Overview of the 2012 ENCODE Rollout

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Papers

Other ENCODE associated papers

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

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

Gencode Pseudogene work

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

Original Pilot Grant Papers

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

Press

Articles about the ENCODE rollout

http://linkstream2.gerstein.info/tag/prencroll0mg

Articles that describe the Gerstein lab's work on the project :

http://linkstream2.gerstein.info/tag/x78qtecore/

An article in Spanish :

http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf

Schematic showing key point of ENCODE networks analysis:

annotation to hairball to interpretable hierarchy

http://archive.gersteinlab.org/mark/out/log/2012/08.28/diag/encodenets--presss-release-schematic--Diagram-4-1.pdf

3 Yale Press Releases on ENCODE (written by Bill Hathaway)

https://docs.google.com/document/d/1q6EYtxN5Ym_0OBwrSm6EtLELfpIG9xmGd38-5O4hAR8/edit#

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