Overview of the 2012 ENCODE Rollout

From GersteinInfo

The rollout for the ENCODE consortium (Human Genome Annotation) papers occurred in early fall 2012. The Gerstein lab is associated with 10 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.

Contents 1 Papers 2 Press 3 Talks 4 Subway Map 5 Easy to Read Introductory Papers

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

• Original Pilot Grant Papers

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

• Yale website for ENCODE pilot project

http://encode.gersteinlab.org/

Press

• Articles about the ENCODE rollout
• ENCODE floods the news networks… - The OpenHelix Blog
• Articles that describe the Gerstein lab's work on the project
• An article in Spanish
• Schematic showing key point of ENCODE networks analysis: annotation to hairball to interpretable hierarchy
• 3 Yale Press Releases on ENCODE (written by Bill Hathaway)

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