From GersteinInfo

Contents 1 Gerstein Lab publications for ENCODE 3 rollout 1.1 Nature Special Issue 1.2 Core Papers 1.3 Companion Papers 1.4 Lectures & Images 1.5 News & Media Coverage 1.6 Figures & Videos

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 (5 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

• Perspectives on ENCODE (https://doi.org/10.1038/s41586-020-2449-8)
• Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes (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

• 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 (Google Slide)
• ENCODEC Network Rewiring (YouTube link) (Source)
• ENCODEC Figure Evolution (YouTube link) (Source)