Overview of the 2012 ENCODE Rollout: Difference between revisions
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[[File:cover_nature_encoderollout.jpg|100px|link=http://www.nature.com/nature/journal/v489/n7414/index.html]] [[File:cover_genomeres_encoderollout.png|100px|link=http://genome.cshlp.org/content/22/9.toc]] | |||
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[[File:cover_science_modencode.png|100px|link=http://www.sciencemag.org/content/330/6012.toc]] [[File:cover_genomeres_modencode.png|100px|link=http://genome.cshlp.org/content/21/2.toc]] | |||
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[[File:cover_nature_encodepilot.jpg|100px|link=http://www.nature.com/nature/journal/v447/n7146/]] [[File:cover_genomeres_encodepilot.png|100px|link=http://genome.cshlp.org/content/17/6.toc]] | |||
* Papers related to the | == Papers == | ||
* Papers related to the 2012 [http://papers.gersteinlab.org/subject/encoderollout ENCODE rollout] | |||
[[File:cover_nature_encoderollout.jpg|100px|link=http://www.nature.com/nature/journal/v489/n7414/index.html]] [[File:cover_genomeres_encoderollout.png|100px|link=http://genome.cshlp.org/content/22/9.toc]] | |||
* Papers related to the 2010 [http://papers.gersteinlab.org/subject/modencode modENCODE rollout] | |||
[[File:cover_science_modencode.png|100px|link=http://www.sciencemag.org/content/330/6012.toc]] [[File:cover_genomeres_modencode.png|100px|link=http://genome.cshlp.org/content/21/2.toc]] | |||
http://papers.gersteinlab.org/subject/encodecore | * Papers related to the 2007 [http://papers.gersteinlab.org/subject/encodecore ENCODE pilot rollout] | ||
[[File:cover_nature_encodepilot.jpg|100px|link=http://www.nature.com/nature/journal/v447/n7146/]] [[File:cover_genomeres_encodepilot.png|100px|link=http://genome.cshlp.org/content/17/6.toc]] | |||
* Other ENCODE associated papers | * [http://papers.gersteinlab.org/subject/otherencodepapers Other ENCODE associated papers] | ||
* [http://papers.gersteinlab.org/subject/encode-pgenes Gencode pseudogenes work] | |||
== Press == | |||
* | * [http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?pagewanted=all&_r=0 NY Times article] on ENCODE | ||
* [http://www.reuters.com/article/2012/09/05/us-usa-health-junk-dna-idUSBRE88414V20120905 Occupy comes to DNA: A genome for the 99 percent] - Reuters article that uses Mark's comment in its title | |||
http:// | * [http://linkstream2.gerstein.info/tag/x78qtecore/ other key articles that describe the Gerstein lab's work on the rollout] | ||
* [http://linkstream2.gerstein.info/tag/prencroll0mg More articles about the ENCODE rollout] and an [http://blog.openhelix.eu/?p=13613 OpenHelix Blog] entry that has lots of press links | |||
* [http://www.genome.gov/27549810 NHGRI press release on ENCODE] | |||
* [http://news.yale.edu/2012/09/05/yale-team-finds-order-amidst-chaos-within-human-genome-mom-and-dad-s-contributions-counte Yale Press Releases on ENCODE] (written by Bill Hathaway) | |||
** including a [http://archive.gersteinlab.org/mark/out/log/2012/08.28/diag/encodenets--presss-release-schematic--Diagram-4-1.pdf schematic] showing a key point of ENCODE networks analysis: annotation to hairball to interpretable hierarchy | |||
== Talks == | == Talks == | ||
* Slide pack on networks and pseudogenes (pdf & | * [http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb/ Slide pack on networks and pseudogenes] ([http://archive.gersteinlab.org/mark/out/log/2012/05.29/talk/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb.pdf pdf] & [http://archive.gersteinlab.org/mark/out/log/2012/05.29/talk/ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb.ppt ppt]) | ||
http:// | * Another slide pack containing information on [http://lectures.gersteinlab.org/summary/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn/ statistical models relating output expression to genomic inputs] ([http://archive.gersteinlab.org/mark/out/log/2012/09.15/talk/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn.pdf pdf] & [http://archive.gersteinlab.org/mark/out/log/2012/09.15/talk/ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn.ppt ppt]) | ||
* Finally, here's a link to the [http://lectures.gersteinlab.org/summary/Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620/ modENCODE symposium], which has a [http://www.genome.gov/27549319 video] containing bits of the talks above | |||
* Another slide pack containing information on statistical models relating output expression to genomic inputs (pdf & ppt) | |||
http://lectures.gersteinlab.org/summary/ | |||
== Subway Map == | == Subway Map == | ||
We have created a subway map figure showing the overall collaboration in the consortium. There are now coauthor | We have created a [http://homes.gersteinlab.org/people/rar62/subwaymap/SubwayMap8_16_12.pdf subway map figure] (pdf) showing the [https://docs.google.com/spreadsheet/ccc?key=0AvRr07RHaF5cdFZlOFJ1YmdOT2pUM1VEODM1bE5CRHc#gid=0 overall collaboration in the consortium] (gdoc). There are now coauthor | ||
networks labeled/colored by both country and state. | networks labeled/colored by both country and state. | ||
== Introductory Papers == | |||
These introductory papers are easy to read and provide context on the ENCODE rollout. | |||
* [http://papers.gersteinlab.org/papers/encode-annouce The ENCODE (ENCyclopedia Of DNA Elements) Project] Science (2004) | |||
* [http://papers.gersteinlab.org/papers/sciam2 The real life of pseudogenes] American Scientist (2006) | |||
* [http://papers.gersteinlab.org/papers/amsci Genomics Confounds Gene Classification] American Scientist (2008) | |||
== Grants == | == Grants == | ||
We had 3 NIH ENCODE grants | |||
* GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes]) | |||
GENCODE ( | * The ENCODE Data Analysis Center ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC]) | ||
* The ENCODE "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip]) | |||
The | in addition to the original pilot grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]). | ||
== Misc == | |||
[http://articles.courant.com/2012-09-23/news/hc-connecticut-genomics-20120923_1_human-genome-genome-research-uconn-and-jackson Hartford Courant article] about how Connecticut is aiming to become a genomics hub. Adjacent to the story was a [http://archive.gersteinlab.org/mark/out/log/2012/09.29/pic/Courant-Genomics-Timeline-photo.JPG timeline] highlighting the major genomic achievements in the state. | |||
http:// | [http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish] about the ENCODE rollout. | ||
Revision as of 21:11, 10 October 2012
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
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
- More articles about the ENCODE rollout and an OpenHelix Blog entry that has lots of press links
- NHGRI press release on ENCODE
- 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.
