From GersteinInfo

Contents 1 Gerstein Lab publications for ENCODE 3 rollout 1.1 Core Papers 1.2 Companion Papers 1.3 Lectures & Images 1.4 News & Media Coverage 1.5 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.

• Summary http://papers.gersteinlab.org/subject/encode3rollout/index.html

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
• 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
• 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

• TBD

Figures & Videos

• Figures on ENCODE3 rollout (Google Slide)
• ENCODEC Rewiring of Gene Regulatory Network (YouTube link)
• ENCODEC Figure Evolution (YouTube link) (Source)