Overview of the 2012 ENCODE Rollout

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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


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

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

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