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Identification of functional elements and regulatory circuits by Drosophila modENCODE.(RESEARCH ARTICLES)(Author abstract)(Report)

Sushmita Roy ; Jason Ernst ; Peter V. Kharchenko ; Pouya Kheradpour ; Nicolas Negre ; Matthew L. Eaton ; Jane M. Landolin ; Christopher A. Bristow ; Lijia Ma ; Michael F. Lin ; Stefan Washietl ; Bradley I. Arshinoff ; Ferhat Ay ; Patrick E. Meyer ; Nicolas Robine ; Nicole L. Washington ; Luisa Di Stefano ; Eugene Berezikov ; Christopher D. Brown ; Rogerio Candeias ; Joseph W. Carlson ; Adrian Carr ; Irwin Jungreis ; Daniel Marbach ; Rachel Sealfon ; Michael Y. Tolstorukov ; Sebastian Will ; Artyom A. Alekseyenko ; Carlo Artieri ; Benjamin W. Booth ; Angela N. Brooks ; Qi Dai ; Carrie A. Davis ; Michael O. Duff ; Xin Feng ; Andrey A. Gorchakov ; Tingting Gu ; Jorja G. Henikoff ; Philipp Kapranov ; Renhua Li ; Heather K. Macalpine ; John Malone ; Aki Minoda ; Jared Nordman ; Katsutomo Okamura ; Marc Perry ; Sara K. Powell ; Nicole C. Riddle ; Akiko Sakai ; Anastasia Samsonova ; Jeremy E. Sandler ; Yuri B. Schwartz ; Noa Sher ; Rebecca Spokony ; David Sturgill ; Marijke van Baren ; Kenneth H. Wan ; Li Yang ; Charles Yu ; Elise Feingold ; Peter Good ; Mark Guyer ; Rebecca Lowdon ; Kami Ahmad ; Justen Andrews ; Bonnie Berger ; Steven E. Brenner ; Michael R. Brent ; Lucy Cherbas ; Sarah C. R. Elgin ; Thomas R. Gingeras ; Robert Grossman ; Roger A. Hoskins ; Thomas C. Kaufman ; William Kent ; Mitzi I. Kuroda ; Terry Orr-Weaver ; Norbert Perrimon ; Vincenzo Pirrotta ; James W. Posakony ; Bing Ren ; Steven Russell ; Peter Cherbas ; Brenton R. Graveley ; Suzanna Lewis ; Gos Micklem ; Brian Oliver ; Peter J. Park ; Susan E. Celniker ; Steven Henikoff ; Gary H. Karpen ; Eric C. Lai ; David M. Macalpine ; Lincoln D. Stein ; Kevin P. White ; Manolis Kellis;

Science, Dec 24, 2010, Vol.330(6012), p.1787(11) [Peer Reviewed Journal]

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Human body epigenome maps reveal noncanonical DNA methylation variation.(RESEARCH: LETTER)(Report)

Schultz, Matthew D. ; He, Yupeng ; Whitaker, John W. ; Hariharan, Manoj ; Mukamel, Eran A. ; Leung, Danny ; Rajagopal, Nisha ; Nery, Joseph R. ; Urich, Mark A. ; Chen, Huaming ; Lin, Shin ; Lin, Yiing ; Jung, Inkyung ; Schmitt, Anthony D. ; Selvaraj, Siddarth ; Ren, Bing ; Sejnowski, Terrence J. ; Wang, Wei ; Ecker, Joseph R.

Nature, July 9, 2015, Vol.523(7559), p.212(16) [Peer Reviewed Journal]

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Integrative analysis of 111 reference human epigenomes.(RESEARCH: ARTICLE)(Report)

Kundaje, Anshul ; Meuleman, Wouter ; Ernst, Jason ; Bilenky, Misha ; Yen, Angela ; Kheradpour, Pouya ; Zhang, Zhizhuo ; Heravi-Moussavi, Alireza ; Liu, Yaping ; Amin, Viren ; Ziller, Michael J ; Whitaker, John W ; Schultz, Matthew D ; Sandstrom, Richard S ; Eaton, Matthew L ; Wu, Yi-Chieh ; Wang, Jianrong ; Ward, Lucas D ; Sarkar, Abhishek ; Quon, Gerald ; Pfenning, Andreas ; Wang, Xinchen ; Claussnitzer, Melina ; Coarfa, Cristian ; Harris, R Alan ; Shoresh, Noam ; Epstein, Charles B ; Gjoneska, Elizabeta ; Leung, Danny ; Xie, Wei ; Hawkins, R David ; Lister, Ryan ; Hong, Chibo ; Gascard, Philippe ; Mungall, Andrew J ; Moore, Richard ; Chuah, Eric ; Tam, Angela ; Canfield, Theresa K ; Hansen, R Scott ; Kaul, Rajinder ; Sabo, Peter J ; Bansal, Mukul S ; Carles, Annaick ; Dixon, Jesse R ; Farh, Kai-How ; Feizi, Soheil ; Karlic, Rosa ; Kim, Ah-Ram ; Kulkarni, Ashwinikumar ; Li, Daofeng ; Lowdon, Rebecca ; Mercer, Tim R ; Neph, Shane J ; Onuchic, Vitor ; Polak, Paz ; Rajagopal, Nisha ; Ray, Pradipta ; Sallari, Richard C ; Siebenthall, Kyle T ; Sinnott-Armstrong, Nicholas ; Stevens, Michael ; Thurman, Robert E ; Wu, Jie ; Zhang, Bo ; Zhou, Xin ; Beaudet, Arthur E ; Boyer, Laurie A ; De Jager, Philip ; Farnham, Peggy J ; Fisher, Susan J ; Haussler, David ; Jones, Steven ; Li, Wei ; Marra, Marco ; Mcmanus, Michael T ; Sunyaev, Shamil ; Thomson, James A ; Tlsty, Thea D ; Tsai, Li-Huei ; Wang, Wei ; Waterland, Robert A ; Zhang, Michael ; Chadwick, Lisa H ; Bernstein, Bradley E ; Costello, Joseph F ; Ecker, Joseph R ; Hirst, Martin ; Meissner, Alexander ; Milosavljevic, Aleksandar ; Ren, Bing ; Stamatoyannopoulos, John A ; Wang, Ting ; Kellis, Manolis;

Nature, Feb 19, 2015, Vol.518(7539), p.317(32) [Peer Reviewed Journal]

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The 4D nucleome project.(Report)

Dekker, Job ; Belmont, Andrew S. ; Guttman, Mitchell ; Leshyk, Victor O. ; Lis, John T. ; Lomvardas, Stavros ; Mirny, Leonid A. ; Oshea, Clodagh C. ; Park, Peter J. ; Ren, Bing ; Politz, Joan C. Ritland ; Shendure, Jay ; Zhong, Sheng

Nature, Sept 14, 2017, Vol.549(7671), p.219(8) [Peer Reviewed Journal]

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Topologically associating domains are stable units of replication-timing regulation

Pope, Benjamin ; Ryba, Tyrone ; Dileep, Vishnu ; Yue, Feng ; Wu, Weisheng ; Denas, Olgert ; Vera, Daniel ; Wang, Yanli ; Hansen, R ; Canfield, Theresa ; Thurman, Robert ; Cheng, Yong ; Gülsoy, Günhan ; Dennis, Jonathan ; Snyder, Michael ; Stamatoyannopoulos, John ; Taylor, James ; Hardison, Ross ; Kahveci, Tamer ; Ren, Bing ; Gilbert, David

Nature, Nov 20, 2014, Vol.515(7527), pp.402-5 [Peer Reviewed Journal]

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RAP2 mediates mechanoresponses of the Hippo pathway

Meng, Zhipeng ; Qiu, Yunjiang ; Lin, Kimberly C. ; Kumar, Aditya ; Placone, Jesse K. ; Fang, Cao ; Wang, Kuei - Chun

Nature, August, 2018, Vol.560(7720), p.655 [Peer Reviewed Journal]

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Fine tuning of craniofacial morphology by distant-acting enhancers.(RESEARCH ARTICLE: SUMMARY)(Report)(Author abstract)

Attanasio, Catia ; Nord, Alex S. ; Zhu, Yiwen ; Blow, Matthew J. ; Li, Zirong ; Liberton, Denise K. ; Morrison, Harris ; Plajzer - Frick, Ingrid ; Holt, Amy ; Hosseini, Roya ; Phouanenavong, Sengthavy ; Akiyama, Jennifer A. ; Shoukry, Malak ; Afzal, Veena ; Rubin, Edward M. ; Fitzpatrick, David R. ; Ren, Bing ; Hallgrimsson, Benedikt ; Pennacchio, Len A. ; Visel, Axel

Science, Oct 25, 2013, Vol.342(6157), p.440(1) [Peer Reviewed Journal]

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A map of the cis-regulatory sequences in the mouse genome.(RESEARCH: LETTER)(Report)

Shen, Yin ; Yue, Feng ; Mccleary, David F. ; Ye, Zhen ; Edsall, Lee ; Kuan, Samantha ; Wagner, Ulrich ; Dixon, Jesse ; Lee, Leonard ; Lobanenkov, Victor V. ; Ren, Bing

Nature, August 2, 2012, Vol.488(7409), p.116(5) [Peer Reviewed Journal]

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A high-resolution map of the three-dimensional chromatin interactome in human cells.(RESEARCH: LETTER)(Report)

Jin, Fulai ; Li, Yan ; Dixon, Jesse R. ; Selvaraj, Siddarth ; Ye, Zhen ; Lee, Ah Young ; Yen, Chia-An ; Schmitt, Anthony D. ; Espinoza, Celso A. ; Ren, Bing

Nature, Nov 14, 2013, Vol.503(7475), p.290(5) [Peer Reviewed Journal]

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