14 Papers
13 Citations
Bing Ren is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Chromatin & Epigenomics. The author has an hindex of 8, co-authored 14 publications. Previous affiliations of Bing Ren include University of California, Berkeley & Ludwig Institute for Cancer Research.
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Papers
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Jill Moore,Michael J. Purcaro,Henry Pratt,Charles B. Epstein,Noam Shoresh,Jessika Adrian,Trupti Kawli,Carrie A. Davis,Alexander Dobin,Rajinder Kaul,Jessica Halow,Eric L. Van Nostrand,Peter Freese,David U. Gorkin,David U. Gorkin,Yin Shen,Yin Shen,Yupeng He,Mark Mackiewicz,Florencia Pauli-Behn,Brian A. Williams,Ali Mortazavi,Cheryl A. Keller,Xiao-Ou Zhang,Shaimae I. Elhajjajy,Jack Huey,Diane E. Dickel,Valentina Snetkova,Xintao Wei,Xiaofeng Wang,Xiaofeng Wang,Juan Carlos Rivera-Mulia,Juan Carlos Rivera-Mulia,Joel Rozowsky,Jing Zhang,Surya B. Chhetri,Jialing Zhang,Alec Victorsen,Kevin P. White,Axel Visel,Axel Visel,Gene W. Yeo,Christopher B. Burge,Eric Lécuyer,Eric Lécuyer,David M. Gilbert,Job Dekker,John L. Rinn,Eric M. Mendenhall,Joseph R. Ecker,Manolis Kellis,Manolis Kellis,Robert J. Klein,William Stafford Noble,Anshul Kundaje,Roderic Guigó,Peggy J. Farnham,J. Michael Cherry,Richard M. Myers,Bing Ren,Bing Ren,Brenton R. Graveley,Mark Gerstein,Len A. Pennacchio,Len A. Pennacchio,Michael Snyder,Bradley E. Bernstein,Barbara J. Wold,Ross C. Hardison,Thomas R. Gingeras,John A. Stamatoyannopoulos,Zhiping Weng,Zhiping Weng,Zhiping Weng +73 more
TL;DR: The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development.
An atlas of dynamic chromatin landscapes in mouse fetal development
David U. Gorkin,David U. Gorkin,Iros Barozzi,Iros Barozzi,Yuan Zhao,Yuan Zhao,Yanxiao Zhang,Hui Huang,Hui Huang,Ah Young Lee,Bin Li,Joshua Chiou,Andre Wildberg,Bo Ding,Bo Zhang,Mengchi Wang,J. Seth Strattan,Jean M. Davidson,Yunjiang Qiu,Yunjiang Qiu,Veena Afzal,Jennifer A. Akiyama,Ingrid Plajzer-Frick,Catherine S. Novak,Momoe Kato,Tyler H. Garvin,Quan T. Pham,Anne N. Harrington,Brandon J. Mannion,Elizabeth Lee,Yoko Fukuda-Yuzawa,Yupeng He,Yupeng He,Sebastian Preissl,Sebastian Preissl,Sora Chee,Jee Yun Han,Brian A. Williams,Diane Trout,Henry Amrhein,Hongbo Yang,J. Michael Cherry,Wei Wang,Kyle J. Gaulton,Joseph R. Ecker,Yin Shen,Diane E. Dickel,Axel Visel,Axel Visel,Axel Visel,Len A. Pennacchio,Len A. Pennacchio,Len A. Pennacchio,Bing Ren +53 more
TL;DR: Analysis of chromatin state and accessibility in mouse tissues from twelve sites and eight developmental stages provides the most comprehensive view of Chromatin dynamics to date.
Perspectives on ENCODE.
Michael Snyder,Thomas R. Gingeras,Jill Moore,Zhiping Weng,Zhiping Weng,Zhiping Weng,Mark Gerstein,Bing Ren,Bing Ren,Ross C. Hardison,John A. Stamatoyannopoulos,Brenton R. Graveley,Elise A. Feingold,Michael J. Pazin,Michael Pagan,Daniel A. Gilchrist,Benjamin C. Hitz,J. Michael Cherry,Bradley E. Bernstein,Eric M. Mendenhall,Daniel R. Zerbino,Adam Frankish,Paul Flicek,Richard M. Myers +23 more
TL;DR: In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
Peng He,Peng He,Brian A. Williams,Diane Trout,Georgi K. Marinov,Henry Amrhein,Libera Berghella,Say Tar Goh,Ingrid Plajzer-Frick,Veena Afzal,Len A. Pennacchio,Len A. Pennacchio,Diane E. Dickel,Axel Visel,Axel Visel,Bing Ren,Ross C. Hardison,Yu Zhang,Barbara J. Wold +18 more
TL;DR: This systematic quantification of mouse polyA-RNA from day 10.5 of embryonic development to birth found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types.
Spatiotemporal DNA methylome dynamics of the developing mouse fetus.
Yupeng He,Yupeng He,Manoj Hariharan,David U. Gorkin,Diane E. Dickel,Chongyuan Luo,Rosa Castanon,Joseph R. Nery,Ah Young Lee,Yuan Zhao,Yuan Zhao,Hui Huang,Hui Huang,Brian A. Williams,Diane Trout,Henry Amrhein,Rongxin Fang,Rongxin Fang,Huaming Chen,Bin Li,Axel Visel,Axel Visel,Len A. Pennacchio,Len A. Pennacchio,Bing Ren,Bing Ren,Joseph R. Ecker +26 more
TL;DR: These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.