Encode3rollout

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= Gerstein Lab publications for ENCODE 3 rollout =
= Gerstein Lab publications for ENCODE 3 rollout =
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* Summary http://papers.gersteinlab.org/subject/encode3rollout/index.html
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[[File:encode3.png|800px]]
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The ENCODE project has been extended to model organisms, particularly the mouse. Through the third phase of ENCODE (ENCODE 3) nearly a million and more than 300K cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community. The rollout for the ENCODE consortium phase 3 papers occurred in 7/29/2020. The Gerstein lab is associated with 9 papers (6 core and 3 companion papers).
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* Paper Summary http://papers.gersteinlab.org/subject/encode3rollout/index.html
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== Nature Special Issue ==
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* Landing Page https://www.nature.com/immersive/d42859-020-00027-2/index.html
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* Collections Page https://www.nature.com/collections/dggcchgghg
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* Additional Research Papers https://www.nature.com/collections/dggcchgghg/additional-research-papers
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* ENCODE Portal Publications Page https://www.encodeproject.org/publications/
== Core Papers ==
== Core Papers ==
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* Encyclopedia Marker Paper TBD
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* Perspectives on ENCODE http://papers.gersteinlab.org/papers/encode3perspective/index.html (https://doi.org/10.1038/s41586-020-2449-8)
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* ENCODEC http://papers.gersteinlab.org/papers/encodec/index.html
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* Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes http://papers.gersteinlab.org/papers/encode3main/index.html (https://doi.org/10.1038/s41586-020-2493-4)
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* RADAR http://papers.gersteinlab.org/papers/radar/index.html
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* ENCODEC http://papers.gersteinlab.org/papers/encodec/index.html (https://www.nature.com/articles/s41467-020-14743-w)
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* MatchFilter http://papers.gersteinlab.org/papers/matchfilter/index.html
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* RADAR http://papers.gersteinlab.org/papers/radar/index.html (https://doi.org/10.1186/s13059-020-01979-4)
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* Mouse Pseudogene http://papers.gersteinlab.org/papers/mspgenes/index.html
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* MatchFilter http://papers.gersteinlab.org/papers/matchfilter/index.html (https://www.nature.com/articles/s41592-020-0907-8)
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* Mouse Pseudogene http://papers.gersteinlab.org/papers/mspgenes/index.html (https://www.nature.com/articles/s41467-020-17157-w)
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== Related Papers ==
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== Companion Papers ==
* ESPRNN http://papers.gersteinlab.org/papers/esprnn/index.html
* ESPRNN http://papers.gersteinlab.org/papers/esprnn/index.html
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* DINER TBD
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* DINER http://papers.gersteinlab.org/papers/diner/index.html
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* TopicNet http://papers.gersteinlab.org/papers/tfmem/index.html
== Lectures & Images ==
== Lectures & Images ==
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http://lectures.gersteinlab.org/summary/Annotation-Variants-Dysregulation-Cancer--20190614-i0lon19+bern/
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* http://lectures.gersteinlab.org/summary/Annotation-Variants-Dysregulation-Cancer--20190614-i0lon19+bern/
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== News & Media Coverage ==
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* Yale News (https://news.yale.edu/2020/07/30/insights-outcomes-new-spin-quantum-research-and-biology-sex)
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* NHGRI News (https://www.genome.gov/news/news-release/NHGRI-funded-project-creates-encyclopedia-detailing-inner-workings-of-human-and-mouse-genomes)
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* Nature News and Views (https://www.nature.com/articles/d41586-020-02139-1)
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== Figures & Videos ==
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* Figures on ENCODE3 rollout [https://docs.google.com/presentation/d/1UIT5QfAr7YgNBazU7XbuBA5u9dcZTaBkFZz6HWsBdRI/edit?usp=sharing (Google Slide)]
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* ENCODEC Network Rewiring [https://youtu.be/g3R0xv3x2Wc (YouTube link)] [http://files.gersteinlab.org/public-docs/2020/07.23/ENCODEC_rewiring_animation.mov (Source)]
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* ENCODEC Figure Evolution [https://youtu.be/MQMBdqO1Tzs (YouTube link)] [http://files.gersteinlab.org/public-docs/2020/06.02/ENCODEC_figure_evolution.mp4 (Source)]

Latest revision as of 23:19, 31 July 2020

Contents

Gerstein Lab publications for ENCODE 3 rollout

The ENCODE project has been extended to model organisms, particularly the mouse. Through the third phase of ENCODE (ENCODE 3) nearly a million and more than 300K cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community. The rollout for the ENCODE consortium phase 3 papers occurred in 7/29/2020. The Gerstein lab is associated with 9 papers (6 core and 3 companion papers).

Nature Special Issue

Core Papers

Companion Papers

Lectures & Images

News & Media Coverage

Figures & Videos

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