User contributions
From GersteinInfo
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- 14:04, 10 June 2010 (hist) (diff) N Encode Information Page (Redirected page to Encode Information) (top)
- 14:02, 10 June 2010 (hist) (diff) N DeadLines (Created page with '= Deadlines on Different Encode Projects = == Calendar == Deadlines are placed in [http://www.google.com/calendar/hosted/gersteinlab.org/embed?src=gersteinlab.org_cf9nqr5n2q0q7bp…') (top)
- 14:02, 10 June 2010 (hist) (diff) N File:Expressed HumanTFs Summary.xls (top)
- 14:00, 10 June 2010 (hist) (diff) N Encode Information (Created page with '==Encode Resources== * [http://encode.gersteinlab.org Yale ENCODE site] * [http://wiki.gersteinlab.org/encode/index.php/Main_Page Lab ENCODE information] * [http://www.genome.gov…') (top)
- 13:59, 10 June 2010 (hist) (diff) N FusionSeq (Created page with '=Introduction= This page provides the source code for FusionSeq. Please note that these tools were tested on a multi-node cluster of computing nodes with Linux Red Hat as operati…')
- 13:58, 10 June 2010 (hist) (diff) N Genome Statistics (Created page with '* From ENCODE paper These 30Mb are divided among 44 genomic regions; approximately 15Mb reside in 14 regions for which there is already substantial biological knowledge, whereas…') (top)
- 13:57, 10 June 2010 (hist) (diff) N Genome Technology Subgroup (Redirected page to Genome Technology) (top)
- 13:55, 10 June 2010 (hist) (diff) N Genome Technology (Created page with '== Recent Publications == ;'''Integrating sequencing technologies in personal genomics - optimal low cost reconstruction of structural variants.''' :J Du, RD Bjornson, ZD Zhang,…') (top)
- 13:39, 10 June 2010 (hist) (diff) N Human TF List (Created page with ''''Here is the [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls list] with various gene names mapped.''' '''Citation:''' Bhardwaj, N., Carson, M. B., …') (top)
- 13:36, 10 June 2010 (hist) (diff) N File:Lunter-indel-genic.png (top)
- 13:35, 10 June 2010 (hist) (diff) N LOF (Created page with '== 1000 Genomes Project indel LOF == === Lunter indels === * Combined indels from low-coverage individuals * Currently 3,853,785 indels = 2,263,850 deletions + 1,589,935 insertio…') (top)
- 13:34, 10 June 2010 (hist) (diff) N Local-copy-cs445 (Created page with 'This page contains general information for the class: ''CPSC445/CPSC545/MBB334/MBB545/CBB545'' Spring 2008 '''Introduction to Data Mining''' == Course websites == * Course wi…') (top)
- 13:31, 10 June 2010 (hist) (diff) MB&B Policy for Graduate Students on Vacation and Travel (top)
- 13:29, 10 June 2010 (hist) (diff) N File:Mark.jpg (top)
- 13:29, 10 June 2010 (hist) (diff) N File:Mbg-name.Greek-Russian.jpg (top)
- 13:28, 10 June 2010 (hist) (diff) N Mark Alphabets (Created page with 'Mark Gerstein in multiple alphabets. ===υαρκοσ γερστειν=== 400px 400px') (top)
- 13:24, 10 June 2010 (hist) (diff) N Paper Byte letter (Created page with '==Other Paper's : Letter in Byte == M Gerstein (1996). "Porting Unix," letter to Byte (August issue of magazine). I use Unix extensively in a scientific research environment, …') (top)
- 13:21, 10 June 2010 (hist) (diff) N Pseudogene Statistics (Created page with '{| border="1" |- ! Organism ! Pseudogenes ! Duplicated ! Processed ! Notes |- | Human | 16,326 | 2,585 | 7,913 |- | Arabidopsis | 4,260 | 1,144 | 704 |- | Chicken | 4,179 | 2,655…') (top)
- 13:18, 10 June 2010 (hist) (diff) N File:TranscriptCoverage.jpg (top)
- 13:18, 10 June 2010 (hist) (diff) N File:SummaryStatistics.jpg (top)
- 13:18, 10 June 2010 (hist) (diff) N File:GenomicRegion.jpg (top)
- 13:17, 10 June 2010 (hist) (diff) N RSEQtools/gallery (Created page with '<center>[http://archive.gersteinlab.org/proj/rnaseq/rseqtools '''RSEQtools Main Page''']</center> __TOC__ == Results Gallery == <center>Top</center> === Visualization…') (top)
- 13:14, 10 June 2010 (hist) (diff) N File:GersteinLab-Resources-21Oct08.doc (top)
- 13:14, 10 June 2010 (hist) (diff) N File:GersteinLab-Resources-1Sep07.doc (top)
- 13:06, 10 June 2010 (hist) (diff) N File:Gene complexity.jpeg (top)
- 13:05, 10 June 2010 (hist) (diff) N What is a gene? (Created page with '''``The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products."'' ''from'': <br> '''What is a gene, post-ENCODE? History an…') (top)
- 12:36, 9 June 2010 (hist) (diff) N File:Tree.png (top)
- 12:35, 9 June 2010 (hist) (diff) N File:Saturation2.jpg (top)
- 12:35, 9 June 2010 (hist) (diff) N File:Saturation.png (top)
- 12:35, 9 June 2010 (hist) (diff) N File:Output.png (top)
- 12:35, 9 June 2010 (hist) (diff) N File:Image006.gif (top)
- 12:35, 9 June 2010 (hist) (diff) N File:Image004.gif (top)
- 12:34, 9 June 2010 (hist) (diff) N File:Heatmap.png (top)
- 12:34, 9 June 2010 (hist) (diff) N File:GSA.png (top)
- 12:34, 9 June 2010 (hist) (diff) N File:GSA results.png (top)
- 12:34, 9 June 2010 (hist) (diff) N File:Errorbar.png (top)
- 12:34, 9 June 2010 (hist) (diff) N File:Bigdendogram.png (top)
- 12:33, 9 June 2010 (hist) (diff) N File:Agg.jpg (top)
- 12:33, 9 June 2010 (hist) (diff) N File:Agg Baf155 exp.jpg (top)
- 12:33, 9 June 2010 (hist) (diff) N File:Act-5000bp-1.jpg (top)
- 12:31, 9 June 2010 (hist) (diff) N File:Act-2500bp-1.jpg (top)
- 12:31, 9 June 2010 (hist) (diff) N File:ACT results.png (top)
- 12:05, 9 June 2010 (hist) (diff) N ActGallery (Created page with '==Aggregation== The standard output for the aggregation script is a three column file corresponding to nucleotide position, bin number, and average signal (or a two column file c…')
- 12:01, 9 June 2010 (hist) (diff) N ACT (Created page with '=== ACT === http://ACT.Gersteinlab.org was developed by Robert Bjornson <robert.bjornson@yale.edu>, Joel Rozowsky, Justin Jee, and others at the Gerstein Lab at Yale. This code …') (top)
- 12:00, 9 June 2010 (hist) (diff) N 1000genomes nonsyn (Created page with '[http://homes.gersteinlab.org/people/suganthi/outbox/1000genomes/REL-0908/all_LOF/nsyn/CEU.0908.all.pc.nsyn CEU.0908.nsyn] Summary of file The pipeline software to map SNPs on…') (top)
- 11:57, 9 June 2010 (hist) (diff) N RSEQtools/workflow (Created page with '<center>[http://archive.gersteinlab.org/proj/rnaseq/rseqtools '''RSEQtools Main Page''']</center> __TOC__ == Example workflow == This section shows a simple workflow for proce…')
- 11:56, 9 June 2010 (hist) (diff) N RSEQtools (Created page with '<center>[http://archive.gersteinlab.org/proj/rnaseq/rseqtools '''RSEQtools Main Page''']</center> __TOC__ == Introduction == The mapped read format (MRF) is a concise represe…')
- 11:49, 9 June 2010 (hist) (diff) N Null Page (Created page with '==Stuff is coming!== This is a null page!') (top)
- 11:48, 9 June 2010 (hist) (diff) N Old lectures and courses (Created page with '* Older lectures http://lectures.gersteinlab.org/old_lectures.html * Older Courses http://lectures.gersteinlab.org/old_courses.html * Updating the lectures page [http://lec…')
- 11:48, 9 June 2010 (hist) (diff) N Some Useful Email Addresses (Created page with '* For submitting data to the public data banks, use: datasubmission (AT) gersteinlab (DOT) org') (top)
- 11:47, 9 June 2010 (hist) (diff) N Lab Address (Created page with '==PI Contact Address== Mark Gerstein ([http://contact.gerstein.info contact.gerstein.info]) ==Senior Admin Assistant== Anne Nicotra MB&B Department Bass 432, 266 Whitney Ave.…')
- 11:46, 9 June 2010 (hist) (diff) N Mbg-research (Created page with ''''Research Summary: Protein Bioinformatics''' The biological sciences are being transformed by the advent of large-scale data. The sequencing of the human genome is a most dra…') (top)
- 11:45, 9 June 2010 (hist) (diff) N MBG-Profile (Created page with '* Here is a 50 word description of my research (31-Aug-2009) Dr. Gerstein is the Albert Williams Professor of Biomedical Informatics, Molecular Biophysics & Biochemistry and Com…')
- 11:45, 9 June 2010 (hist) (diff) N Outbox information (Created page with 'Additional information on Mark's outboxes beyond that in http://outbox.gerstein.info http://homes.gersteinlab.org/people/mark/scr scratch workspace http://bioinfo.mbb.yale.edu/…') (top)
- 11:45, 9 June 2010 (hist) (diff) N Contact information (Created page with 'The main contact information for Mark Gerstein is on '''http://contact.gerstein.info''' . Additional information is on the page, as it is easier to edit . * Confidential inform…')
- 11:44, 9 June 2010 (hist) (diff) N AlleleSeq (Created page with 'insert text here...')
- 11:43, 9 June 2010 (hist) (diff) N Calendar maintainers (Created page with 'The individuals below have responsibilities for maintaining different parts of the lab calendar. These should *also* try to turn up on their call. {| class="wikitable" border="…')
- 11:43, 9 June 2010 (hist) (diff) N Calendar (Created page with '==Overview (Gerstein Lab Calendars and Listings of General Yale Bioinformatics Events)== These two calendars are primarily for scheduling Gerstein Lab meetings, but include a num…')
- 11:41, 9 June 2010 (hist) (diff) N Q2C panel from Other Papers for M Gerstein (Created page with ''''"Whose DNA is it?"''' A Panel on the Agenda with Steve Paikin ( [http://www.tvo.org/cfmx/tvoorg/theagenda/index.cfm?page_id=7&bpn=104107&ts=2009-10-21%2020:00:00.0| Agenda s…') (top)
- 11:40, 9 June 2010 (hist) (diff) N Commonwealth Club of California from Other Papers for M Gerstein (Created page with '* L Avey, D Ballon, D Magnus, M Gerstein, J Rae-Dupree (2009). A Closer Look at Personal Genomic Testing, -- Commonwealth Club of California, Inforum Genomics Panel [http://www.y…') (top)
- 11:40, 9 June 2010 (hist) (diff) N Fib Podcast from Other Papers for M Gerstein (Created page with '* M Gerstein (interviewed by M Pelletier) (2008) [http://twit.tv/fib34 Futures in Biotech 34: A Great Historical Document - The Human Genome] ([http://papers.gersteinlab.org/e-pr…') (top)
- 11:39, 9 June 2010 (hist) (diff) N Byte letter from Other Papers for M Gerstein (Created page with 'M Gerstein (1996). [http://www.byte.com/art/9608/sec2/art4.htm|"Porting Unix,"] letter to Byte (August issue of magazine). Below is original text of the letter. I use Unix ext…') (top)
- 11:39, 9 June 2010 (hist) (diff) N Hartford Courant OpEd2 from Other Papers for M Gerstein (Created page with 'M Seringhaus, M Gerstein. (2009) "Putting too much information online can erode individual privacy", Hartford Courant, 5 June Original Article link no longer available Reposte…')
- 11:38, 9 June 2010 (hist) (diff) N SF Chron OpEd from Other Papers for M Gerstein (Created page with 'D Greenbaum, M Gerstein. (2008) [http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2008/11/02/INLM12IL8T.DTL "Personal genomics requires redefining privacy The human blueprint: da…')
- 11:38, 9 June 2010 (hist) (diff) N Hartford Courant OpEd from Other Papers for M Gerstein (Created page with 'D Greenbaum, M Gerstein. (2008) "Danger: Sharing Gene Data", Hartford Courant, 10 July, pg. A11 (OPED) Original Article link (probably now broken): http://www.courant.com/news/…') (top)
- 11:37, 9 June 2010 (hist) (diff) N Other Papers (Created page with '==Other Writings (book chapters, popular articles, Op-Eds, miscellaneous)== * C Chothia & M Gerstein. (1992). "Protein Design for Domain Closure," in Muscle as a Machine: Energy…')
- 11:36, 9 June 2010 (hist) (diff) Motions Supplement (top)
- 11:05, 9 June 2010 (hist) (diff) N Motions Supplement (Created page with 'coracoloroz ==Proteins in 3 (or more) conformations (includes links to RCSB and MolMovDB)== <table border="1" width="100%" id="table1"> <tr> <td width="150" style="borde…')
- 11:04, 9 June 2010 (hist) (diff) N ActFaq (Created page with 'This page is under construction') (top)
- 23:38, 3 June 2010 (hist) (diff) Mihali A. Felipe (top)
- 23:38, 3 June 2010 (hist) (diff) N Mihali A. Felipe (Created page with '[http://homes.gersteinlab.org/people/mihali]')
- 23:37, 3 June 2010 (hist) (diff) N User:Infoadmin (Created page with 'Mihali A. Felipe')
- 23:12, 3 June 2010 (hist) (diff) N Cs545-07 (Created page with 'This page contains general information for the class: ''CPSC445/CPSC545/MBB334/MBB545/CBB545'' '''Introduction to Data Mining''' == Course websites == * Main website ** http:…') (top)
- 23:35, 2 June 2010 (hist) (diff) File:ACT option.png (uploaded a new version of "File:ACT option.png") (top)
- 23:27, 2 June 2010 (hist) (diff) N File:ACT option.png
- 10:20, 2 June 2010 (hist) (diff) Policy on Postdoc Appointments (top)
- 10:20, 2 June 2010 (hist) (diff) Policy on Postdoc Appointments
- 10:19, 2 June 2010 (hist) (diff) Main Page (→Info for Lab Members and Collaborators)
- 19:20, 1 June 2010 (hist) (diff) N File:Policy-on-Minors-in-Labs.pdf (Yale's policy regarding minors in the lab.) (top)
- 19:18, 1 June 2010 (hist) (diff) N Meeting Invites (Created page with '=Information on Standard Meeting Invitations= This document has more detail on Mark's standard meeting invites. These usually tend to be rather terse and cryptic emails auto-gene…') (top)
- 19:17, 1 June 2010 (hist) (diff) N What grant to charge something to (Created page with 'Current procedure (1-Nov-07, updated Sep-08) * For "committed" effort people and casuals (e.g. summer job undergrads) ** MG will assign people to projects in consultation with Za…')
- 19:16, 1 June 2010 (hist) (diff) N MB&B Policy for Graduate Students on Vacation and Travel (Created page with 'From [http://www.mbb.yale.edu/grad/reqts/index.html www.mbb.yale.edu/grad/reqts] * VACATION The Departmental policy regarding student vacations conforms to the stipulations of…')
- 19:15, 1 June 2010 (hist) (diff) N Policy on Postdoc Appointments (Created page with '<pre> Subject: Ph.D. certificates for new postdocs Date: Fri, 21 Nov 2008 12:02:18 -0500 From: Lane, Melody An important reminder of the Postdoctoral Policy to be sure you acqu…')
- 19:15, 1 June 2010 (hist) (diff) Resources Document
- 19:14, 1 June 2010 (hist) (diff) N Resources Document (Created page with 'Information about lab resources can be found here: *NIH resources document (revised 21Oct2008) *[[Image:GersteinLab-Resources-1Sep…')
- 19:13, 1 June 2010 (hist) (diff) N Recommendation Letters (Created page with '* Overview ** To help Mark write as good a letter as possible, he would appreciate if you could draft an initial skeleton of the letter -- the base letter. * Preparing a '''DRA…')
- 19:12, 1 June 2010 (hist) (diff) N Pointers on Grant Sections (Created page with '* Just use straight text (no greek, etc), avoid complex equations. * Use Times and Ariel fonts. Use word '04 format (.doc) file -- not Word '08 (.docx) or open office. * Put …')
- 19:12, 1 June 2010 (hist) (diff) Main Page (→Info for Lab Members and Collaborators)
- 19:11, 1 June 2010 (hist) (diff) N Pointers on Powerpoints (Created page with '* Number Slides * Make a secondary PDF when mailing to a list * For a template use the initial slides from any of the recent lectures on http://lectures.gersteinlab.org/summary (…') (top)
- 19:10, 1 June 2010 (hist) (diff) N Xxmg at gersteinlab.org (Created page with '* '''xx'''mg@gersteinlab.org address for paper correspondence. ** Try to use '''xx'''mg@gersteinlab.org, where '''xx''' is your lab initials . For instance, hymg (at) gersteinla…')
- 19:10, 1 June 2010 (hist) (diff) N Affiliation (Created page with 'Way to List Affiliations for Mark Gerstein on papers Mark B. Gerstein 1,2,3 1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Bi…')
- 19:09, 1 June 2010 (hist) (diff) N Streamlining Draft Flow (Created page with '== General == This document has been prepared by Mark Gerstein. It describes some general ideas to streamline the flow of drafts, papers, and related documents through the lab. …')
- 19:08, 1 June 2010 (hist) (diff) N Public wiki pages linked from elsewhere (Created page with 'These pages have been established on the wiki are best accessed first from outside the wiki *cs545-07 : Course page for CS545 *[http://wiki.gersteinlab.org/pubinfo/Human_TF_…')
- 19:08, 1 June 2010 (hist) (diff) N General Information for Interested Undergrads and Masters Students (Created page with 'A bit of a five-step plan: 1 * Look at past and present undergrads http://www.gersteinlab.org/people/alumni.htm http://www.gersteinlab.org/people/ (These have included STARs …')
- 19:07, 1 June 2010 (hist) (diff) N FAQ (Created page with '==OLD FAQs== Frequently asked questions about lab programs ([http://bioinfo.mbb.yale.edu/pipermail/faq/ mailman version], [http://gersteinlabfaqs.blogspot.com/ blogger version]) …')
- 19:06, 1 June 2010 (hist) (diff) N ACT Tool (Created page with 'Here is some info. on http://act.gersteinlab.org ('''A'''ggregation & '''C'''orrelation '''T'''oolbox) ==Overview== [[Image:ACT_option.png|thumb|Getting Started: select from on…')
- 19:05, 1 June 2010 (hist) (diff) N Analysis of Lab Publications (Created page with '==Overview== Below is quick analysis of lab publication patterns, showing our websites and most commonly picked journals. Raw data is in : [http://archive.gersteinlab.org/doc…') (top)
- 19:04, 1 June 2010 (hist) (diff) N Documents (Created page with '(This page contains sundry public documents related to the Gerstein Lab. See to [http://wiki.gersteinlab.org/labinfo/Uploading_documents upload documents]) Here is a [http://arc…')
- 19:04, 1 June 2010 (hist) (diff) Main Page
- 19:02, 1 June 2010 (hist) (diff) N User:Mbg (Created page with '=Mark B. Gerstein= Principal Investigator') (top)
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