voluntary compliance? Because AI systems are fundamentally different from traditional tools. A hammer doesn’t pretend to be a carpenter. AI systems do, projecting authority through confident prose, whether retrieving or fabricating facts. Without regulatory requirements, companies optimizing for engagement will necessarily sacrifice accuracy for market share.

The trick is regulating without crushing innovation. The EU’s AI Act shows how hard that is. Under the Act, companies building high-risk AI systems must document how their systems work, assess risks and monitor them closely. A small startup might spend more on lawyers and paperwork than on building the actual product. Big companies with legal teams can handle this. Small teams can’t.

Pharmaceutical regulation shows the same pattern. Post-market surveillance prevented tens of thousands of deaths when the FDA discovered that Vioxx — an arthritis medication prescribed to more than 80 million patients worldwide — doubled the risk of heart attacks. Still, billion-dollar regulatory costs mean only large companies can compete, and beneficial treatments for rare diseases, perhaps best tackled by small biotechs, go undeveloped.

Graduated oversight addresses this problem, scaling requirements and costs with demonstrated harm. An AI assistant with low error rates gets extra monitoring. Higher rates trigger mandatory fixes. Persistent problems? Pull it from the market until it’s fixed. Companies either improve their systems to stay in business, or they exit. Innovation continues, but now there’s more accountability.

Responsible stewardship cannot be voluntary. Once you create something powerful, you’re responsible for it. The question isn’t whether to build advanced AI systems — we’re already building them. The question is whether we’ll require the careful stewardship those systems demand.

The pharmaceutical framework — prescribed training standards, structured testing, continuous surveillance — offers a proven model for critical technologies we cannot fully predict. Shelley’s lesson was never about the creation itself. It was about what happens when creators walk away. Two centuries later, as Del Toro’s adaptation reaches millions this month, the lesson remains urgent. This time, with synthetic intelligence rapidly spreading through our society, we might not get another chance to choose the other path.

Dov Greenbaum is professor of law and director of the Zvi Meitar Institute for Legal Implications of Emerging Technologies at Reichman University in Israel.

Mark Gerstein is the Albert L. Williams Professor of Biomedical Informatics at Yale University.

LA Times Oped on AI

2025-11-26T04:56:17Z

Mbg:

===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)===

''Link to original article:
https://www.latimes.com/opinion/story/2025-11-15/artificial-intelligence-frankenstein''
----
==== Cached Copies ====

Reprint (
[https://www.dropbox.com/scl/fi/woocw8alkg395kbli8phd/frankenstein.normal.pdf?rlkey=3gbuxsszcfpj881b4jpd1oiqz&dl=0 Full-PDF],
[https://www.dropbox.com/scl/fi/74cymotsxislbwhv6i8f5/frankenstein.simple.pdf?rlkey=c9noj432zn6z8hbnbv05afu8x&dl=0 Simple-PDF],
[https://www.dropbox.com/scl/fi/93uoc8e9edft21sbn3qop/frankenstein.normal.html?rlkey=bo6ot7q2ljvfojr0sissgrtn2&dl=0 Full-HTML],
[https://www.dropbox.com/scl/fi/w4dx2w33u8k2zcdbr1yk2/frankenstein.simple.html?rlkey=a3lee30t0rnf19dw1xb9jif71&dl=0 Simple-HTML]
)

Revisions tag: [https://linkstream2.gerstein.info/tag/frankenstein/ frankenstein] + https://mail.google.com/mail/u/0/#search/frankenstein (frankenstein)

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

----
==== Wiki Text of OPED ====
'''Can AI developers avoid Frankenstein’s fateful mistake?'''

By Dov Greenbaum and Mark Gerstein

Audiences already know the story of Frankenstein. The gothic novel — adapted dozens of times, most recently in director Guillermo del Toro’s haunting revival now available on Netflix — is embedded in our cultural DNA as the cautionary tale of science gone wrong. But popular culture misreads author Mary Shelley’s warning. The lesson isn’t “don’t create dangerous things.” It’s “don’t walk away from what you create.”

This distinction matters: The fork in the road comes after creation, not before. All powerful technologies can become destructive — the choice between outcomes lies in stewardship or abdication. Victor Frankenstein’s sin wasn’t simply bringing life to a grotesque creature. It was refusing to raise it, insisting that the consequences were someone else’s problem. Every generation produces its Victors. Ours work in artificial intelligence.

Recently, a California appeals court fined an attorney $10,000 after 21 of 23 case citations in their brief proved to be AI fabrications — nonexistent precedents. Hundreds of similar instances have been documented nationwide, growing from a few cases a month to a few cases a day. This summer, a Georgia appeals court vacated a divorce ruling after discovering that 11 of 15 citations were AI fabrications. How many more went undetected, ready to corrupt the legal record?

The problem runs deeper than irresponsible deployment. For decades, computer systems were provably correct — a pocket calculator can consistently offer users the mathematically correct answers every time. Engineers could demonstrate how an algorithm would behave. Failures meant implementation errors, not uncertainty about the system itself.

Modern AI changes that paradigm. A recent study reported in Science confirms what AI experts have long known: plausible falsehoods — what the industry calls “hallucinations” — are inevitable in these systems. They’re trained to predict what sounds plausible, not to verify what’s true. When confident answers aren’t justified, the systems guess anyway. Their training rewards confidence over uncertainty. As one AI researcher quoted in the report put it, fixing this would “kill the product.”

This creates a fundamental veracity problem. These systems work by extracting patterns from vast training datasets — patterns so numerous and interconnected that even their designers cannot reliably predict what they’ll produce. We can only observe how they actually behave in practice, sometimes not until well after damage is done.

This unpredictability creates cascading consequences. These failures don’t disappear, they become permanent. Every legal fabrication that slips in undetected enters databases as precedent. Fake medical advice spreads across health sites. AI-generated “news” circulates through social media. This synthetic content is even scraped back into training data for future models. Today’s hallucinations become tomorrow’s facts.

So how do we address this without stifling innovation? We already have a model in pharmaceuticals. Drug companies cannot be certain of all biological effects in advance, so they test extensively, with most drugs failing before reaching patients. Even approved drugs face unexpected real-world problems. That’s why continuous monitoring remains essential. AI needs a similar framework.

Responsible stewardship — the opposite of Victor Frankenstein’s abandonment — requires three interconnected pillars. First: prescribed training standards. Drug manufacturers must control ingredients, document production practices and conduct quality testing. AI companies should face parallel requirements: documented provenance for training data, with contamination monitoring to prevent reuse of problematic synthetic content, prohibited content categories and bias testing across demographics. Pharmaceutical regulators require transparency while current AI companies need to disclose little.

Second: pre-deployment testing. Drugs undergo extensive trials before reaching patients. Randomized controlled trials were a major achievement, developed to demonstrate safety and efficacy. Most fail. That’s the point. Testing catches subtle dangers before deployment. AI systems for high-stakes applications, including legal research, medical advice and financial management, need structured testing to document error rates and establish safety thresholds.

Third: continuous surveillance after deployment. Drug companies are obligated to track adverse events of their products and report them to regulators. In turn, the regulators can mandate warnings, restrictions or withdrawal when problems emerge. AI needs equivalent oversight.

Why does this need regulation rather than voluntary compliance? Because AI systems are fundamentally different from traditional tools. A hammer doesn’t pretend to be a carpenter. AI systems do, projecting authority through confident prose, whether retrieving or fabricating facts. Without regulatory requirements, companies optimizing for engagement will necessarily sacrifice accuracy for market share.

The trick is regulating without crushing innovation. The EU’s AI Act shows how hard that is. Under the Act, companies building high-risk AI systems must document how their systems work, assess risks and monitor them closely. A small startup might spend more on lawyers and paperwork than on building the actual product. Big companies with legal teams can handle this. Small teams can’t.

Pharmaceutical regulation shows the same pattern. Post-market surveillance prevented tens of thousands of deaths when the FDA discovered that Vioxx — an arthritis medication prescribed to more than 80 million patients worldwide — doubled the risk of heart attacks. Still, billion-dollar regulatory costs mean only large companies can compete, and beneficial treatments for rare diseases, perhaps best tackled by small biotechs, go undeveloped.

Graduated oversight addresses this problem, scaling requirements and costs with demonstrated harm. An AI assistant with low error rates gets extra monitoring. Higher rates trigger mandatory fixes. Persistent problems? Pull it from the market until it’s fixed. Companies either improve their systems to stay in business, or they exit. Innovation continues, but now there’s more accountability.

Responsible stewardship cannot be voluntary. Once you create something powerful, you’re responsible for it. The question isn’t whether to build advanced AI systems — we’re already building them. The question is whether we’ll require the careful stewardship those systems demand.

The pharmaceutical framework — prescribed training standards, structured testing, continuous surveillance — offers a proven model for critical technologies we cannot fully predict. Shelley’s lesson was never about the creation itself. It was about what happens when creators walk away. Two centuries later, as Del Toro’s adaptation reaches millions this month, the lesson remains urgent. This time, with synthetic intelligence rapidly spreading through our society, we might not get another chance to choose the other path.

Dov Greenbaum is professor of law and director of the Zvi Meitar Institute for Legal Implications of Emerging Technologies at Reichman University in Israel.

Mark Gerstein is the Albert L. Williams Professor of Biomedical Informatics at Yale University.

LA Times Oped on AI

2025-11-26T04:55:51Z

Mbg:

===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)===

Link to original article:
https://www.latimes.com/opinion/story/2025-11-15/artificial-intelligence-frankenstein
----
==== Cached Copies ====

Reprint (
[https://www.dropbox.com/scl/fi/woocw8alkg395kbli8phd/frankenstein.normal.pdf?rlkey=3gbuxsszcfpj881b4jpd1oiqz&dl=0 Full-PDF],
[https://www.dropbox.com/scl/fi/74cymotsxislbwhv6i8f5/frankenstein.simple.pdf?rlkey=c9noj432zn6z8hbnbv05afu8x&dl=0 Simple-PDF],
[https://www.dropbox.com/scl/fi/93uoc8e9edft21sbn3qop/frankenstein.normal.html?rlkey=bo6ot7q2ljvfojr0sissgrtn2&dl=0 Full-HTML],
[https://www.dropbox.com/scl/fi/w4dx2w33u8k2zcdbr1yk2/frankenstein.simple.html?rlkey=a3lee30t0rnf19dw1xb9jif71&dl=0 Simple-HTML]
)

Revisions tag: [https://linkstream2.gerstein.info/tag/frankenstein/ frankenstein] + https://mail.google.com/mail/u/0/#search/frankenstein (frankenstein)

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

----
==== Wiki Text of OPED ====
'''Can AI developers avoid Frankenstein’s fateful mistake?'''

By Dov Greenbaum and Mark Gerstein

Audiences already know the story of Frankenstein. The gothic novel — adapted dozens of times, most recently in director Guillermo del Toro’s haunting revival now available on Netflix — is embedded in our cultural DNA as the cautionary tale of science gone wrong. But popular culture misreads author Mary Shelley’s warning. The lesson isn’t “don’t create dangerous things.” It’s “don’t walk away from what you create.”

This distinction matters: The fork in the road comes after creation, not before. All powerful technologies can become destructive — the choice between outcomes lies in stewardship or abdication. Victor Frankenstein’s sin wasn’t simply bringing life to a grotesque creature. It was refusing to raise it, insisting that the consequences were someone else’s problem. Every generation produces its Victors. Ours work in artificial intelligence.

Recently, a California appeals court fined an attorney $10,000 after 21 of 23 case citations in their brief proved to be AI fabrications — nonexistent precedents. Hundreds of similar instances have been documented nationwide, growing from a few cases a month to a few cases a day. This summer, a Georgia appeals court vacated a divorce ruling after discovering that 11 of 15 citations were AI fabrications. How many more went undetected, ready to corrupt the legal record?

The problem runs deeper than irresponsible deployment. For decades, computer systems were provably correct — a pocket calculator can consistently offer users the mathematically correct answers every time. Engineers could demonstrate how an algorithm would behave. Failures meant implementation errors, not uncertainty about the system itself.

Modern AI changes that paradigm. A recent study reported in Science confirms what AI experts have long known: plausible falsehoods — what the industry calls “hallucinations” — are inevitable in these systems. They’re trained to predict what sounds plausible, not to verify what’s true. When confident answers aren’t justified, the systems guess anyway. Their training rewards confidence over uncertainty. As one AI researcher quoted in the report put it, fixing this would “kill the product.”

This creates a fundamental veracity problem. These systems work by extracting patterns from vast training datasets — patterns so numerous and interconnected that even their designers cannot reliably predict what they’ll produce. We can only observe how they actually behave in practice, sometimes not until well after damage is done.

This unpredictability creates cascading consequences. These failures don’t disappear, they become permanent. Every legal fabrication that slips in undetected enters databases as precedent. Fake medical advice spreads across health sites. AI-generated “news” circulates through social media. This synthetic content is even scraped back into training data for future models. Today’s hallucinations become tomorrow’s facts.

So how do we address this without stifling innovation? We already have a model in pharmaceuticals. Drug companies cannot be certain of all biological effects in advance, so they test extensively, with most drugs failing before reaching patients. Even approved drugs face unexpected real-world problems. That’s why continuous monitoring remains essential. AI needs a similar framework.

Responsible stewardship — the opposite of Victor Frankenstein’s abandonment — requires three interconnected pillars. First: prescribed training standards. Drug manufacturers must control ingredients, document production practices and conduct quality testing. AI companies should face parallel requirements: documented provenance for training data, with contamination monitoring to prevent reuse of problematic synthetic content, prohibited content categories and bias testing across demographics. Pharmaceutical regulators require transparency while current AI companies need to disclose little.

Second: pre-deployment testing. Drugs undergo extensive trials before reaching patients. Randomized controlled trials were a major achievement, developed to demonstrate safety and efficacy. Most fail. That’s the point. Testing catches subtle dangers before deployment. AI systems for high-stakes applications, including legal research, medical advice and financial management, need structured testing to document error rates and establish safety thresholds.

Third: continuous surveillance after deployment. Drug companies are obligated to track adverse events of their products and report them to regulators. In turn, the regulators can mandate warnings, restrictions or withdrawal when problems emerge. AI needs equivalent oversight.

Why does this need regulation rather than voluntary compliance? Because AI systems are fundamentally different from traditional tools. A hammer doesn’t pretend to be a carpenter. AI systems do, projecting authority through confident prose, whether retrieving or fabricating facts. Without regulatory requirements, companies optimizing for engagement will necessarily sacrifice accuracy for market share.

The trick is regulating without crushing innovation. The EU’s AI Act shows how hard that is. Under the Act, companies building high-risk AI systems must document how their systems work, assess risks and monitor them closely. A small startup might spend more on lawyers and paperwork than on building the actual product. Big companies with legal teams can handle this. Small teams can’t.

Pharmaceutical regulation shows the same pattern. Post-market surveillance prevented tens of thousands of deaths when the FDA discovered that Vioxx — an arthritis medication prescribed to more than 80 million patients worldwide — doubled the risk of heart attacks. Still, billion-dollar regulatory costs mean only large companies can compete, and beneficial treatments for rare diseases, perhaps best tackled by small biotechs, go undeveloped.

Graduated oversight addresses this problem, scaling requirements and costs with demonstrated harm. An AI assistant with low error rates gets extra monitoring. Higher rates trigger mandatory fixes. Persistent problems? Pull it from the market until it’s fixed. Companies either improve their systems to stay in business, or they exit. Innovation continues, but now there’s more accountability.

Responsible stewardship cannot be voluntary. Once you create something powerful, you’re responsible for it. The question isn’t whether to build advanced AI systems — we’re already building them. The question is whether we’ll require the careful stewardship those systems demand.

The pharmaceutical framework — prescribed training standards, structured testing, continuous surveillance — offers a proven model for critical technologies we cannot fully predict. Shelley’s lesson was never about the creation itself. It was about what happens when creators walk away. Two centuries later, as Del Toro’s adaptation reaches millions this month, the lesson remains urgent. This time, with synthetic intelligence rapidly spreading through our society, we might not get another chance to choose the other path.

Dov Greenbaum is professor of law and director of the Zvi Meitar Institute for Legal Implications of Emerging Technologies at Reichman University in Israel.

Mark Gerstein is the Albert L. Williams Professor of Biomedical Informatics at Yale University.

Other Papers

2025-11-26T04:48:15Z

Mbg: /* Opinion Pieces (Op-Eds) */

==Opinion Pieces (Op-Eds)==

* D Greenbaum & M Gerstein (2008). [[Hartford_Courant_OpEd_from_Other_Papers_for_M_Gerstein|"Danger: Sharing Gene Data"]], ''Hartford Courant'', July 10, pg. A11 (oped)

* D Greenbaum & M Gerstein (2008). [[SF Chron OpEd from Other Papers for M Gerstein|"Personal genomics requires redefining privacy -- The human blueprint: dangerous secrets"]], ''SF Chronicle'', Nov. 2, Page 2 (Insight)

* M Seringhaus & M Gerstein (2009). [[Hartford_Courant_OpEd2_from_Other_Papers_for_M_Gerstein|"Putting too much information online can erode individual privacy"]], ''Hartford Courant'', June 5 (oped)

* D Greenbaum & M Gerstein (2010). [[SF Chron OpEd2 from Other Papers for M Gerstein|"Exploring genetics of professional athletes"]], ''SF Chronicle'', May 2, Page E-4 (Insight)

* D Greenbaum & M Gerstein (2012). [[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)

* D Greenbaum & M Gerstein (2013). [[USA Today Oped from Other Papers for M Gerstein|"Your DNA vulnerable to snooping, too?"]], ''USA Today'', July 27 (Opinion)

* D Greenbaum & M Gerstein (2015). [[SF Chron Oped on gcode from Other Papers for M Gerstein|"Too big to close down: Websites need regulation like utilities"]], ''SF Chronicle'', April 24 (Opinion)

* D Greenbaum & M Gerstein (2015). [[SF Chron Oped on GINA from Other Papers for M Gerstein|"Why can employers fingerprint, but not test workers’ DNA?"]], ''SF Chronicle'', July 10 (Opinion)

* D Greenbaum & M Gerstein (2016). [[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

* D Greenbaum & M Gerstein (2017). [[SF Chron Oped on Wearable Data from Other Papers for M Gerstein|"Pooling data from wearables could boost health benefits"]], ''SF Chronicle'', Feb. 24 (Opinion)

* D Greenbaum & M Gerstein (2018). [[SF Chron Oped on Data Residue from Other Papers for M Gerstein|"Our smart devices must be made to forget us"]], ''SF Chronicle'', Oct. 18 (Opinion)

* G Gursoy & M Gerstein (2020). [[Hartford Courant Oped on Molecular Privacy|"As coronavirus testing expands, new personal privacy issues arise"]], ''Hartford Courant'', July 19 (oped)

* M Gerstein & J Peccia (2020). [[New Haven Register Oped on Aerosol Transmission of Coronavirus|"What secondhand smoke tells us about the coronavirus"]], ''New Haven Register'', Dec. 12 (Opinion)

* M Gerstein & D Greenbaum (2021). [[JPost Oped on Data Science and polling|"Georgia Senate runoff: Using predictive analytics and big data properly"]], ''Jerusalem Post Opinion'', Jan. 6 (Opinion)

* D Greenbaum & M Gerstein (2024). [[The Hill Oped on 23andme|"23andMe must secure its DNA databases immediately"]], ''The Hill'', Dec 14 (Opinion)

* D Greenbaum & M Gerstein (2025). [[LA Times Oped on AI|"Can AI developers avoid Frankenstein’s fateful mistake?"]], ''The LA Times'', Nov 15 (Opinion)

==Letters to the Editor (in the Popular Press)==

* M Gerstein (1996). [[Byte_letter_from_Other_Papers_for_M_Gerstein|"Porting Unix"]], ''Byte'' (Aug.)

* M Gerstein (1997). [http://textstream.blogspot.com/2007/01/letter-how-smart-can-it-be-responding.html "How Smart Can It Be?"], ''NY Times'' (13 May)

* M Gerstein (1998). [http://textstream.blogspot.com/2006/10/letter-new-stadium-lets-vote-on-it-in.html "A New Stadium? Let's Vote on It"], ''NY Times'' (11 June)

* M Gerstein (1999). [http://textstream.blogspot.com/2006/09/letter-in-response-to-daemon-seed.html "Daemon Seedlings"], ''Wired'' (Issue 7.08, Aug.)

* M Gerstein (1999). [http://textstream.blogspot.com/2006/10/letter-life-beyond-abacus-in-response.html "Life Beyond the Abacus"], ''NY Times'' (6 Dec.)

* M Gerstein (1999). [http://textstream.blogspot.com/2007/03/letter-responding-to-riding-mo-in-lime.html "Re: Riding the Mo In the Lime Green Glow"], ''NY Times'' (19 Dec.)

* M Gerstein (2006). [http://textstream.blogspot.com/2006/09/reclusive-genius-letter-in-response-to.html "Reclusive Genius"] , ''NY Times'' (3 Sept.)

* M Gerstein (2006). [http://textstream.blogspot.com/2006/10/letter-in-response-to-homo-conexus.html "Re: Homo Conexus"], ''Tech Review'' (Sept.-Oct.)

* M Gerstein (2006). [http://textstream.blogspot.com/2007/03/letter-programming-pedigrees-responding.html "Programming Pedigrees"], ''American Scientist'' (Nov.-Dec.)

* M Gerstein & A Smith (2007). [http://textstream.blogspot.com/2007/07/let-to-ed-re-smarter-web-tech-review.html "The Semantic Web"], ''Tech Review'' (Jul.-Aug.)

* M Gerstein (2007). [http://textstream.blogspot.com/2007/09/let-to-ed-re-moms-genes-or-dads-map-can.html "DNA Rights and Wrongs"], ''Washington Post'' (7 Sept., A20)

* M Gerstein (2008). [http://textstream.blogspot.com/2008/02/let-to-ed-23andmashup-re-23andme-will.html "23andMashup"], ''Wired'' (issue 16.02, Feb., pg. 17)

* D Greenbaum & M Gerstein (2009). [http://textstream.blogspot.com/2009/11/let-to-ed-re-your-genome-isnt-that.html "Can't run from DNA"], ''New Scientist'' (issue 2727, 23 Sept., pgs. 28-29)

* M Gerstein (2010). [http://blog.gerstein.info/2010/09/harness-dna-memory-letter-re-avoiding.html "Harness DNA Memory"], ''American Scientist'' (Mar.-Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/09/testing-isnt-everything-letter-re.html "Testing Isn’t Everything"], ''NY Times'' (17 Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/09/regulating-genome-letter-re-diagnosis.html "Regulating the Genome"], ''Forbes'' (26 Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/10/thrills-and-traps-lurking-on-web-letter.html "Thrills and Traps, Lurking on the Web"], ''NY Times'' (12 May, pg. A24)

* M Gerstein (2010). [http://blog.gerstein.info/2010/09/outlook-for-libraries-letter-re.html "The Outlook for Libraries"], ''Harvard Magazine'' (July-August issue)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/10/concern-for-privacy-letter-re-dna.html "Concern for Privacy"], ''NY Times'' (17 Oct., pg. SP11)

* D Greenbaum & M Gerstein (2011). [http://blog.gerstein.info/2011/07/benefits-of-snooping-letter-re-how-to.html "The Benefits of Snooping"], ''Tech Review'' (Jul.-Aug.)

* D Greenbaum & M Gerstein (2011). [http://blog.gerstein.info/2011/11/sharing-too-much-online-letter-re-at.html "Sharing Too Much Online"], ''NY Times'' (7 Oct.)

* M Gerstein (2013). [http://blog.gerstein.info/2013/07/cyberattacks-on-universities-and-how-to.html "Cyberattacks on Universities, and How to Thwart Them"], ''NY Times'' (24 Jul., pg A22)

* M Gerstein (2014). [http://blog.gerstein.info/2014/05/getting-personal-letter-re-uniquely-me.html "Getting Personal"], ''American Scientist'' (May-Jun., vol. 12, pg. 163)

* D Greenbaum & M Gerstein (2015). [http://blog.gerstein.info/2015/06/an-emerging-field-letter-re-cultures-of.html "An Emerging Field"], ''American Scientist'' (May-Jun., vol. 103, pg. 164)

* M Gerstein (2015). [http://blog.gerstein.info/2015/12/the-full-monte-carlo-letter-re-programs.html "The Full Monte Carlo"], ''American Scientist'' (Nov-Dec., vol. 103, Num. 6, pg. 374)

* D Greenbaum & M Gerstein (2016). [http://blog.gerstein.info/2016/11/a-cyberattack-medical-devices-letter-re.html "A Cyberattack & Medical Devices"], ''NY Times'' (2 Nov., Opinion Pages)

==Recorded Panel Discussions & Interviews==

* M Gerstein (2008). [[Fib_Podcast_from_Other_Papers_for_M_Gerstein|"A Great Historical Document - The Human Genome"]], ''Futures in Biotech'' 34 (podcast moderated by M Pelletier)

* [[Commonwealth_Club_of_California_from_Other_Papers_for_M_Gerstein|"A Closer Look at Personal Genomic Testing"]], Inforum Genomics Panel, at the Commonwealth Club of California, including L Avey, D Ballon, D Magnus, M Gerstein, J Rae-Dupree (2009)

* [[Q2C_panel_from_Other_Papers_for_M_Gerstein|"Whose DNA is it?"]], a panel discussion on Personal Genomics, on the Agenda with Steve Paikin, as part of the Quantum to Cosmos Festival (Q2C) in Waterloo, ON, 21 Oct. 2009

* [[Fib_Podcast2_from_Other_Papers_for_M_Gerstein|"Genomics, Proteomics, Cellular Immunity, and Anti-Matter"]], a panel discussion moderated by M Pelletier, including V Racaniello, A Nantel, M Gerstein, and G Farr. ''Futures in Biotech'' 71 (22 Nov. 2010)

* M Gerstein (2011). [[Fib83_Podcast_from_Other_Papers_for_M_Gerstein|"Bioinformatics: Essential Gene names Skewed in a Network of Blame"]], ''Futures in Biotech'' 83 (podcast moderated by M Pelletier)

* [[Fib_Podcast3_from_Other_Papers_for_M_Gerstein|"6 PhDs Piled High And Deep"]], a panel discussion moderated by M Pelletier, including G Farr, D Thomas, M Gerstein, S Melov, and J Sanchez. ''Futures in Biotech'' 91 (16 Dec. 2011)

* M Gerstein (2014). [[SiriusXM_Podcast_from_Other_Papers_for_M_Gerstein|"What in the World"]], ''Sirius XM Radio Canada'', 60' on 20 Nov. (Interview by Richard Garner)

* M Gerstein (2015). [[Mendelspod_Podcast_from_Other_Papers_for_M_Gerstein|"What Now? Going Beyond the $1,000 Genome"]], ''Mendelspod,'' 17 Sept. (podcast moderated by T Timpson)

* M Gerstein (2020). [https://linkstream2.gerstein.info/2020/12/22/bbc-media-request-data-sanitisation/ "Data sanitisation tool plugs privacy gap"], ''Naked Genetics,'' 17 Dec. (podcast moderated by P Sansom)

==Other Writings (book chapters, popular articles, miscellaneous)==

* C Chothia & M Gerstein. (1992). "Protein Design for Domain Closure," in Muscle as a Machine: Energy Transduction in the Contractile System. (ed. M Morales), 149-153 (NIH, Bethesda, MD).

* M Gerstein. (1994). "Benefits of the Internet," in 51 Reasons: How we use the Internet and What it says about the information superhighway. (ed. M Stone-Martin & L Breeden, Lexington, MA, Federation of American Research Networks).

* M Gerstein (1995). "A Protein Motions Database," Protein Data Bank Quarterly Newsletter 73: 2 (July 1995).

==Patent Applications==

'''Granted'''

* [http://www.wipo.int/pctdb/en/wo.jsp?wo=2002092118 Global Analysis of Protein Activities Using Proteome Chips]

* [http://www.wipo.int/pctdb/en/wo.jsp?wo=2007127367 Method of Prediction of the Three-Dimensional Conformation of Flexible Proteins]

'''Submitted'''

* A Drawid, M Gerstein. "A Method for Predicting Subcellular Localization of Proteins using a Bayesian System that Integrates Expression Data with Sequence Patterns."

* M Kimber, M Gerstein, C Arrowsmith, A Edwards. "Protein Data Analysis". PCT/US01//30311 filed on 27 Sept. 2001 A edwards, C Arrowsmith, M Kimber, M Gerstein US Patent 09/965564

==Note==
All of this is in addition to main scientific papers at http://papers.gersteinlab.org and lectures at http://lectures.gersteinlab.org .

LA Times Oped on AI

2025-11-26T04:46:30Z

Mbg: Created page with '===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)=== Link to original article: https://www.latimes…'

===D Greenbaum & M Gerstein (2025). "Can AI developers avoid Frankenstein’s fateful mistake?", The LA Times, Nov. 15 (Opinion)===

Link to original article:
https://www.latimes.com/opinion/story/2025-11-15/artificial-intelligence-frankenstein

==== Cached Copies ====

Reprint (
[https://www.dropbox.com/scl/fi/woocw8alkg395kbli8phd/frankenstein.normal.pdf?rlkey=3gbuxsszcfpj881b4jpd1oiqz&dl=0 Full-PDF],
[https://www.dropbox.com/scl/fi/74cymotsxislbwhv6i8f5/frankenstein.simple.pdf?rlkey=c9noj432zn6z8hbnbv05afu8x&dl=0 Simple-PDF],
[https://www.dropbox.com/scl/fi/93uoc8e9edft21sbn3qop/frankenstein.normal.html?rlkey=bo6ot7q2ljvfojr0sissgrtn2&dl=0 Full-HTML],
[https://www.dropbox.com/scl/fi/w4dx2w33u8k2zcdbr1yk2/frankenstein.simple.html?rlkey=a3lee30t0rnf19dw1xb9jif71&dl=0 Simple-HTML]
)

Revisions tag: [https://linkstream2.gerstein.info/tag/frankenstein/ frankenstein] + https://mail.google.com/mail/u/0/#search/frankenstein (frankenstein)

(Home: [http://papers.gersteinlab.org Papers.GersteinLab.org] / [[Other Papers]] )

----
==== Wiki Text of OPED ====
'''Can AI developers avoid Frankenstein’s fateful mistake?'''

By Dov Greenbaum and Mark Gerstein

Audiences already know the story of Frankenstein. The gothic novel — adapted dozens of times, most recently in director Guillermo del Toro’s haunting revival now available on Netflix — is embedded in our cultural DNA as the cautionary tale of science gone wrong. But popular culture misreads author Mary Shelley’s warning. The lesson isn’t “don’t create dangerous things.” It’s “don’t walk away from what you create.”

This distinction matters: The fork in the road comes after creation, not before. All powerful technologies can become destructive — the choice between outcomes lies in stewardship or abdication. Victor Frankenstein’s sin wasn’t simply bringing life to a grotesque creature. It was refusing to raise it, insisting that the consequences were someone else’s problem. Every generation produces its Victors. Ours work in artificial intelligence.

Recently, a California appeals court fined an attorney $10,000 after 21 of 23 case citations in their brief proved to be AI fabrications — nonexistent precedents. Hundreds of similar instances have been documented nationwide, growing from a few cases a month to a few cases a day. This summer, a Georgia appeals court vacated a divorce ruling after discovering that 11 of 15 citations were AI fabrications. How many more went undetected, ready to corrupt the legal record?

The problem runs deeper than irresponsible deployment. For decades, computer systems were provably correct — a pocket calculator can consistently offer users the mathematically correct answers every time. Engineers could demonstrate how an algorithm would behave. Failures meant implementation errors, not uncertainty about the system itself.

Modern AI changes that paradigm. A recent study reported in Science confirms what AI experts have long known: plausible falsehoods — what the industry calls “hallucinations” — are inevitable in these systems. They’re trained to predict what sounds plausible, not to verify what’s true. When confident answers aren’t justified, the systems guess anyway. Their training rewards confidence over uncertainty. As one AI researcher quoted in the report put it, fixing this would “kill the product.”

This creates a fundamental veracity problem. These systems work by extracting patterns from vast training datasets — patterns so numerous and interconnected that even their designers cannot reliably predict what they’ll produce. We can only observe how they actually behave in practice, sometimes not until well after damage is done.

This unpredictability creates cascading consequences. These failures don’t disappear, they become permanent. Every legal fabrication that slips in undetected enters databases as precedent. Fake medical advice spreads across health sites. AI-generated “news” circulates through social media. This synthetic content is even scraped back into training data for future models. Today’s hallucinations become tomorrow’s facts.

So how do we address this without stifling innovation? We already have a model in pharmaceuticals. Drug companies cannot be certain of all biological effects in advance, so they test extensively, with most drugs failing before reaching patients. Even approved drugs face unexpected real-world problems. That’s why continuous monitoring remains essential. AI needs a similar framework.

Responsible stewardship — the opposite of Victor Frankenstein’s abandonment — requires three interconnected pillars. First: prescribed training standards. Drug manufacturers must control ingredients, document production practices and conduct quality testing. AI companies should face parallel requirements: documented provenance for training data, with contamination monitoring to prevent reuse of problematic synthetic content, prohibited content categories and bias testing across demographics. Pharmaceutical regulators require transparency while current AI companies need to disclose little.

Second: pre-deployment testing. Drugs undergo extensive trials before reaching patients. Randomized controlled trials were a major achievement, developed to demonstrate safety and efficacy. Most fail. That’s the point. Testing catches subtle dangers before deployment. AI systems for high-stakes applications, including legal research, medical advice and financial management, need structured testing to document error rates and establish safety thresholds.

Third: continuous surveillance after deployment. Drug companies are obligated to track adverse events of their products and report them to regulators. In turn, the regulators can mandate warnings, restrictions or withdrawal when problems emerge. AI needs equivalent oversight.

Why does this need regulation rather than voluntary compliance? Because AI systems are fundamentally different from traditional tools. A hammer doesn’t pretend to be a carpenter. AI systems do, projecting authority through confident prose, whether retrieving or fabricating facts. Without regulatory requirements, companies optimizing for engagement will necessarily sacrifice accuracy for market share.

The trick is regulating without crushing innovation. The EU’s AI Act shows how hard that is. Under the Act, companies building high-risk AI systems must document how their systems work, assess risks and monitor them closely. A small startup might spend more on lawyers and paperwork than on building the actual product. Big companies with legal teams can handle this. Small teams can’t.

Pharmaceutical regulation shows the same pattern. Post-market surveillance prevented tens of thousands of deaths when the FDA discovered that Vioxx — an arthritis medication prescribed to more than 80 million patients worldwide — doubled the risk of heart attacks. Still, billion-dollar regulatory costs mean only large companies can compete, and beneficial treatments for rare diseases, perhaps best tackled by small biotechs, go undeveloped.

Graduated oversight addresses this problem, scaling requirements and costs with demonstrated harm. An AI assistant with low error rates gets extra monitoring. Higher rates trigger mandatory fixes. Persistent problems? Pull it from the market until it’s fixed. Companies either improve their systems to stay in business, or they exit. Innovation continues, but now there’s more accountability.

Responsible stewardship cannot be voluntary. Once you create something powerful, you’re responsible for it. The question isn’t whether to build advanced AI systems — we’re already building them. The question is whether we’ll require the careful stewardship those systems demand.

The pharmaceutical framework — prescribed training standards, structured testing, continuous surveillance — offers a proven model for critical technologies we cannot fully predict. Shelley’s lesson was never about the creation itself. It was about what happens when creators walk away. Two centuries later, as Del Toro’s adaptation reaches millions this month, the lesson remains urgent. This time, with synthetic intelligence rapidly spreading through our society, we might not get another chance to choose the other path.

Dov Greenbaum is professor of law and director of the Zvi Meitar Institute for Legal Implications of Emerging Technologies at Reichman University in Israel.

Mark Gerstein is the Albert L. Williams Professor of Biomedical Informatics at Yale University.

Other Papers

2025-11-26T04:39:36Z

Mbg: /* Opinion Pieces (Op-Eds) */

==Opinion Pieces (Op-Eds)==

* D Greenbaum & M Gerstein (2008). [[Hartford_Courant_OpEd_from_Other_Papers_for_M_Gerstein|"Danger: Sharing Gene Data"]], ''Hartford Courant'', July 10, pg. A11 (oped)

* D Greenbaum & M Gerstein (2008). [[SF Chron OpEd from Other Papers for M Gerstein|"Personal genomics requires redefining privacy -- The human blueprint: dangerous secrets"]], ''SF Chronicle'', Nov. 2, Page 2 (Insight)

* M Seringhaus & M Gerstein (2009). [[Hartford_Courant_OpEd2_from_Other_Papers_for_M_Gerstein|"Putting too much information online can erode individual privacy"]], ''Hartford Courant'', June 5 (oped)

* D Greenbaum & M Gerstein (2010). [[SF Chron OpEd2 from Other Papers for M Gerstein|"Exploring genetics of professional athletes"]], ''SF Chronicle'', May 2, Page E-4 (Insight)

* D Greenbaum & M Gerstein (2012). [[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)

* D Greenbaum & M Gerstein (2013). [[USA Today Oped from Other Papers for M Gerstein|"Your DNA vulnerable to snooping, too?"]], ''USA Today'', July 27 (Opinion)

* D Greenbaum & M Gerstein (2015). [[SF Chron Oped on gcode from Other Papers for M Gerstein|"Too big to close down: Websites need regulation like utilities"]], ''SF Chronicle'', April 24 (Opinion)

* D Greenbaum & M Gerstein (2015). [[SF Chron Oped on GINA from Other Papers for M Gerstein|"Why can employers fingerprint, but not test workers’ DNA?"]], ''SF Chronicle'', July 10 (Opinion)

* D Greenbaum & M Gerstein (2016). [[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

* D Greenbaum & M Gerstein (2017). [[SF Chron Oped on Wearable Data from Other Papers for M Gerstein|"Pooling data from wearables could boost health benefits"]], ''SF Chronicle'', Feb. 24 (Opinion)

* D Greenbaum & M Gerstein (2018). [[SF Chron Oped on Data Residue from Other Papers for M Gerstein|"Our smart devices must be made to forget us"]], ''SF Chronicle'', Oct. 18 (Opinion)

* G Gursoy & M Gerstein (2020). [[Hartford Courant Oped on Molecular Privacy|"As coronavirus testing expands, new personal privacy issues arise"]], ''Hartford Courant'', July 19 (oped)

* M Gerstein & J Peccia (2020). [[New Haven Register Oped on Aerosol Transmission of Coronavirus|"What secondhand smoke tells us about the coronavirus"]], ''New Haven Register'', Dec. 12 (Opinion)

* M Gerstein & D Greenbaum (2021). [[JPost Oped on Data Science and polling|"Georgia Senate runoff: Using predictive analytics and big data properly"]], ''Jerusalem Post Opinion'', Jan. 6 (Opinion)

* D Greenbaum & M Gerstein (2024). [[The Hill Oped on 23andme|"23andMe must secure its DNA databases immediately"]], ''The Hill'', Dec 14 (Opinion)

* D Greenbaum & M Gerstein (2024). [[LA Times Oped on AI|"Can AI developers avoid Frankenstein’s fateful mistake?"]], ''The LA Times'', Nov 15 (Opinion)

==Letters to the Editor (in the Popular Press)==

* M Gerstein (1996). [[Byte_letter_from_Other_Papers_for_M_Gerstein|"Porting Unix"]], ''Byte'' (Aug.)

* M Gerstein (1997). [http://textstream.blogspot.com/2007/01/letter-how-smart-can-it-be-responding.html "How Smart Can It Be?"], ''NY Times'' (13 May)

* M Gerstein (1998). [http://textstream.blogspot.com/2006/10/letter-new-stadium-lets-vote-on-it-in.html "A New Stadium? Let's Vote on It"], ''NY Times'' (11 June)

* M Gerstein (1999). [http://textstream.blogspot.com/2006/09/letter-in-response-to-daemon-seed.html "Daemon Seedlings"], ''Wired'' (Issue 7.08, Aug.)

* M Gerstein (1999). [http://textstream.blogspot.com/2006/10/letter-life-beyond-abacus-in-response.html "Life Beyond the Abacus"], ''NY Times'' (6 Dec.)

* M Gerstein (1999). [http://textstream.blogspot.com/2007/03/letter-responding-to-riding-mo-in-lime.html "Re: Riding the Mo In the Lime Green Glow"], ''NY Times'' (19 Dec.)

* M Gerstein (2006). [http://textstream.blogspot.com/2006/09/reclusive-genius-letter-in-response-to.html "Reclusive Genius"] , ''NY Times'' (3 Sept.)

* M Gerstein (2006). [http://textstream.blogspot.com/2006/10/letter-in-response-to-homo-conexus.html "Re: Homo Conexus"], ''Tech Review'' (Sept.-Oct.)

* M Gerstein (2006). [http://textstream.blogspot.com/2007/03/letter-programming-pedigrees-responding.html "Programming Pedigrees"], ''American Scientist'' (Nov.-Dec.)

* M Gerstein & A Smith (2007). [http://textstream.blogspot.com/2007/07/let-to-ed-re-smarter-web-tech-review.html "The Semantic Web"], ''Tech Review'' (Jul.-Aug.)

* M Gerstein (2007). [http://textstream.blogspot.com/2007/09/let-to-ed-re-moms-genes-or-dads-map-can.html "DNA Rights and Wrongs"], ''Washington Post'' (7 Sept., A20)

* M Gerstein (2008). [http://textstream.blogspot.com/2008/02/let-to-ed-23andmashup-re-23andme-will.html "23andMashup"], ''Wired'' (issue 16.02, Feb., pg. 17)

* D Greenbaum & M Gerstein (2009). [http://textstream.blogspot.com/2009/11/let-to-ed-re-your-genome-isnt-that.html "Can't run from DNA"], ''New Scientist'' (issue 2727, 23 Sept., pgs. 28-29)

* M Gerstein (2010). [http://blog.gerstein.info/2010/09/harness-dna-memory-letter-re-avoiding.html "Harness DNA Memory"], ''American Scientist'' (Mar.-Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/09/testing-isnt-everything-letter-re.html "Testing Isn’t Everything"], ''NY Times'' (17 Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/09/regulating-genome-letter-re-diagnosis.html "Regulating the Genome"], ''Forbes'' (26 Apr.)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/10/thrills-and-traps-lurking-on-web-letter.html "Thrills and Traps, Lurking on the Web"], ''NY Times'' (12 May, pg. A24)

* M Gerstein (2010). [http://blog.gerstein.info/2010/09/outlook-for-libraries-letter-re.html "The Outlook for Libraries"], ''Harvard Magazine'' (July-August issue)

* D Greenbaum & M Gerstein (2010). [http://blog.gerstein.info/2010/10/concern-for-privacy-letter-re-dna.html "Concern for Privacy"], ''NY Times'' (17 Oct., pg. SP11)

* D Greenbaum & M Gerstein (2011). [http://blog.gerstein.info/2011/07/benefits-of-snooping-letter-re-how-to.html "The Benefits of Snooping"], ''Tech Review'' (Jul.-Aug.)

* D Greenbaum & M Gerstein (2011). [http://blog.gerstein.info/2011/11/sharing-too-much-online-letter-re-at.html "Sharing Too Much Online"], ''NY Times'' (7 Oct.)

* M Gerstein (2013). [http://blog.gerstein.info/2013/07/cyberattacks-on-universities-and-how-to.html "Cyberattacks on Universities, and How to Thwart Them"], ''NY Times'' (24 Jul., pg A22)

* M Gerstein (2014). [http://blog.gerstein.info/2014/05/getting-personal-letter-re-uniquely-me.html "Getting Personal"], ''American Scientist'' (May-Jun., vol. 12, pg. 163)

* D Greenbaum & M Gerstein (2015). [http://blog.gerstein.info/2015/06/an-emerging-field-letter-re-cultures-of.html "An Emerging Field"], ''American Scientist'' (May-Jun., vol. 103, pg. 164)

* M Gerstein (2015). [http://blog.gerstein.info/2015/12/the-full-monte-carlo-letter-re-programs.html "The Full Monte Carlo"], ''American Scientist'' (Nov-Dec., vol. 103, Num. 6, pg. 374)

* D Greenbaum & M Gerstein (2016). [http://blog.gerstein.info/2016/11/a-cyberattack-medical-devices-letter-re.html "A Cyberattack & Medical Devices"], ''NY Times'' (2 Nov., Opinion Pages)

==Recorded Panel Discussions & Interviews==

* M Gerstein (2008). [[Fib_Podcast_from_Other_Papers_for_M_Gerstein|"A Great Historical Document - The Human Genome"]], ''Futures in Biotech'' 34 (podcast moderated by M Pelletier)

* [[Commonwealth_Club_of_California_from_Other_Papers_for_M_Gerstein|"A Closer Look at Personal Genomic Testing"]], Inforum Genomics Panel, at the Commonwealth Club of California, including L Avey, D Ballon, D Magnus, M Gerstein, J Rae-Dupree (2009)

* [[Q2C_panel_from_Other_Papers_for_M_Gerstein|"Whose DNA is it?"]], a panel discussion on Personal Genomics, on the Agenda with Steve Paikin, as part of the Quantum to Cosmos Festival (Q2C) in Waterloo, ON, 21 Oct. 2009

* [[Fib_Podcast2_from_Other_Papers_for_M_Gerstein|"Genomics, Proteomics, Cellular Immunity, and Anti-Matter"]], a panel discussion moderated by M Pelletier, including V Racaniello, A Nantel, M Gerstein, and G Farr. ''Futures in Biotech'' 71 (22 Nov. 2010)

* M Gerstein (2011). [[Fib83_Podcast_from_Other_Papers_for_M_Gerstein|"Bioinformatics: Essential Gene names Skewed in a Network of Blame"]], ''Futures in Biotech'' 83 (podcast moderated by M Pelletier)

* [[Fib_Podcast3_from_Other_Papers_for_M_Gerstein|"6 PhDs Piled High And Deep"]], a panel discussion moderated by M Pelletier, including G Farr, D Thomas, M Gerstein, S Melov, and J Sanchez. ''Futures in Biotech'' 91 (16 Dec. 2011)

* M Gerstein (2014). [[SiriusXM_Podcast_from_Other_Papers_for_M_Gerstein|"What in the World"]], ''Sirius XM Radio Canada'', 60' on 20 Nov. (Interview by Richard Garner)

* M Gerstein (2015). [[Mendelspod_Podcast_from_Other_Papers_for_M_Gerstein|"What Now? Going Beyond the $1,000 Genome"]], ''Mendelspod,'' 17 Sept. (podcast moderated by T Timpson)

* M Gerstein (2020). [https://linkstream2.gerstein.info/2020/12/22/bbc-media-request-data-sanitisation/ "Data sanitisation tool plugs privacy gap"], ''Naked Genetics,'' 17 Dec. (podcast moderated by P Sansom)

==Other Writings (book chapters, popular articles, miscellaneous)==

* C Chothia & M Gerstein. (1992). "Protein Design for Domain Closure," in Muscle as a Machine: Energy Transduction in the Contractile System. (ed. M Morales), 149-153 (NIH, Bethesda, MD).

* M Gerstein. (1994). "Benefits of the Internet," in 51 Reasons: How we use the Internet and What it says about the information superhighway. (ed. M Stone-Martin & L Breeden, Lexington, MA, Federation of American Research Networks).

* M Gerstein (1995). "A Protein Motions Database," Protein Data Bank Quarterly Newsletter 73: 2 (July 1995).

==Patent Applications==

'''Granted'''

* [http://www.wipo.int/pctdb/en/wo.jsp?wo=2002092118 Global Analysis of Protein Activities Using Proteome Chips]

* [http://www.wipo.int/pctdb/en/wo.jsp?wo=2007127367 Method of Prediction of the Three-Dimensional Conformation of Flexible Proteins]

'''Submitted'''

* A Drawid, M Gerstein. "A Method for Predicting Subcellular Localization of Proteins using a Bayesian System that Integrates Expression Data with Sequence Patterns."

* M Kimber, M Gerstein, C Arrowsmith, A Edwards. "Protein Data Analysis". PCT/US01//30311 filed on 27 Sept. 2001 A edwards, C Arrowsmith, M Kimber, M Gerstein US Patent 09/965564

==Note==
All of this is in addition to main scientific papers at http://papers.gersteinlab.org and lectures at http://lectures.gersteinlab.org .

Selected Press Coverage for the PEC2 publication package in Science

2025-11-06T21:47:22Z

Mbg:

This page summarizes press coverage related to the publication of the PsychENCODE consortium's publication package in Science in May 2024:

[https://news.yale.edu/2024/05/23/tracking-cellular-and-genetic-roots-neuropsychiatric-disease Tracking the cellular and genetic roots of neuropsychiatric disease (Yale Press Release)]

[https://www.science.org/toc/science/384/6698 Science Cover] + [https://www.science.org/doi/10.1126/science.adp9365 Feature on Decoding the Brain (Science Magazine)]

<HR>
[https://www.youtube.com/watch?v=IqfNuw7ZjCk YouTube video summary of the Integrative Analysis Paper]

[https://x.com/MarkGerstein/status/1793740161588887644 "Tweetorial + short videos"] going over key results in the paper (need to be logged into x.com to see)

[https://medicine.yale.edu/psychiatry/news-article/single-cell-genomics-and-regulatory-networks-for-388-human-brains/ Yale School of Medicine news on "Single-cell genomics and regulatory networks for 388 human brains."]

[https://www.sciencesetavenir.fr/sante/cerveau-et-psy/psychencode-un-travail-sans-precedent-qui-decortique-l-adn-cerebral-des-maladies-mentales_178619 PsychENCODE : un travail "sans précédent" qui décortique l'ADN cérébral des maladies mentales (Sciences et Avenir)]

[https://mp.weixin.qq.com/s?__biz=MzA3MzQyNjY1MQ==&mid=2652760936&idx=1&sn=7e3e84848bd4d5400d12139c93172d49&chksm=85412b0dbc02d715e7a079ea83258385f97f1d07f116215d97129f5ea39e982d92fbfb297d07&scene=0&xtrack=1 WeChat Official Account “BioArt” introducing our study and other consortium papers]

[https://www.163.com/dy/article/J2UJ4UR905349C3F.html EaseNet news on our Science paper and the 8 other papers from the PsychENCODE consortium in the same package]

[[Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work|(Up)]]

Representative
[https://lectures.gersteinlab.org/summary/Exploring-Intermediate-Endophenotypes-connecting-Genotype-to-Diseases-20250731-eur25-ebi/ slide pack]
going over the paper from many at [https://lectures.gersteinlab.org lectures.gersteinlab.org]

Proof Stage Checklist

2025-09-09T21:37:28Z

Mbg: /* Long version of checklist */

==Short version==
* Get grant right!
* correct MG email + ORCID
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
* github should have a license/permissions
* lab homepage image
* tweet
* slide deck

(see '''<code>Proofsx57m</code>''' tag on correspondence)

==Long version of checklist==

* Press & PR
** 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.

* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Check that MG's [[Affiliation]] is accurate

* Funding
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
*** We should usually acknowledge grant XXX and ALW
** 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.
*** 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.)
** Funding is usually applicable when MG is the last author.

*** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.

*PMC & License
** For license, go for open access for non-commercial use unless prohibitively expensive.
** 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]
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)

* Papers Page (papers.gersteinlab.org)
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
** 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.
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
*** Send the following information to whoever is in charge of rebuilding the papers page:
**** PubMed ID or doi of the preprint
**** A link to the paper
**** A link to the tools or resources (see "Tools & Resources" section below)
**** 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.
**** Any additional information such as co-first authorship
*** 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
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
** Co-first and co-corresponding authors can be indicated with the footnote field
** Use the link field to directly link the journal site (particularly if there is no pubmed)

* Tools & Resources
** Website
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
*** Best is where the paper ID is what, eg, ABCDE
*** Try to use the GitHub standard for code data
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
** You can use the "website" field on the papers page to link your github site.

* Preprints
** Do a biorxiv submission (or another equiv. preprint server)
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).

* Slides & Images
** Make sure Mark has "slide packs" for the paper
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .

* Tweet
**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.
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
https://twitter.com/markgerstein/status/789117961843900417
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344

* Wikipedia
** Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate

* Tag for this page
** [[Proofsx57m]]
** Linked from [[Streamlining_Draft_Flow]] = [[x57m]]

Main Page

2025-08-03T03:04:24Z

Mbg: /* Important Public Items */

== Important Public Items ==
*Gerstein Lab '''[https://twitter.com/GersteinLab Twitter/X]''' and '''[https://bsky.app/profile/gersteinlab.bsky.social Bluesky]'''
*'''[[FAQ]]''' on tools and data
*'''Lab [https://www.gersteinlab.org/calendar/ Calendar]'''
*[http://www.gersteinlab.org/media/images '''Gallery of Homepage Images'''] (Also, [[Homepage image gallery |info. on these images]] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions '''Permissions'''] on using material generated by the lab

__TOC__

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 [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*[[Posters]] showing lab research
*Misc. Public [[Documents]] about the lab
*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])
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== Info for New People ==
* Please follow the steps of [http://info.gersteinlab.org/Onboarding Onboarding] to apply and fill in the new members’ entry process.
* [[Glossary]] of terms.
* Initialed people should have access to [http://bit.ly/mglab-folder Google Drive]

== Info for Lab Signature ==
*For all lab signatures this the procedure: ask LI & CC. MG will reply w/ an email say "sign0mg" LI will sign.

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
*** Contains a proof stage [http://info.gersteinlab.org/Proofsx57m checklist] ('''Proofsx57m''')
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [[Gerstein Lab Computing in HPC]]
** [[Gerstein Lab Computing in GersteinLab West Campus]]
** [http://sites.gersteinlab.org/account-summary/ Wordpress Accounts Summary]

* Calls, meetings, &c
**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]])
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [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&on=downloads Other info])
**[[Bass434]] introduction
**Booking [[Meeting Room]]
**Booking a [[Conference Room at 100 College]]

* Some Useful University Policies
** [https://covid19.yale.edu/ COVID] [https://symptomtracking.yale.edu Symptom Tracking] [https://dailyhealthcheck.yale.edu/web-survey Web Survey] [[Covid-19 Guidelines | Guidelines]]
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** 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]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
** [https://your.yale.edu/policies-procedures/policies/3401-general-payment#3401.3 Yale Purchasing Buy/Pay Matrix 3401.3]

* Documents
** [[Uploading_documents]]
** Letterhead templates [https://docs.google.com/document/d/1Uj1kaFiPIBmBFv2yccVkYXkJulIW1jk6/edit Current Version] (Older versions at http://wiki.gersteinlab.org/labinfo/index.php/Templates)

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** 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]
** Yale helpdesk 203-432-4700 helpdesk@yale.edu (For issues regarding Yale's network, computing, power, and phones.)
**[[OpenStack]]
**[[IDP report]]
**[[PEC package preprints]]
**[[Summary of undergraduate involvement]]
**Lab [http://bit.ly/mglab-folder google folder]
**List of bioinformatics conferences: [https://docs.google.com/spreadsheets/d/1_dAyUts51jgici9dy-l0IVPypUCRvmLsVXSrmVEXjoI/edit?usp=sharing Link to Google Drive document]

Lecture Today

2025-07-18T22:59:59Z

Mbg:

In general,
the top of the twitter query ("from @MarkGerstein, containing lectures.gersteinlab.org") :

https://x.com/search?q=lectures.gersteinlab.org%20(from%3Amarkgerstein)&f=live&src=typed_query

has the slides for my current lectures (ie this week). See last slide for references & more info.

Also, see https://bsky.app/search?q=lectures.gersteinlab.org

or top of this page:

https://lectures.gersteinlab.org/summary/

(You need to be signed into X or BlueSky for this to work.)

MBG-Profile

2025-06-29T00:19:44Z

Mbg: /* Random "Profile" Pages */

== Research Description ==

* Current description http://gersteinlab.org/research

* Here is a 48-word description of Mark Gerstein's research (18-May-2025)

Dr. Gerstein is the Williams Professor of Biomedical Informatics at Yale University, affiliated with Molecular Biophysics &
Biochemistry and Statistics & Data Science. His research involves applying AI and machine-learning approaches to large-scale biomedical data. He is specifically
interested in disease genome annotation, gene networks, macromolecular simulation, and biosensor analysis.

* Recent short profiles ([https://www.dropbox.com/s/0qtunvhz7t10svo/99-word-bio-for-M-Gerstein-30Apr23-i0ismb23.docx?dl=0 100-words], [[125-word-2022-profile|125-words]], and [[275-word profile overview|275-words]]) and [[150-word-2022-research|150-word]] research description.

* Other short profiles: [[short 150-word profile|150-word]], [[micro-bio-Mar-2016 | 120-word]], [[100-word profile|100-word]], [[250-word research description|250-word]].

* Other short research descriptions: [[180-word research description|180-word]]

== [[Key Contributions]] ==

== [[Headshots]] ==

== Random "Profile" Pages ==

There are many random profile pages that are associated with me. Most of these are out of date.
My main Page is http://gersteinlab.org/about

[http://www.zoominfo.com/Search/ReferencesView.aspx?PersonID=14758619 ZoomInfo] (contains a comprehensive listing of articles referring to the lab)

* [http://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia] (my Wikipedia editing name is [https://en.wikipedia.org/wiki/User:Mbgmbg mbgmbg])
* [http://cpsc.yale.edu/people/mark-gerstein CS]
* [https://statistics.yale.edu/people/mark-gerstein S&DS]
* [https://medicine.yale.edu/profile/mark_gerstein BBS]
* [https://physics-engineering-biology.yale.edu/profile/mark-gerstein PEB]

==[[Affiliation]]==

== CV ==

[[Current M Gerstein CV|Current Full CV]]

[http://files.gersteinlab.org/public-docs/2019/08.11/MBG-Short-CV--cv57-31Jul19.html HTML header]

[http://papers.gersteinlab.org/papers/papers-simple.html Current list of Scientific Publications]

Partial NIH Biosketch (25 Aug. '19) ([http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.docx docx], [http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.pdf pdf])

1-page CV with a Cancer Focus (April 2025) ([https://www.dropbox.com/scl/fi/363fd3zbexbyvnzrm9oo8/M-Gerstein-1pg-CV-w-Cancer-Focus-29Apr25-for-g0cgc-CGC_2025_Biosketch_Template.docx?rlkey=rh8j9489o0kxhudo6xf84ly6j&dl=0 docx])

==[[Old Profile Stuff]]==

Lecture Today

2025-06-26T16:24:42Z

Mbg:

See:

https://x.com/MarkGerstein/status/1938073117139861565

In general,
the top of the twitter query ("from @MarkGerstein, containing lectures.gersteinlab.org") :

https://x.com/search?q=lectures.gersteinlab.org%20(from%3Amarkgerstein)&f=live&src=typed_query

has the slides for my current lectures (ie this week). See last slide for references & more info.

Also, see https://bsky.app/search?q=lectures.gersteinlab.org

or top of this page:

https://lectures.gersteinlab.org/summary/

(You need to be signed into X or BlueSky for this to work.)

Lecture Today

2025-06-26T16:23:19Z

Mbg:

See:

https://x.com/MarkGerstein/status/1938073117139861565

In general,
the top of the twitter query ("from @MarkGerstein, containing lectures.gersteinlab.org") :

https://x.com/search?q=lectures.gersteinlab.org%20(from%3Amarkgerstein)&f=live&src=typed_query

has the slides for my current lectures (ie this week). See last slide for references & more info.

Also, see https://bsky.app/search?q=lectures.gersteinlab.org

(You need to be signed into X or BlueSky for this to work.)

Lecture Today

2025-06-09T02:10:25Z

Mbg:

See:

https://x.com/MarkGerstein/status/1931893365978878385

https://bsky.app/profile/markgerstein.bsky.social/post/3lr5bomeijc2t

In general,
the top of the twitter query ("from @MarkGerstein, containing lectures.gersteinlab.org") :

https://x.com/search?q=lectures.gersteinlab.org%20(from%3Amarkgerstein)&f=live&src=typed_query

has the slides for my current lectures (ie this week). See last slide for references & more info.

Also, see https://bsky.app/search?q=lectures.gersteinlab.org

(You need to be signed into X or BlueSky for this to work.)

Resources

2025-05-27T15:21:26Z

Mbg:

__NOTOC__
==Github==
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])

<HR>
The tools & 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'''].

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'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

See [https://info.gersteinlab.org/Old_Resources '''the old tools page here'''].

==Portals==

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://www.molmovdb.org/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

Resources

2025-05-27T15:21:04Z

Mbg:

__NOTOC__
=Github=
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])

<HR>
The tools & 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'''].

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'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

See [https://info.gersteinlab.org/Old_Resources '''the old tools page here'''].

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://www.molmovdb.org/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

Resources

2025-05-27T15:20:22Z

Mbg:

=Github=
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])

<HR>
The tools & 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'''].

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'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

See [https://info.gersteinlab.org/Old_Resources '''the old tools page here'''].

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://www.molmovdb.org/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

Selected Press Accounts Highlighting Gerstein Lab Work

2025-05-27T03:25:49Z

Mbg: /* 2025 */

__NOTOC__
=== 2025 ===

*[https://medicine.yale.edu/news/yale-medicine-magazine/article/can-ai-predict-the-future/ Can AI Predict the Future? (Yale Medicine Magazine)]
*[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]

=== 2024 ===
*'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''
*[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)]
*'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''
*[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]
*[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]

=== 2023 ===
* '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''
* [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]
** [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)]

=== 2022 ===
*[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]
*[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)]
*[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)]
**[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]
=== 2021 ===
*[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]
*[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]
=== 2020 ===
* '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''
* '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''
=== 2019 ===
* '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]'''
=== 2018 ===
* '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''
*[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]
*[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)]
*[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)]
=== 2017 ===
*[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]
*[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]
*[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]

=== 2016 ===
* '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''
* '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''
* [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)]

=== 2014 ===

* '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''
*[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]

=== 2013 ===

* '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''
*[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)]
*[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]

=== 2012 ===

* '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''
** [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)]
* [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]
** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]
** [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)]
* [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)]

=== 2011 ===
*[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)]
*[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)]
* [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)]

=== 2010 ===

*[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]
*[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]
*[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]
* [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)]
* [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)]
* [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)]
** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]
* [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)]

=== 2009 ===

* [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)]
* [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)]

=== 2008 ===

* [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]

=== 2007 ===

* [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)]

=== 2003 ===

* [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]

=== 2001 ===

* [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)]

=== 2000 ===

* Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])

=== 1998 ===

* [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)]

== More Stuff ==
* 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.)
* A [https://news.google.com/search?q=mark%20gerstein%20yale&hl=en-US&gl=US&ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)

Old Profile Stuff

2025-05-18T21:06:14Z

Mbg: /* Old Research Descriptions */

== Old Research Descriptions ==

* [https://files.gersteinlab.org/public-docs/2025/02.17/sites-gersteinlab-org-research.pdf Gerstein Lab Research page prior to Feb 2025 update]

* Listing of Key Research Contributions (as of 30-Nov-2019) ([http://files.gersteinlab.org/public-docs/2019/12.28/Key-Research-Contributions--EXTRACT-FROM--mb0mg--Gerstein-final-30nov19.pdf PDF], [http://files.gersteinlab.org/public-docs/2019/12.28/Key-Research-Contributions--EXTRACT-FROM--mb0mg--Gerstein-final-30nov19.docx DOC])

* [http://www.gersteinlab.org/about/index.html.006 Older research description]

* [http://www.gersteinlab.org/about/short-bio.txt Micro-BIO]

* Here is a 50-word description of Mark Gerstein's research (31-Aug-2009)

Dr. Gerstein is the Albert Williams Professor of Biomedical Informatics, Molecular Biophysics &
Biochemistry and Computer Science at Yale University. His research involves applying quantitative
approaches such as data mining and simulation to problems in molecular biology. He is specifically
interested in human genome annotation, molecular networks, and macromolecular geometry.

* Longer Wiki Description of [[Mbg-research]] (out of date as of Aug-2009)

* [[Gerstein Lab Research - 22 Jul. 2013 | Long 1648 Word Research Description]] with References (current as of 22-July-2013)

* [[NIH grant justification text for MG]]

* Old Wiki description of research interests - http://info.gersteinlab.org/Current_Research_Interests_for_Mark_Gerstein

Research Program [http://papers.gersteinlab.org/about/sum2006 2006], [http://papers.gersteinlab.org/papers/papers-research.shtml 2002a],
[http://bioinfo.mbb.yale.edu/about/sum/res-sum-020128.htm 2002b], [http://papers.gersteinlab.org/about/sum2001 2001]

[http://bioinfo.mbb.yale.edu/about/nih-style-full-cv-apr-05.doc Complete CV, MS Word format] (pubs only up to 2005)

[http://archive.gersteinlab.org/mark/out/log/2011/08.08/cv/cv-nih-format.html NIH-style Old Short CV]

* Older Research Description (010108) with figures and many file formats:
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108.doc doc]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.pdf pdf]
** [http://www.gersteinlab.org/about/sum/mbg-research-summary-010108-figs.ppt ppt]
* [http://www.gersteinlab.org/about/long-descrip.pdf An even older (1999) version in pdf]

== Old CVs ==
=== Recent OLD CVs ===

https://www.dropbox.com/scl/fi/7fanrd14hzrpp9e5b3uti/M-Gerstein-Full-public-CV-bld11may24.cv57.pdf?rlkey=9tbgrqco6odc17r9gl4vrcgy0&dl=0

https://www.dropbox.com/scl/fi/0pnka2ijlk3egdhyo9645/M-Gerstein-CV-bld6Jan24-Public-CV-Jan-2024.cv57.pdf?rlkey=08un1ufxhvc13mrpog1fwf1zs&dl=0

https://www.dropbox.com/s/hrmczyzq2zj1x93/M-Gerstein-Full-public-CV-bld12Jan23-FAR.onweb.pdf?dl=0

https://www.dropbox.com/s/5r8kwh4tfqcprqf/M-Gerstein-Full-public-CV-bld14Aug22-SS.onweb.pdf?dl=0

=== CV Build as of 31 Dec 2019 ===

http://files.gersteinlab.org/public-docs/2019/12.28/M-Gerstein-CV-bld31Dec19--public.pdf

=== CV Build as of 1 Jan 2019 ===

http://files.gersteinlab.org/public-docs/2019/01.03/M-Gerstein-full-public-CV--bld1Jan19-cv57.pdf

=== CV Build as of 8 Jan 2018 ===

http://files.gersteinlab.org/public-docs/2018/01.10/Full-CV-M-Gerstein--for-FAR-bld8Jan18-cv57.pdf

https://linkstream.gersteinlab.org/2018/01/10/highlights-of-2017/

Current as of 8 Jan. 2018 (w. some sections less current)

=== CV Build as of 28 Jan 2016 ===

http://archive.gersteinlab.org/public-docs/2016/01.31/cv57/M-Gerstein-Full-CV-28Jan16-publ.pdf

=== CV Build as of 30 Sep 2015 ===

http://archive.gersteinlab.org/public-docs/2015/10.21/M-Gerstein-full-CV-30Sep2015-publ.pdf

=== CV Build as of 30 Jan 2015 ===

[http://archive.gersteinlab.org/public-docs/2015/01.30/cv/M-Gerstein-public-CV-31Dec2014.pdf Built CV with publications and people]

=== CV Build as of 28 Nov 2014 ===

[http://archive.gersteinlab.org/public-docs/2014/11.28/M-Gerstein-public-CV-28nov14.pdf Built CV with publications and people]

=== CV Build as of 31 Dec 2013 ===

[http://archive.gersteinlab.org/mark/out/log/2014/06.20/cv/M-Gerstein-public-CV-31Dec2013.pdf Built CV with publications and people]

=== CV Build as of Jan 2013 ===

[http://archive.gersteinlab.org/mark/out/log/2013/01.23/M-Gerstein-public-cv-1jan13.pdf Built CV with publications and people]

=== Old CV Build in Jan 2012 (obsolete but maybe useful)===

[http://archive.gersteinlab.org/mark/out/log/2012/01.30/cv/M-Gerstein-publ-CV-29jan2012.pdf Built CV with publications and people]

[http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Lab-Personnel-and-Alumni-1Dec2011.pdf Listing of Lab Personnel and Alumni]

[http://archive.gersteinlab.org/mark/out/log/2012/01.01/cv/M-Gerstein-Scientific-Pubs-1Jan2012.pdf Scientific Publications up to Jan. '12]

[http://archive.gersteinlab.org/mark/out/log/2012/01.30/cv/M-Gerstein-Other-Writings-1jan2012.pdf Other Writings up to Jan. '12]


==Old overview lectures==

http://lectures.gersteinlab.org/summary/7-slide-overview-of-the-GersteinLab-20170203/

http://lectures.gersteinlab.org/summary/Talk-at-Levitt-alumni-gathering--20140911-i0levalum-final/

http://lectures.gersteinlab.org/summary/5-slide-overview-of-the-lab/

==Old Profile Pages==
* DEFUNCT profile links

** Yale Pantheon page (via eli.yale.edu), which can be used as an outbox: http://pantheon.yale.edu/~mg269
** [http://www.google.com/profiles/bluehat Google] (defunct Google profile page)
** [http://info.med.yale.edu/bbs/faculty/ger_ma.html BBS Page]
** [http://expertise.cos.com/cgi-bin/exp.cgi?id=414253 COS]
** [http://www.mbb.yale.edu/faculty/pages/gerstein.html MB&B]
** [http://bigthink.com/markgerstein Delphi Fellow]

MBG-Profile

2025-05-18T21:05:26Z

Mbg: /* Research Description */

== Research Description ==

* Current description http://gersteinlab.org/research

* Here is a 48-word description of Mark Gerstein's research (18-May-2025)

Dr. Gerstein is the Williams Professor of Biomedical Informatics at Yale University, affiliated with Molecular Biophysics &
Biochemistry and Statistics & Data Science. His research involves applying AI and machine-learning approaches to large-scale biomedical data. He is specifically
interested in disease genome annotation, gene networks, macromolecular simulation, and biosensor analysis.

* Recent short profiles ([https://www.dropbox.com/s/0qtunvhz7t10svo/99-word-bio-for-M-Gerstein-30Apr23-i0ismb23.docx?dl=0 100-words], [[125-word-2022-profile|125-words]], and [[275-word profile overview|275-words]]) and [[150-word-2022-research|150-word]] research description.

* Other short profiles: [[short 150-word profile|150-word]], [[micro-bio-Mar-2016 | 120-word]], [[100-word profile|100-word]], [[250-word research description|250-word]].

* Other short research descriptions: [[180-word research description|180-word]]

== [[Key Contributions]] ==

== [[Headshots]] ==

== Random "Profile" Pages ==

There are many random profile pages that are associated with me. Most of these are out of date.
My main Page is http://gersteinlab.org/about

[http://www.zoominfo.com/Search/ReferencesView.aspx?PersonID=14758619 ZoomInfo] (contains a comprehensive listing of articles referring to the lab)

* [http://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia] (my Wikipedia editing name is [https://en.wikipedia.org/wiki/User:Mbgmbg mbgmbg])
* [http://cpsc.yale.edu/people/mark-gerstein CS]
* [https://statistics.yale.edu/people/mark-gerstein S&DS]
* [https://medicine.yale.edu/profile/mark_gerstein BBS]

==[[Affiliation]]==

== CV ==

[[Current M Gerstein CV|Current Full CV]]

[http://files.gersteinlab.org/public-docs/2019/08.11/MBG-Short-CV--cv57-31Jul19.html HTML header]

[http://papers.gersteinlab.org/papers/papers-simple.html Current list of Scientific Publications]

Partial NIH Biosketch (25 Aug. '19) ([http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.docx docx], [http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.pdf pdf])

1-page CV with a Cancer Focus (April 2025) ([https://www.dropbox.com/scl/fi/363fd3zbexbyvnzrm9oo8/M-Gerstein-1pg-CV-w-Cancer-Focus-29Apr25-for-g0cgc-CGC_2025_Biosketch_Template.docx?rlkey=rh8j9489o0kxhudo6xf84ly6j&dl=0 docx])

==[[Old Profile Stuff]]==

Lecture Today

2025-05-04T00:46:28Z

Mbg:

See:

https://bsky.app/profile/markgerstein.bsky.social/post/3locmh3lv3c2d

https://lectures.gersteinlab.org/summary/Better-G-to-P-w-biosensor-n-privacy-20250505-i0ucla24/

https://lectures.gersteinlab.org/summary/SCZ-AD-ADHD-20250506-i0ucla24-uci/

In general,
the top of the twitter query ("from @MarkGerstein, containing lectures.gersteinlab.org") :

https://x.com/search?q=lectures.gersteinlab.org%20(from%3Amarkgerstein)&f=live&src=typed_query

has the slides for my current lectures (ie this week). See last slide for references & more info.

Also, see https://bsky.app/search?q=lectures.gersteinlab.org

(You need to be signed into X or BlueSky for this to work.)

MBG-Profile

2025-04-28T21:44:15Z

Mbg: /* CV */

== Research Description ==

* Current description http://gersteinlab.org/research

* Here is a 50-word description of Mark Gerstein's research (31-Aug-2009)

Dr. Gerstein is the Albert Williams Professor of Biomedical Informatics, Molecular Biophysics &
Biochemistry and Computer Science at Yale University. His research involves applying quantitative
approaches such as data mining and simulation to problems in molecular biology. He is specifically
interested in human genome annotation, molecular networks, and macromolecular geometry.

* Recent short profiles ([https://www.dropbox.com/s/0qtunvhz7t10svo/99-word-bio-for-M-Gerstein-30Apr23-i0ismb23.docx?dl=0 100-words], [[125-word-2022-profile|125-words]], and [[275-word profile overview|275-words]]) and [[150-word-2022-research|150-word]] research description.

* Other short profiles: [[short 150-word profile|150-word]], [[micro-bio-Mar-2016 | 120-word]], [[100-word profile|100-word]], [[250-word research description|250-word]].

* Other short research descriptions: [[180-word research description|180-word]]

== [[Key Contributions]] ==

== [[Headshots]] ==

== Random "Profile" Pages ==

There are many random profile pages that are associated with me. Most of these are out of date.
My main Page is http://gersteinlab.org/about

[http://www.zoominfo.com/Search/ReferencesView.aspx?PersonID=14758619 ZoomInfo] (contains a comprehensive listing of articles referring to the lab)

* [http://en.wikipedia.org/wiki/Mark_Bender_Gerstein Wikipedia] (my Wikipedia editing name is [https://en.wikipedia.org/wiki/User:Mbgmbg mbgmbg])
* [http://cpsc.yale.edu/people/mark-gerstein CS]
* [https://statistics.yale.edu/people/mark-gerstein S&DS]
* [https://medicine.yale.edu/profile/mark_gerstein BBS]

==[[Affiliation]]==

== CV ==

[[Current M Gerstein CV|Current Full CV]]

[http://files.gersteinlab.org/public-docs/2019/08.11/MBG-Short-CV--cv57-31Jul19.html HTML header]

[http://papers.gersteinlab.org/papers/papers-simple.html Current list of Scientific Publications]

Partial NIH Biosketch (25 Aug. '19) ([http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.docx docx], [http://files.gersteinlab.org/public-docs/2019/08.27/cv/M-Gerstein-1st-half-NIH-biosketch-25Aug2019-cv57-biosketch0mg.pdf pdf])

1-page CV with a Cancer Focus (April 2025) ([https://www.dropbox.com/scl/fi/363fd3zbexbyvnzrm9oo8/M-Gerstein-1pg-CV-w-Cancer-Focus-29Apr25-for-g0cgc-CGC_2025_Biosketch_Template.docx?rlkey=rh8j9489o0kxhudo6xf84ly6j&dl=0 docx])

==[[Old Profile Stuff]]==

Key Contributions

2025-02-17T02:39:42Z

Mbg:

Listing of '''Key Research Contributions''':
*'''[https://www.dropbox.com/scl/fi/z0216ldqr54ihm8qe78gv/5-key-papers-for-M-Gerstein-as-of-Feb2025.sds0mg.docx?rlkey=dimn7s6lpaffn4y48w4mb2oxh&dl=0 5 best papers]''' (as of Jan. 2025)
*'''10 best papers [https://www.dropbox.com/s/yseofry0421vczm/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.pdf?dl=0 PDF]''' or [https://www.dropbox.com/s/00nntgu7u3djmij/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.docx?dl=0 DOC] (as of 27-Nov-2020)
*Shorter version from NIH biosketch ([https://www.dropbox.com/s/vb0o09tjd9oq98l/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.pdf?dl=0 PDF], [https://www.dropbox.com/s/z4zkkvnjlrfpkzw/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.docx?dl=0 DOC]) (as of 15-Nov-2020)

Some key bits from '''[[Other Papers|non-technical writings]]''':
*[[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)
*[[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

Also, see:

*Relevant [[Summaries]] of our research.
*[http://papers.gersteinlab.org/subject/best Best Papers] and [http://papers.gersteinlab.org/subject/best-revs Reviews]
*[http://papers.gersteinlab.org/subject/intro-to-lab Intro to the Lab] (another [http://papers.gersteinlab.org/subject/intro-cs one with a CS focus])
*Lab [http://research.gersteinlab.org research statement]

[[Old Profile Stuff|Old Stuff]] (Perhaps still relevant)

Key Contributions

2025-02-13T18:59:42Z

Mbg:

Listing of '''Key Research Contributions''':
*'''[https://www.dropbox.com/scl/fi/z0216ldqr54ihm8qe78gv/5-key-papers-for-M-Gerstein-as-of-Feb2025.sds0mg.docx?rlkey=dimn7s6lpaffn4y48w4mb2oxh&dl=0 5 best papers]''' (as of Jan. 2025)
*'''[https://www.dropbox.com/s/yseofry0421vczm/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.pdf?dl=0 PDF]''' or [https://www.dropbox.com/s/00nntgu7u3djmij/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.docx?dl=0 DOC] (as of 27-Nov-2020)
*Shorter version from NIH biosketch ([https://www.dropbox.com/s/vb0o09tjd9oq98l/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.pdf?dl=0 PDF], [https://www.dropbox.com/s/z4zkkvnjlrfpkzw/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.docx?dl=0 DOC]) (as of 15-Nov-2020)

Some key bits from '''[[Other Papers|non-technical writings]]''':
*[[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)
*[[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

Also, see:

*Relevant [[Summaries]] of our research.
*[http://papers.gersteinlab.org/subject/best Best Papers] and [http://papers.gersteinlab.org/subject/best-revs Reviews]
*[http://papers.gersteinlab.org/subject/intro-to-lab Intro to the Lab] (another [http://papers.gersteinlab.org/subject/intro-cs one with a CS focus])
*Lab [http://research.gersteinlab.org research statement]

[[Old Profile Stuff|Old Stuff]] (Perhaps still relevant)

Key Contributions

2025-02-13T18:59:08Z

Mbg:

Listing of '''Key Research Contributions''':
*'''[https://www.dropbox.com/scl/fi/z0216ldqr54ihm8qe78gv/5-key-papers-for-M-Gerstein-as-of-Feb2025.sds0mg.docx?rlkey=dimn7s6lpaffn4y48w4mb2oxh&dl=0 5 best papers] (as of Jan. 2025)
*'''[https://www.dropbox.com/s/yseofry0421vczm/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.pdf?dl=0 PDF]''' or [https://www.dropbox.com/s/00nntgu7u3djmij/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.docx?dl=0 DOC] (as of 27-Nov-2020)
*Shorter version from NIH biosketch ([https://www.dropbox.com/s/vb0o09tjd9oq98l/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.pdf?dl=0 PDF], [https://www.dropbox.com/s/z4zkkvnjlrfpkzw/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.docx?dl=0 DOC]) (as of 15-Nov-2020)

Some key bits from '''[[Other Papers|non-technical writings]]''':
*[[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)
*[[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

Also, see:

*Relevant [[Summaries]] of our research.
*[http://papers.gersteinlab.org/subject/best Best Papers] and [http://papers.gersteinlab.org/subject/best-revs Reviews]
*[http://papers.gersteinlab.org/subject/intro-to-lab Intro to the Lab] (another [http://papers.gersteinlab.org/subject/intro-cs one with a CS focus])
*Lab [http://research.gersteinlab.org research statement]

[[Old Profile Stuff|Old Stuff]] (Perhaps still relevant)

Key Contributions

2025-02-13T18:37:15Z

Mbg:

Listing of '''Key Research Contributions''':
*'''[https://www.dropbox.com/scl/fi/z0216ldqr54ihm8qe78gv/5-key-papers-for-M-Gerstein-as-of-Feb2025.sds0mg.docx?rlkey=dimn7s6lpaffn4y48w4mb2oxh&dl=0 5 best papers as of Jan. 2025]
*'''[https://www.dropbox.com/s/yseofry0421vczm/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.pdf?dl=0 PDF]''' or [https://www.dropbox.com/s/00nntgu7u3djmij/Key-Research-Contributions--EXTRACT-FROM--Gerstein-final-27nov2020.mb0mg.onweb.docx?dl=0 DOC] (as of 27-Nov-2020)
*Shorter version from NIH biosketch ([https://www.dropbox.com/s/vb0o09tjd9oq98l/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.pdf?dl=0 PDF], [https://www.dropbox.com/s/z4zkkvnjlrfpkzw/Key-publications--EXTRACT-FROM--M-Gerstein-NIH-biosketch-15nov20-cv57-biosketch0mg.onweb.docx?dl=0 DOC]) (as of 15-Nov-2020)

Some key bits from '''[[Other Papers|non-technical writings]]''':
*[[WSJ OpEd from Other Papers for M Gerstein|"The Age of Genetically Optimized Sports"]], ''Wall Street Journal'', July 24, Page A13 (Opinion)
*[[SF Chron Oped on Geek Chic from Other Papers for M Gerstein|"Going beyond geek chic -- CeBIT"]], ''SF Chronicle'', March 10 (Opinion)

Also, see:

*Relevant [[Summaries]] of our research.
*[http://papers.gersteinlab.org/subject/best Best Papers] and [http://papers.gersteinlab.org/subject/best-revs Reviews]
*[http://papers.gersteinlab.org/subject/intro-to-lab Intro to the Lab] (another [http://papers.gersteinlab.org/subject/intro-cs one with a CS focus])
*Lab [http://research.gersteinlab.org research statement]

[[Old Profile Stuff|Old Stuff]] (Perhaps still relevant)

Selected Press Coverage for the ABCD paper in Cell

2025-02-05T01:50:07Z

Mbg: /* Other Stuff */

This page summarizes media coverage and associated material for the publication of our [https://papers.gersteinlab.org/papers/ABCD "ABCD" paper in Cell], "Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations"

===Main PR Material===
[https://news.yale.edu/2024/12/19/using-smartwatches-better-understand-psychiatric-illness Using smartwatches to better understand psychiatric illness] (Yale Press Release)

[https://www.wtnh.com/video/smart-watches-and-understanding-psychiatric-illnesses/10371676 Good Morning Connecticut interview] (News 8, January 15, 2025)

[https://connecticut.news12.com/yale-researchers-use-ai-in-studies-regarding-heart-and-mental-health Yale researchers use AI in studies regarding heart and mental health] (News 12, 4 Feb. 2025)

[https://web.ub.edu/en/web/actualitat/w/smartwatches-research Smartwatches to better understand psychiatric illnesses and their genetic basis] (Press release from University of Barcelona - January 20, 2025 - English)

[https://web.ub.edu/ca/web/actualitat/w/recerca-rellotges-intelligents Rellotges intel·ligents per comprendre millor les malalties psiquiàtriques i les seves bases genètiques] (Press release from University of Barcelona - January 20, 2025 - Catalan)

[https://web.ub.edu/es/web/actualitat/w/investigacion-relojes-inteligentes Relojes inteligentes para comprender mejor las enfermedades psiquiátricas y sus bases genéticas] (Press release from University of Barcelona - January 20, 2025 - Spanish)

Press release by EUREKALERT in [https://www.eurekalert.org/news-releases/1071471 English] and [https://www.eurekalert.org/news-releases/1071471?language=spanish Spanish]. Also artwork [https://www.eurekalert.org/multimedia/1057517 here] and [https://www.eurekalert.org/multimedia/1057517?language=spanish here].

Video by University of Barcelona describing the research. [[https://www.instagram.com/reel/DFXyefdvq9u/?utm_source=ig_web_copy_link&igsh=MzRlODBiNWFlZA== Instagram]] [[https://www.youtube.com/shorts/BOhZJV5u3YY YouTube]] [[https://www.linkedin.com/posts/university-of-barcelona_rellotges-digitals-per-predir-malalties-psiquiàtriques-activity-7290002480057221120-cfMm?utm_source=share&utm_medium=member_desktop LinkedIn]] [[https://bsky.app/profile/ub.edu/post/3lgscopeftk2x BlueSky]]

<HR>
===Social Media===
[https://x.com/CellCellPress/status/1869897639715844209 @CellCellPress tweet of the paper]

[https://bsky.app/profile/gersteinlab.bsky.social/post/3ldohsv4hgs2j Bluesky post of the paper]

[https://x.com/MarkGerstein/status/1869801315112759808 Mark Gerstein tweet of the paper]

[https://x.com/Yale/status/1877367254725116102 Yale tweet of the paper]

[https://x.com/YaleBIDS/status/1879909038714159562 Yale BIDS tweet of the project]

<HR>
===Other Stuff===
[https://www.youtube.com/watch?v=3Gv-8F4xEwA YouTube video summary of the paper]

A useful [https://lectures.gersteinlab.org/summary/AI-for-Brain-Disorders-20250106-i0msft slide pack] on AI for Brain Disorders.

[https://files.gersteinlab.org/public-docs/2025/01.29/LiuJ_Cell2025_public_slides.pdf Public slides for the paper]

Some fun images from S Liu: [https://files.gersteinlab.org/public-docs/2025/01.27/S-Liu-pic-abcd-1.jpg 1] and
[https://files.gersteinlab.org/public-docs/2025/01.27/S-Liu-pic-abcd-2.jpg 2]

[https://files.gersteinlab.org/public-docs/2025/01.29/LiuJ_Graphical_Abstract.jpg Summary image] from the paper

[[Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work|(Up)]]

Selected Press Coverage for the ABCD paper in Cell

2025-02-05T01:48:58Z

Mbg:

This page summarizes media coverage and associated material for the publication of our [https://papers.gersteinlab.org/papers/ABCD "ABCD" paper in Cell], "Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations"

===Main PR Material===
[https://news.yale.edu/2024/12/19/using-smartwatches-better-understand-psychiatric-illness Using smartwatches to better understand psychiatric illness] (Yale Press Release)

[https://www.wtnh.com/video/smart-watches-and-understanding-psychiatric-illnesses/10371676 Good Morning Connecticut interview] (News 8, January 15, 2025)

[https://connecticut.news12.com/yale-researchers-use-ai-in-studies-regarding-heart-and-mental-health Yale researchers use AI in studies regarding heart and mental health] (News 12, 4 Feb. 2025)

[https://web.ub.edu/en/web/actualitat/w/smartwatches-research Smartwatches to better understand psychiatric illnesses and their genetic basis] (Press release from University of Barcelona - January 20, 2025 - English)

[https://web.ub.edu/ca/web/actualitat/w/recerca-rellotges-intelligents Rellotges intel·ligents per comprendre millor les malalties psiquiàtriques i les seves bases genètiques] (Press release from University of Barcelona - January 20, 2025 - Catalan)

[https://web.ub.edu/es/web/actualitat/w/investigacion-relojes-inteligentes Relojes inteligentes para comprender mejor las enfermedades psiquiátricas y sus bases genéticas] (Press release from University of Barcelona - January 20, 2025 - Spanish)

Press release by EUREKALERT in [https://www.eurekalert.org/news-releases/1071471 English] and [https://www.eurekalert.org/news-releases/1071471?language=spanish Spanish]. Also artwork [https://www.eurekalert.org/multimedia/1057517 here] and [https://www.eurekalert.org/multimedia/1057517?language=spanish here].

Video by University of Barcelona describing the research. [[https://www.instagram.com/reel/DFXyefdvq9u/?utm_source=ig_web_copy_link&igsh=MzRlODBiNWFlZA== Instagram]] [[https://www.youtube.com/shorts/BOhZJV5u3YY YouTube]] [[https://www.linkedin.com/posts/university-of-barcelona_rellotges-digitals-per-predir-malalties-psiquiàtriques-activity-7290002480057221120-cfMm?utm_source=share&utm_medium=member_desktop LinkedIn]] [[https://bsky.app/profile/ub.edu/post/3lgscopeftk2x BlueSky]]

<HR>
===Social Media===
[https://x.com/CellCellPress/status/1869897639715844209 @CellCellPress tweet of the paper]

[https://bsky.app/profile/gersteinlab.bsky.social/post/3ldohsv4hgs2j Bluesky post of the paper]

[https://x.com/MarkGerstein/status/1869801315112759808 Mark Gerstein tweet of the paper]

[https://x.com/Yale/status/1877367254725116102 Yale tweet of the paper]

[https://x.com/YaleBIDS/status/1879909038714159562 Yale BIDS tweet of the project]

<HR>
===Other Stuff===
[https://www.youtube.com/watch?v=3Gv-8F4xEwA YouTube video summary of the paper]

A useful [https://lectures.gersteinlab.org/summary/AI-for-Brain-Disorders-20250106-i0msft slide pack]. AI for Brain Disorders.

[https://files.gersteinlab.org/public-docs/2025/01.29/LiuJ_Cell2025_public_slides.pdf Public slides for the paper]

Some fun images from S Liu: [https://files.gersteinlab.org/public-docs/2025/01.27/S-Liu-pic-abcd-1.jpg 1] and
[https://files.gersteinlab.org/public-docs/2025/01.27/S-Liu-pic-abcd-2.jpg 2]

[https://files.gersteinlab.org/public-docs/2025/01.29/LiuJ_Graphical_Abstract.jpg Summary image] from the paper

[[Selected_Press_Accounts_Highlighting_Gerstein_Lab_Work|(Up)]]

Selected Press Accounts Highlighting Gerstein Lab Work

2025-01-19T04:28:11Z

Mbg:

__NOTOC__
=== 2025 ===

*[https://doi.org/10.1038/s41591-024-03369-w Can quantum computing crack the biggest challenges in health? (Nature Medicine)]

=== 2024 ===
*'''[[Selected Press Coverage for the ABCD paper in Cell]] (Overview)'''
*[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)]
*'''[[Selected Press Coverage for the PEC2 publication package in Science]] (Overview)'''
*[https://www.nature.com/articles/s41592-024-02421-4 LLMs predict protein phases (Nature Methods)]
*[https://www.nytimes.com/2024/10/05/business/23andme-dna-bankrupt.html As 23andMe Struggles, Concerns Surface About Its Genetic Data (NY Times)]

=== 2023 ===
* '''[[Selected Press Coverage for EN-TEx paper in Cell | Selected Press Coverage for EN-TEx paper in Cell (Overview)]] '''
* [https://academic.oup.com/bioinformatics/article/39/Supplement_1/i9/7210511 2023 ISCB accomplishments by a senior scientist award (Write up in Bioinformatics)]
** [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)]

=== 2022 ===
*[https://www.nature.com/articles/d41586-022-00729-9 How hybrid working took hold in science (Nature)]
*[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)]
*[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)]
**[https://www.nytimes.com/2022/06/06/science/bitcoin-nakamoto-blackburn-crypto.html How ‘Trustless’ Is Bitcoin, Really? (NY Times)]
=== 2021 ===
*[https://www.nature.com/articles/d41586-021-01752-y Digital secrets of successful lab management (Nature)]
*[https://www.nature.com/articles/s41592-021-01199-z Biology begins to tangle with quantum computing (Nature Methods)]
=== 2020 ===
* '''[[Overview of the 2020 PCAWG Rollout | Lab contributions to the '20 PCAWG rollout (Overview)]]'''
* '''[[Selected Press Coverage for Gursoy et al Cell 2020 | Selected Press Coverage for Gursoy et al Cell 2020 (Overview)]] '''
=== 2019 ===
* '''[[Comparison of DTC based ancestry result for identical twins | Comparison of DTC based ancestry result for identical twins (Overview)]]'''
=== 2018 ===
* '''[[Overview of the 2018 PsychENCODE Rollout | Lab contributions to the '18 PsychENCODE rollout (Overview)]]'''
*[http://medicine.yale.edu/news/article.aspx?id=16666 Inauguration of the Yale Center for Biomedical Data Science (Yale Release)]
*[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)]
*[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)]
=== 2017 ===
*[http://ymm.yale.edu/autumn2017/features/feature/317720/ Putting the precise in precision medicine (Yale Medicine)]
*[http://protomag.com/articles/genetic-privacy-myth Is Genetic Privacy a Myth (Proto Magazine)]
*[http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379 Cybersecurity for the travelling scientist (Nature)]

=== 2016 ===
* '''[[STAT Series on Analyzing the Personal Genome of Carl Zimmer | STAT Series on Analyzing the Personal Genome of Carl Zimmer]]'''
* '''[[Selected Press Coverage for Harmanci et al Nature Methods 2016 | Selected Press Coverage for Harmanci et al Nature Methods 2016 (Overview)]]'''
* [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)]

=== 2014 ===

* '''[[Selected Press Coverage for the 2014 modENCODE Nature papers | Selected Press Coverage for the 2014 modENCODE Nature papers (Overview)]] '''
*[http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239 Geneticists tap human knockouts (Nature)]

=== 2013 ===

* '''[[Selected Press Coverage for Khurana et al Science 2013 | Selected Press Coverage for Khurana et al Science 2013 (Overview)]] '''
*[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)]
*[http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484?WT.ec_id=NATURE-20130228 Big biology: The 'omes puzzle (Nature)]

=== 2012 ===

* '''[[Overview of the 2012 ENCODE Rollout | Lab contributions to the '12 ENCODE rollout (Overview)]]'''
** [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)]
* [http://news.yale.edu/2012/02/16/yale-study-proves-nobody-genetically-perfect Yale study proves nobody is genetically perfect (Yale Press Release)]
** [http://news.yale.edu/2012/10/31/lessons-1000-genomes-small-differences-matter Lessons from 1000 Genomes: Small differences matter (Yale Press Release)]
** [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)]
* [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)]

=== 2011 ===
*[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)]
*[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)]
* [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)]

=== 2010 ===

*[http://twit.tv/fib71 Genomics, Proteomics, Cellular Immunity, and Anti-Matter (Futures in Biotech, TWiT.TV)]
*[http://www.nature.com/news/2010/100428/full/4641260a.html Cybersecurity: How safe are your data? (Nature)]
*[http://www.nature.com/news/2010/100715/full/news.2010.356.html Mystery RNA spawns gene-activating peptides (Nature)]
* [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)]
* [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)]
* [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)]
** [http://www.wired.com/wiredscience/2010/05/linux-vs-life/ Linux vs. Genome in Network Challenge (Wired)]
* [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)]

=== 2009 ===

* [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)]
* [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)]

=== 2008 ===

* [http://www.nytimes.com/2008/11/11/science/11gene.html Now: The Rest of the Genome (The New York Times)]

=== 2007 ===

* [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)]

=== 2003 ===

* [http://news.yale.edu/2003/12/01/yale-scientists-report-evolution-preserved-pseudogenes Yale Scientists Report Evolution Preserved in Pseudogenes (Yale Press Release)]

=== 2001 ===

* [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)]

=== 2000 ===

* Description of our research featured in [http://pubs.acs.org/cen/coverstory/7839/7839scit1.html C&E News] ([http://www.gersteinlab.org/about/7839scit1.html local copy])

=== 1998 ===

* [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)]

== More Stuff ==
* 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.)
* A [https://news.google.com/search?q=mark%20gerstein%20yale&hl=en-US&gl=US&ceid=US%3Aen Google News Query], which returns many of the mentions of the lab in the press (albeit with some noise)

Selected Press Coverage for the ABCD paper in Cell

2025-01-18T23:09:19Z

Mbg:

Resources

2025-01-05T03:06:37Z

Mbg:

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])
<HR>
The tools & 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'''].

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'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://molmovdb.mbb.yale.edu/molmovdb/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Networks===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 10px;"
|style="width:15%; text-align:center;"| [[File:Network.jpg|center|x75px]] [http://networks.gersteinlab.org/ Networks] ||
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.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

===Structural Variants (SV)===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:SVpage logo.png‎|center|x85px]] [http://sv.gersteinlab.org/ Structural Variants]||
Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).
|}

=Data Sets=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style="width:7%; text-align:center;"|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://resource.psychencode.org/ '''PsychENCODE resource''']||style="width:7%; text-align:center;"|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.
|}

=Evolution=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style="width:7%; text-align:center;"|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.
|}

=Genome Technology=

===Gene Regulation===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/Loregic '''Loregic''']||style="width:7%; text-align:center;"|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.
|}

===Allele-Specific Effects===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleledb.gersteinlab.org '''AlleleDB''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style="width:7%; text-align:center;"|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.
|}

===ChIP-Seq ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://music.gersteinlab.org '''MUSIC'''] [http://github.gersteinlab.org/MUSIC/ Github repo] ||style="width:7%; text-align:center;"|2014||
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style="width:7%; text-align:center;"|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.
|}

===Functional Annotation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq'''] - & - [http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style="width:7%; text-align:center;"|2013 & 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.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://larva.gersteinlab.org/ '''LARVA'''] [https://github.com/gersteinlab/LARVA Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT'''] [http://github.gersteinlab.org/vat/ Github repo] ||style="width:7%; text-align:center;"|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://aloft.gersteinlab.org/ '''ALoFT'''] [https://github.com/gersteinlab/aloft Github repo] ||style="width:7%; text-align:center;"|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://moat.gersteinlab.org/ '''MOAT'''] [https://github.com/gersteinlab/MOAT Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://github.gersteinlab.org/uORFs/ '''uORFs'''] [https://github.com/gersteinlab/uORFs Github repo] ||style="width:7%; text-align:center;"|2018|| A catalog of predicted functional upstream open reading frames (uORFs) in humans.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/GRAM '''GRAM'''] [https://github.com/gersteinlab/GRAM Github repo] ||style="width:7%; text-align:center;"|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).

|}

===Microarrays & Proteomics===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''MOTIPS''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|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.
|}

===RNA-Seq===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://act.gersteinlab.org/ '''ACT''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq'''] [http://github.gersteinlab.org/FusionSeq/ Github repo]||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq'''] [http://github.gersteinlab.org/IQSeq/ Github repo]||style="text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools'''] [http://github.gersteinlab.org/RSEQtools/ Github repo]||style="text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[https://github.com/gersteinlab/texp/blob/master/README.md '''TeXP'''] [https://github.com/gersteinlab/texp Github repo]||style="text-align:center;"|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.
|}

=== Structural Variation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE'''] [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style="width:7%; text-align:center;"|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] [http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style="width:7%; text-align:center;"|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.
|}

=Networks=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style="width:7%; text-align:center;"|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://pubnet.gersteinlab.org/ '''PubNet''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|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.
|}

=Structure and Macromolecular Motions=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [http://3vee.molmovdb.org/ '''3V''']||style="width:7%; text-align:center;"|2010||
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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://stress.molmovdb.org/ '''STRESS'''] [https://github.com/gersteinlab/STRESS Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://intensification.gersteinlab.org// '''Intensification'''] [https://github.com/gersteinlab/Intensification Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|}

=more=
[http://info.gersteinlab.org/More_tools more tools & resources]

Resources

2025-01-05T03:01:59Z

Mbg:

The tools & 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'''].

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'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

<HR>

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])

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://molmovdb.mbb.yale.edu/molmovdb/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Networks===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 10px;"
|style="width:15%; text-align:center;"| [[File:Network.jpg|center|x75px]] [http://networks.gersteinlab.org/ Networks] ||
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.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

===Structural Variants (SV)===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:SVpage logo.png‎|center|x85px]] [http://sv.gersteinlab.org/ Structural Variants]||
Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).
|}

=Data Sets=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style="width:7%; text-align:center;"|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://resource.psychencode.org/ '''PsychENCODE resource''']||style="width:7%; text-align:center;"|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.
|}

=Evolution=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style="width:7%; text-align:center;"|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.
|}

=Genome Technology=

===Gene Regulation===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/Loregic '''Loregic''']||style="width:7%; text-align:center;"|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.
|}

===Allele-Specific Effects===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleledb.gersteinlab.org '''AlleleDB''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style="width:7%; text-align:center;"|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.
|}

===ChIP-Seq ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://music.gersteinlab.org '''MUSIC'''] [http://github.gersteinlab.org/MUSIC/ Github repo] ||style="width:7%; text-align:center;"|2014||
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style="width:7%; text-align:center;"|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.
|}

===Functional Annotation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq'''] - & - [http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style="width:7%; text-align:center;"|2013 & 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.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://larva.gersteinlab.org/ '''LARVA'''] [https://github.com/gersteinlab/LARVA Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT'''] [http://github.gersteinlab.org/vat/ Github repo] ||style="width:7%; text-align:center;"|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://aloft.gersteinlab.org/ '''ALoFT'''] [https://github.com/gersteinlab/aloft Github repo] ||style="width:7%; text-align:center;"|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://moat.gersteinlab.org/ '''MOAT'''] [https://github.com/gersteinlab/MOAT Github repo] ||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://github.gersteinlab.org/uORFs/ '''uORFs'''] [https://github.com/gersteinlab/uORFs Github repo] ||style="width:7%; text-align:center;"|2018|| A catalog of predicted functional upstream open reading frames (uORFs) in humans.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/GRAM '''GRAM'''] [https://github.com/gersteinlab/GRAM Github repo] ||style="width:7%; text-align:center;"|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).

|}

===Microarrays & Proteomics===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''MOTIPS''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|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.
|}

===RNA-Seq===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://act.gersteinlab.org/ '''ACT''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq'''] [http://github.gersteinlab.org/FusionSeq/ Github repo]||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq'''] [http://github.gersteinlab.org/IQSeq/ Github repo]||style="text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools'''] [http://github.gersteinlab.org/RSEQtools/ Github repo]||style="text-align:center;"|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.
|-style="height: 100px;"
|style="text-align: center;"|[https://github.com/gersteinlab/texp/blob/master/README.md '''TeXP'''] [https://github.com/gersteinlab/texp Github repo]||style="text-align:center;"|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.
|}

=== Structural Variation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE'''] [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style="width:7%; text-align:center;"|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] [http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style="width:7%; text-align:center;"|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.
|}

=Networks=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style="width:7%; text-align:center;"|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://pubnet.gersteinlab.org/ '''PubNet''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style="width:7%; text-align:center;"|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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|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.
|}

=Structure and Macromolecular Motions=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [http://3vee.molmovdb.org/ '''3V''']||style="width:7%; text-align:center;"|2010||
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.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|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.
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|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style="width:7%; text-align:center;"|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.
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|style="width:15%; text-align:center;"|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style="width:7%; text-align:center;"|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.
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|style="width:15%; text-align:center;"|[http://stress.molmovdb.org/ '''STRESS'''] [https://github.com/gersteinlab/STRESS Github repo] ||style="width:7%; text-align:center;"|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.
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|style="width:15%; text-align:center;"|[http://intensification.gersteinlab.org// '''Intensification'''] [https://github.com/gersteinlab/Intensification Github repo] ||style="width:7%; text-align:center;"|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.
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=more=
[http://info.gersteinlab.org/More_tools more tools & resources]