Overview of the 2012 ENCODE Rollout

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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 Times article] on ENCODE and [http://linkstream2.gerstein.info/tag/x78qtecore/ other key articles that describe the lab's work on the 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] and [http://linkstream2.gerstein.info/tag/x78qtecore/ other key articles] that describe the lab's work on the ENCODE rollout'''
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* [http://linkstream2.gerstein.info/tag/prencroll0mg More articles] about the ENCODE 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 press links  
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* More
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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), which includes [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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** [http://linkstream2.gerstein.info/tag/prencroll0mg 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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* Article about how CT is aiming to become a genomics hub; adjacent to the story was [http://archive.gersteinlab.org/mark/out/log/2012/09.29/pic/Courant-Genomics-Timeline-photo.JPG a timeline highlighting the major genomic achievements in the state].  
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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), which includes [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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* [http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf Article in Spanish] on the rollout.
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* Misc
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** Article about how CT is aiming to become a genomics hub; adjacent to the story was [http://archive.gersteinlab.org/mark/out/log/2012/09.29/pic/Courant-Genomics-Timeline-photo.JPG a timeline highlighting the major genomic achievements in the state].  
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** [http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf Article in Spanish] on the rollout.
== Talks ==
== Talks ==

Revision as of 04:00, 10 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

  • Papers related to the actual ENCODE rollout

http://papers.gersteinlab.org/subject/encoderollout


  • Listing of ENCODE and modENCODE "rollout" papers from the ENCODE pilot and modENCODE rollouts

http://papers.gersteinlab.org/subject/encodecore


  • Other ENCODE associated papers

http://papers.gersteinlab.org/subject/otherencodepapers


  • Gencode Pseudogene work

http://papers.gersteinlab.org/subject/encode-pgenes


Press

Talks

  • Slide pack on networks and pseudogenes (pdf & ppt):

http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb/

  • Another slide pack containing information on statistical models relating output expression to genomic inputs (pdf & ppt):

http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn/

  • Finally, here's a link to the modENCODE symposium, which has a video

containing bits of the talks above: http://lectures.gersteinlab.org/summary/Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620/

Subway Map

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

http://homes.gersteinlab.org/people/rar62/subwaymap/SubwayMap8_16_12.pdf

https://docs.google.com/spreadsheet/ccc?key=0AvRr07RHaF5cdFZlOFJ1YmdOT2pUM1VEODM1bE5CRHc#gid=0

Easy to Read Introductory Papers

http://papers.gersteinlab.org/papers/sciam2

http://papers.gersteinlab.org/papers/amsci

Grants

We had 3 NIH ENCODE grants :

GENCODE (NIH-encode-pgenes): http://papers.gersteinlab.org/subject/encode-pgenes

The DAC (NIH-encode-DAC): http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695

The ENCODE "chip center" (NIH-encode-chip) : http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805

In addition the original pilot grant : http://papers.gersteinlab.org/subject/encode + http://encode.gersteinlab.org

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