Overview of the 2012 ENCODE Rollout

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[[File:cover_nature_encoderollout.jpg|100px|link=http://www.nature.com/nature/journal/v489/n7414/index.html]] [[File:cover_genomeres_encoderollout.png|100px|link=http://genome.cshlp.org/content/22/9.toc]]
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[[File:cover_science_modencode.png|100px|link=http://www.sciencemag.org/content/330/6012.toc]] [[File:cover_genomeres_modencode.png|100px|link=http://genome.cshlp.org/content/21/2.toc]]   
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[[File:cover_nature_encodepilot.jpg|100px|link=http://www.nature.com/nature/journal/v447/n7146/]] [[File:cover_genomeres_encodepilot.png|100px|link=http://genome.cshlp.org/content/17/6.toc]]     
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== Papers ==
 
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* Papers related to the actual ENCODE rollout
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== Papers ==
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* Papers related to the 2012 [http://papers.gersteinlab.org/subject/encoderollout ENCODE rollout]
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* Papers related to the 2010 [http://papers.gersteinlab.org/subject/modencode modENCODE rollout]
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* Papers related to the 2007 [http://papers.gersteinlab.org/subject/encodecore ENCODE pilot rollout]
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* [http://papers.gersteinlab.org/subject/otherencodepapers Other ENCODE associated papers]
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* [http://papers.gersteinlab.org/subject/encode-pgenes Gencode pseudogenes work]
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http://papers.gersteinlab.org/subject/encoderollout
 
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* Listing of ENCODE and modENCODE "rollout" papers from the ENCODE pilot and modENCODE rollouts
 
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http://papers.gersteinlab.org/subject/encodecore
 
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* Other ENCODE associated papers
 
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http://papers.gersteinlab.org/subject/otherencodepapers
 
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* Gencode Pseudogene work
 
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http://papers.gersteinlab.org/subject/encode-pgenes
 
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* Original Pilot Grant Papers
 
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http://papers.gersteinlab.org/subject/encode
 
== Press ==  
== Press ==  
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* [http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?pagewanted=all&_r=0 NY Times] and [http://www.reuters.com/article/2012/09/05/us-usa-health-junk-dna-idUSBRE88414V20120905 Reuters] articles on the ENCODE rollout
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* [http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?pagewanted=all&_r=0 Times article] on ENCODE  
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* [http://linkstream2.gerstein.info/tag/x78qtecore/ Other key articles] that describe the lab's work on the rollout
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* [http://linkstream2.gerstein.info/tag/x78qtecore/ Articles that describe the Gerstein lab's work on Rollout]
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* [http://linkstream2.gerstein.info/tag/prencroll0mg Even more articles] about the rollout (including a  [http://linkstream2.gerstein.info/tag/x78qtenc subset of them] specifically mentioning the lab) and a comprehensive [http://blog.openhelix.eu/?p=13613 OpenHelix Blog] entry that has lots of annotated press links  
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* [http://news.yale.edu/2012/09/05/yale-team-finds-order-amidst-chaos-within-human-genome-mom-and-dad-s-contributions-counte Yale Press Releases on ENCODE] (written by Bill Hathaway), including a [http://archive.gersteinlab.org/mark/out/log/2012/08.28/diag/encodenets--presss-release-schematic--Diagram-4-1.pdf schematic] showing a key point of ENCODE networks analysis (annotation to hairball to interpretable hierarchy)
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* [http://linkstream2.gerstein.info/tag/prencroll0mg More articles about the ENCODE rollout] and [http://blog.openhelix.eu/?p=13613 OpenHelix Blog] entry that has lots of press links
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* [http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish]
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* [http://archive.gersteinlab.org/mark/out/log/2012/08.28/diag/encodenets--presss-release-schematic--Diagram-4-1.pdf Schematic] showing key point of ENCODE networks analysis: annotation to hairball to interpretable hierarchy
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* [https://docs.google.com/document/d/1q6EYtxN5Ym_0OBwrSm6EtLELfpIG9xmGd38-5O4hAR8/edit# 3 Yale Press Releases on ENCODE] (written by Bill Hathaway)
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== Talks ==
== Talks ==
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* [http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb/ Slide pack on networks and pseudogenes] ([http://archive.gersteinlab.org/mark/out/log/2012/05.29/talk/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb.pdf pdf] & [http://archive.gersteinlab.org/mark/out/log/2012/05.29/talk/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb.ppt ppt])
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* Another slide pack containing information on [http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn/ statistical models relating output expression to genomic inputs] ([http://archive.gersteinlab.org/mark/out/log/2012/09.15/talk/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn.pdf pdf] & [http://archive.gersteinlab.org/mark/out/log/2012/09.15/talk/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn.ppt ppt])
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* Finally, here's a link to the [http://lectures.gersteinlab.org/summary/Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620/ modENCODE symposium], which has a [http://www.genome.gov/27549319 video] containing bits of the talks above
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* Slide pack on networks and pseudogenes (pdf & ppt):
 
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http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb/
 
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* Another slide pack containing information on statistical models relating output expression to genomic inputs (pdf & ppt):
 
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http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn/
 
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* Finally, here's a link to the modENCODE symposium, which has a video
 
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containing bits of the talks above:
 
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http://lectures.gersteinlab.org/summary/Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620/
 
== Subway Map ==
== Subway Map ==
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We have created a subway map figure showing the overall collaboration in the consortium. There are now coauthor
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We have created a [[Media:SubwayMap8_16_12.pdf|subway map figure]] (pdf) showing the [https://docs.google.com/spreadsheet/ccc?key=0AvRr07RHaF5cdFZlOFJ1YmdOT2pUM1VEODM1bE5CRHc#gid=0 overall collaboration in the consortium] (gdoc). There are now coauthor
networks labeled/colored by both country and state.
networks labeled/colored by both country and state.
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http://homes.gersteinlab.org/people/rar62/subwaymap/SubwayMap8_16_12.pdf
 
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https://docs.google.com/spreadsheet/ccc?key=0AvRr07RHaF5cdFZlOFJ1YmdOT2pUM1VEODM1bE5CRHc#gid=0
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== Introductory Papers ==
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These introductory papers are easy to read and provide context on the ENCODE rollout.
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* [http://papers.gersteinlab.org/papers/encode-annouce The ENCODE (ENCyclopedia Of DNA Elements) Project] Science (2004)
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* [http://papers.gersteinlab.org/papers/sciam2 The real life of pseudogenes] American Scientist (2006)
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* [http://papers.gersteinlab.org/papers/amsci Genomics Confounds Gene Classification] American Scientist (2008)
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== Easy to Read Introductory Papers ==
 
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http://papers.gersteinlab.org/papers/sciam2
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== Grants ==
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* For the current ENCODE "build out", we are part of the [http://projectreporter.nih.gov/project_info_description.cfm?aid=8402447 data analysis grant]
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* For the ENCODE scale up, we had 3 NIH grants
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** GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes])
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** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC])
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** The "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip])
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* For modENCODE, we have been part of 3 NIH grants
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** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?projectnumber=1RC2HG005639-01 NIH-modencode-DAC])
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** Transcriptome Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=7853828&icde=0 NIH-modencode-GT]
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** Regulation Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=8249231&icde=0 NIH-modENCODE-TR]
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* For the initial ENCODE pilot, we had one grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]).
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http://papers.gersteinlab.org/papers/amsci
 
== Misc ==
== Misc ==
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[http://articles.courant.com/2012-09-23/news/hc-connecticut-genomics-20120923_1_human-genome-genome-research-uconn-and-jackson Hartford Courant article] about how Connecticut is aiming to become a genomics hub. Adjacent to the story was a [http://archive.gersteinlab.org/mark/out/log/2012/09.29/pic/Courant-Genomics-Timeline-photo.JPG timeline] highlighting the major genomic achievements in the state.
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Yale website for ENCODE pilot project: http://encode.gersteinlab.org/
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[http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish] about the ENCODE rollout.

Latest revision as of 01:09, 12 October 2012

The rollout for the ENCODE consortium (Human Genome Annotation) papers occurred in early fall 2012. This was the culmination of a decade of work in the ENCODE scaleup, the ENCODE pilot project, and modENCODE.

Contents


         


Papers


Press

Talks


Subway Map

We have created a subway map figure (pdf) showing the overall collaboration in the consortium (gdoc). There are now coauthor networks labeled/colored by both country and state.


Introductory Papers

These introductory papers are easy to read and provide context on the ENCODE rollout.


Grants


Misc

Hartford Courant article about how Connecticut is aiming to become a genomics hub. Adjacent to the story was a timeline highlighting the major genomic achievements in the state.

An article in Spanish about the ENCODE rollout.

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