Encode3rollout
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= Gerstein Lab publications for ENCODE 3 rollout = | = Gerstein Lab publications for ENCODE 3 rollout = | ||
| - | * Summary http://papers.gersteinlab.org/subject/encode3rollout/index.html | + | |
| + | [[File:encode3.png|800px]] | ||
| + | |||
| + | 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). | ||
| + | |||
| + | * Paper Summary http://papers.gersteinlab.org/subject/encode3rollout/index.html | ||
| + | |||
| + | == Nature Special Issue == | ||
| + | * Landing Page https://www.nature.com/immersive/d42859-020-00027-2/index.html | ||
| + | * Collections Page https://www.nature.com/collections/dggcchgghg | ||
| + | * Additional Research Papers https://www.nature.com/collections/dggcchgghg/additional-research-papers | ||
| + | * ENCODE Portal Publications Page https://www.encodeproject.org/publications/ | ||
== Core Papers == | == Core Papers == | ||
| - | * | + | * Perspectives on ENCODE http://papers.gersteinlab.org/papers/encode3perspective/index.html (https://doi.org/10.1038/s41586-020-2449-8) |
| - | * ENCODEC http://papers.gersteinlab.org/papers/encodec/index.html | + | * 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) |
| - | * RADAR http://papers.gersteinlab.org/papers/radar/index.html | + | * ENCODEC http://papers.gersteinlab.org/papers/encodec/index.html (https://www.nature.com/articles/s41467-020-14743-w) |
| - | * MatchFilter http://papers.gersteinlab.org/papers/matchfilter/index.html | + | * RADAR http://papers.gersteinlab.org/papers/radar/index.html (https://doi.org/10.1186/s13059-020-01979-4) |
| - | * Mouse Pseudogene http://papers.gersteinlab.org/papers/ | + | * MatchFilter http://papers.gersteinlab.org/papers/matchfilter/index.html (https://www.nature.com/articles/s41592-020-0907-8) |
| + | * Mouse Pseudogene http://papers.gersteinlab.org/papers/mspgenes/index.html (https://www.nature.com/articles/s41467-020-17157-w) | ||
| - | == | + | == Companion Papers == |
* ESPRNN http://papers.gersteinlab.org/papers/esprnn/index.html | * ESPRNN http://papers.gersteinlab.org/papers/esprnn/index.html | ||
| - | * DINER | + | * DINER http://papers.gersteinlab.org/papers/diner/index.html |
| + | * TopicNet http://papers.gersteinlab.org/papers/tfmem/index.html | ||
| + | |||
| + | == Lectures & Images == | ||
| + | * http://lectures.gersteinlab.org/summary/Annotation-Variants-Dysregulation-Cancer--20190614-i0lon19+bern/ | ||
| + | |||
| + | == News & Media Coverage == | ||
| + | * Yale News (https://news.yale.edu/2020/07/30/insights-outcomes-new-spin-quantum-research-and-biology-sex) | ||
| + | * NHGRI News (https://www.genome.gov/news/news-release/NHGRI-funded-project-creates-encyclopedia-detailing-inner-workings-of-human-and-mouse-genomes) | ||
| + | * Nature News and Views (https://www.nature.com/articles/d41586-020-02139-1) | ||
| + | |||
| + | == Figures & Videos == | ||
| + | * Figures on ENCODE3 rollout [https://docs.google.com/presentation/d/1UIT5QfAr7YgNBazU7XbuBA5u9dcZTaBkFZz6HWsBdRI/edit?usp=sharing (Google Slide)] | ||
| + | * ENCODEC Network Rewiring [https://youtu.be/g3R0xv3x2Wc (YouTube link)] [http://files.gersteinlab.org/public-docs/2020/07.23/ENCODEC_rewiring_animation.mov (Source)] | ||
| + | * 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
- Landing Page https://www.nature.com/immersive/d42859-020-00027-2/index.html
- Collections Page https://www.nature.com/collections/dggcchgghg
- Additional Research Papers https://www.nature.com/collections/dggcchgghg/additional-research-papers
- ENCODE Portal Publications Page https://www.encodeproject.org/publications/
Core Papers
- Perspectives on ENCODE http://papers.gersteinlab.org/papers/encode3perspective/index.html (https://doi.org/10.1038/s41586-020-2449-8)
- 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)
- ENCODEC http://papers.gersteinlab.org/papers/encodec/index.html (https://www.nature.com/articles/s41467-020-14743-w)
- RADAR http://papers.gersteinlab.org/papers/radar/index.html (https://doi.org/10.1186/s13059-020-01979-4)
- MatchFilter http://papers.gersteinlab.org/papers/matchfilter/index.html (https://www.nature.com/articles/s41592-020-0907-8)
- Mouse Pseudogene http://papers.gersteinlab.org/papers/mspgenes/index.html (https://www.nature.com/articles/s41467-020-17157-w)
Companion Papers
- ESPRNN http://papers.gersteinlab.org/papers/esprnn/index.html
- DINER http://papers.gersteinlab.org/papers/diner/index.html
- TopicNet http://papers.gersteinlab.org/papers/tfmem/index.html
Lectures & Images
News & Media Coverage
- Yale News (https://news.yale.edu/2020/07/30/insights-outcomes-new-spin-quantum-research-and-biology-sex)
- NHGRI News (https://www.genome.gov/news/news-release/NHGRI-funded-project-creates-encyclopedia-detailing-inner-workings-of-human-and-mouse-genomes)
- Nature News and Views (https://www.nature.com/articles/d41586-020-02139-1)
Figures & Videos
- Figures on ENCODE3 rollout (Google Slide)
- ENCODEC Network Rewiring (YouTube link) (Source)
- ENCODEC Figure Evolution (YouTube link) (Source)
