Overview of the 2012 ENCODE Rollout
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| - | The rollout for the ENCODE consortium (Human Genome Annotation) papers occurred in early fall 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. |
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__TOC__ | __TOC__ | ||
| + | [[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]] | ||
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| - | * Papers related to the | + | == Papers == |
| - | + | * Papers related to the 2012 [http://papers.gersteinlab.org/subject/encoderollout ENCODE rollout] | |
| - | http://papers.gersteinlab.org/subject/encoderollout | + | * Papers related to the 2010 [http://papers.gersteinlab.org/subject/modencode modENCODE rollout] |
| - | + | * Papers related to the 2007 [http://papers.gersteinlab.org/subject/encodecore ENCODE pilot rollout] | |
| - | + | * [http://papers.gersteinlab.org/subject/otherencodepapers Other ENCODE associated papers] | |
| - | * | + | * [http://papers.gersteinlab.org/subject/encode-pgenes Gencode pseudogenes work] |
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| - | http://papers.gersteinlab.org/subject/ | + | |
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| - | http://papers.gersteinlab.org/subject/ | + | |
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| - | http://papers.gersteinlab.org/subject/ | + | |
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| - | http://papers.gersteinlab.org/subject/encode | + | |
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== Press == | == 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] and [http://www.reuters.com/article/2012/09/05/us-usa-health-junk-dna-idUSBRE88414V20120905 Reuters] articles on the ENCODE rollout | |
| - | * [http:// | + | * [http://linkstream2.gerstein.info/tag/x78qtecore/ Other key articles] that describe the lab's work on the rollout |
| - | + | * [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 | |
| - | * [http://linkstream2.gerstein.info/tag/x78qtecore/ | + | * [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) |
| - | * [http:// | + | |
| - | * [http://archive.gersteinlab.org/mark/out/log/2012/08.28/diag/encodenets--presss-release-schematic--Diagram-4-1.pdf | + | |
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== Talks == | == Talks == | ||
| + | * [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]) | ||
| + | * 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 | ||
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| - | + | == Subway Map == | |
| + | 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. | ||
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| - | http:// | + | == 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) | |
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| - | + | == Grants == | |
| + | * For the current ENCODE "build out", we are part of the [http://projectreporter.nih.gov/project_info_description.cfm?aid=8402447 data analysis grant] | ||
| + | * For the ENCODE scale up, we had 3 NIH grants | ||
| + | ** GENCODE ([http://papers.gersteinlab.org/subject/encode-pgenes NIH-encode-pgenes]) | ||
| + | ** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8107695 NIH-encode-DAC]) | ||
| + | ** The "chip center" ([http://projectreporter.nih.gov/project_info_description.cfm?aid=8325805 NIH-encode-chip]) | ||
| + | * For modENCODE, we have been part of 3 NIH grants | ||
| + | ** The Data Analysis Center (DAC) ([http://projectreporter.nih.gov/project_info_description.cfm?projectnumber=1RC2HG005639-01 NIH-modencode-DAC]) | ||
| + | ** Transcriptome Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=7853828&icde=0 NIH-modencode-GT] | ||
| + | ** Regulation Project [http://projectreporter.nih.gov/project_info_description.cfm?aid=8249231&icde=0 NIH-modENCODE-TR] | ||
| + | * For the initial ENCODE pilot, we had one grant ([http://papers.gersteinlab.org/subject/encode papers], [http://encode.gersteinlab.org website]). | ||
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| - | http:// | + | == 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. |
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
- 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.
