Overview of the 2012 ENCODE Rollout

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The rollout for the ENCODE consortium (Human Genome Annotation) papers occurred in early fall 2012.  The Gerstein lab is associated with 9 papers. The 3 Nature submissions comprise >35 formatted journal pages in total.  In addition to the core ENCODE papers, the Gerstein lab contributed a small comment on the “big data” aspect of ENCODE, which appeared in a subsequent issue of Nature, and a review on the machine-learning aspects of ENCODE which will come out in Genome Biology.
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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.  
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__TOC__
__TOC__
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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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http://papers.gersteinlab.org/subject/encoderollout
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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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* Listing of ENCODE and modENCODE "rollout" papers from the ENCODE pilot and modENCODE rollouts
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* [http://papers.gersteinlab.org/subject/encode-pgenes Gencode pseudogenes work]
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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
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* Yale website for ENCODE pilot project
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http://encode.gersteinlab.org/
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== 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://linkstream2.gerstein.info/tag/prencroll0mg Articles about the ENCODE rollout]
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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://blog.openhelix.eu/?p=13613 ENCODE floods the news networks…] - The OpenHelix Blog
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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://linkstream2.gerstein.info/tag/x78qtecore/ Articles that describe the Gerstein lab's work on the project]
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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://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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== Subway Map ==
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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
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networks labeled/colored by both country and state.
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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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== Introductory Papers ==
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These introductory papers are easy to read and provide context on the ENCODE rollout.
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* Finally, here's a link to the modENCODE symposium, which has a video
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* [http://papers.gersteinlab.org/papers/encode-annouce The ENCODE (ENCyclopedia Of DNA Elements) Project] Science (2004)
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containing bits of the talks above:
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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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http://lectures.gersteinlab.org/summary/Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620/
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== 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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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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== 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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== Easy to Read Introductory Papers ==
 
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http://papers.gersteinlab.org/papers/sciam2
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== 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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http://papers.gersteinlab.org/papers/amsci
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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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