Overview of the 2012 ENCODE Rollout

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.

         

Papers

• Papers related to the 2012 ENCODE rollout
• Papers related to the 2010 modENCODE rollout
• Papers related to the 2007 ENCODE pilot rollout
• Other ENCODE associated papers
• Gencode pseudogenes work

Press

• NY Times and Reuters articles on the ENCODE rollout
• Other key articles that describe the lab's work on the rollout
• Even 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), including a schematic showing a key point of ENCODE networks analysis (annotation to hairball to interpretable hierarchy)

Talks

• Slide pack on networks and pseudogenes (pdf & ppt)
• Another slide pack containing information on statistical models relating output expression to genomic inputs (pdf & ppt)
• Finally, here's a link to the modENCODE symposium, which has a video containing bits of the talks above

Subway Map

We have created a subway map figure (pdf) showing the overall collaboration in the consortium (gdoc). There are now coauthor networks labeled/colored by both country and state.

Introductory Papers

These introductory papers are easy to read and provide context on the ENCODE rollout.

• The ENCODE (ENCyclopedia Of DNA Elements) Project Science (2004)
• The real life of pseudogenes American Scientist (2006)
• Genomics Confounds Gene Classification American Scientist (2008)

Grants

• For the current ENCODE "build out", we are part of the data analysis grant
• For the ENCODE scale up, we had 3 NIH grants
  • GENCODE (NIH-encode-pgenes)
  • The Data Analysis Center (DAC) (NIH-encode-DAC)
  • The "chip center" (NIH-encode-chip)
• For modENCODE, we have been part of 3 NIH grants
  • The Data Analysis Center (DAC) (NIH-modencode-DAC)
  • Transcriptome Project NIH-modencode-GT
  • Regulation Project NIH-modENCODE-TR
• For the initial ENCODE pilot, we had one grant (papers, website).

Misc

Hartford Courant article about how Connecticut is aiming to become a genomics hub. Adjacent to the story was a timeline highlighting the major genomic achievements in the state.

An article in Spanish about the ENCODE rollout.