Overview of the 2012 ENCODE Rollout

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== Press ==  
== Press ==  
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* [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] and [http://www.reuters.com/article/2012/09/05/us-usa-health-junk-dna-idUSBRE88414V20120905 Reuters] articles on the ENCODE rollout
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* [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
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* [http://linkstream2.gerstein.info/tag/x78qtecore/ Other key articles] that describe the lab's work on the rollout
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* [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
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* [http://linkstream2.gerstein.info/tag/prencroll0mg Even more articles] about the rollout (including a  [http://linkstream2.gerstein.info/tag/x78qtenc subset of them] specifically mentioning the lab) and a comprehensive [http://blog.openhelix.eu/?p=13613 OpenHelix Blog] entry that has lots of annotated press links  
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* [http://linkstream2.gerstein.info/tag/x78qtecore/ other key articles that describe the Gerstein lab's work on the rollout]
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* [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)
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* [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
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* [http://www.genome.gov/27549810 NHGRI press release on ENCODE]
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* [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)
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** 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
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== Talks ==
== Talks ==
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* [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://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])
* 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])
* 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])
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== Subway Map ==
== Subway Map ==
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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
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We have created a [[Media: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.
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== Grants ==
== Grants ==
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* For the current ENCODE "build out", we are part of the [http://projectreporter.nih.gov/project_info_description.cfm?aid=8402447 data analysis grant]
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We had 3 NIH ENCODE grants
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* For the ENCODE scale up, we had 3 NIH grants
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* GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes])
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** GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes])
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* The ENCODE Data Analysis Center ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC])
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** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC])
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* The ENCODE "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip])  
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** The "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip])  
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in addition to the original pilot grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]).
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* For modENCODE, we have been part of 3 NIH grants
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** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?projectnumber=1RC2HG005639-01 NIH-modencode-DAC])
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** Transcriptome Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=7853828&icde=0 NIH-modencode-GT]
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** Regulation Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=8249231&icde=0 NIH-modENCODE-TR]
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* For the initial ENCODE pilot, we had one grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]).
== Misc ==
== Misc ==
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[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://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://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish] about the ENCODE rollout.
[http://archive.gersteinlab.org/mark/out/log/2012/09.09/encoderollout-PR/P038MAD_SOC06092012038_1.pdf An article in Spanish] about the ENCODE rollout.

Latest revision as of 01:09, 12 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.

Contents


         


Papers


Press

Talks


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.


Grants


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.

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