View source for Overview of the 2012 ENCODE Rollout

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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== Papers ==
* 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]
[[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]]      


* [http://papers.gersteinlab.org/subject/otherencodepapers Other ENCODE associated papers]
* [http://papers.gersteinlab.org/subject/encode-pgenes Gencode pseudogenes work]


== Press == 

* [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 article] on ENCODE 
* [http://www.reuters.com/article/2012/09/05/us-usa-health-junk-dna-idUSBRE88414V20120905 Occupy comes to DNA: A genome for the 99 percent] - Reuters article that uses Mark's comment in its title
* [http://linkstream2.gerstein.info/tag/x78qtecore/ other key articles that describe the Gerstein lab's work on the rollout]
* [http://linkstream2.gerstein.info/tag/prencroll0mg More articles about the ENCODE rollout] and an [http://blog.openhelix.eu/?p=13613 OpenHelix Blog] entry that has lots of press links
* [http://www.genome.gov/27549810 NHGRI press release on ENCODE]
* [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


== Talks ==

* [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])
* 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])
* 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


== Subway Map ==
We have created a [http://homes.gersteinlab.org/people/rar62/subwaymap/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.


== Introductory Papers ==
These introductory papers are easy to read and provide context on the ENCODE rollout.
* [http://papers.gersteinlab.org/papers/encode-annouce The ENCODE (ENCyclopedia Of DNA Elements) Project] Science (2004)
* [http://papers.gersteinlab.org/papers/sciam2 The real life of pseudogenes] American Scientist (2006)
* [http://papers.gersteinlab.org/papers/amsci Genomics Confounds Gene Classification] American Scientist (2008)


== Grants ==

We had 3 NIH ENCODE grants
* GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes])
* The ENCODE Data Analysis Center ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC])
* The ENCODE "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip]) 
in addition to the original pilot grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]).


== Misc ==

[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. 

[http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish] about the ENCODE rollout.