Overview of the 2012 ENCODE Rollout

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.

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

2 * Slide pack on networks and pseudogenes (pdf & ppt): http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb/

3 * 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--20120604-i0ucla/

4 * Finally, here's a link to the modENCODE symposium, which has a video containing bits of the talks above: http://www.genome.gov/27549319

Subway Map

We have created another iteration of the subway map figures using the most recent data located in the google docs. There are now coauthor networks labeled/colored by both country and state.

The new figures are located here: 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