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 article on ENCODE
- Occupy comes to DNA: A genome for the 99 percent - Reuters article that uses Mark's comment in its title
- other key articles that describe the Gerstein 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
We had 3 NIH ENCODE grants
- GENCODE (NIH-encode-pgenes)
- The ENCODE Data Analysis Center (NIH-encode-DAC)
- The ENCODE "chip center" (NIH-encode-chip)
in addition to the original pilot 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.