Overview of the 2012 ENCODE Rollout

From GersteinInfo

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.

Contents 1 Papers 2 Press 3 Talks 4 Subway Map 5 Easy to Read Introductory Papers 6 Grants

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

Press

• Times article and other key articles that describe the lab's work on the ENCODE rollout
• More
  • More articles about the rollout (including a subset of them specifically mentioning the lab) and a comprehensive OpenHelix Blog entry that has lots of annotated press links
  • Yale Press Releases on ENCODE (written by Bill Hathaway), which includes Schematic showing key point of ENCODE networks analysis: annotation to hairball to interpretable hierarchy
• Misc
  • Article about how CT is aiming to become a genomics hub; adjacent to the story was a timeline highlighting the major genomic achievements in the state.
  • Article in Spanish on the rollout.

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

Grants

• For the scale up, we had 3 NIH ENCODE grants :

GENCODE (NIH-encode-pgenes): http://papers.gersteinlab.org/subject/encode-pgenes

The DAC (NIH-encode-DAC): http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695

The ENCODE "chip center" (NIH-encode-chip) : http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805

• For the initial pilot, we had one grant: http://papers.gersteinlab.org/subject/encode + http://encode.gersteinlab.org

• For the current "build out", we are part of the data analysis grant :

http://projectreporter.nih.gov/project_info_description.cfm?aid=8402447