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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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Evidence of abundant purifying selection in humans for recently acquired regulatory functions.(REPORTS)(Report)(Author abstract)

Ward, Lucas D. ; Kellis, Manolis

Science, Sept 28, 2012, Vol.337(6102), p.1675(4) [Peer Reviewed Journal]

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Response to Comment on "Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions"

Ward, Lucas ; Kellis, Manolis

Science, May 10, 2013, Vol.340(6133), pp.682-682 [Peer Reviewed Journal]

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Survey of variation in human transcription factors reveals prevalent DNA binding changes.(PROTEIN EVOLUTION)(Author abstract)

Barrera, Luis ; Vedenko, Anastasia ; Kurland, Jesse ; Rogers, Julia ; Gisselbrecht, Stephen ; Rossin, Elizabeth ; Woodard, Jaie ; Mariani, Luca ; Inukai, Sachi ; Siggers, Trevor ; Shokri, Leila ; Gordân, Raluca ; Sahni, Nidhi ; Cotsapas, Chris ; Tong, Hao ; Song, Yi ; Kellis, Manolis ; Daly, Mark ; Vidal, Marc ; Hill, David ; Bulyk, Martha ; Barrera, Luis ; Vedenko, Anastasia ; Kurland, Jesse ; Rogers, Julia ; Gisselbrecht, Stephen ; Rossin, Elizabeth ; Woodard, Jaie ; Mariani, Luca ; Inukai, Sachi ; Siggers, Trevor ; Shokri, Leila ; Gordân, Raluca ; Sahni, Nidhi ; Cotsapas, Chris ; Tong, Hao;

Science, March 25, 2016, Vol.351(6280), p.1450(5) [Peer Reviewed Journal]

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Common genetic variants modulate pathogen-sensing responses in human dendritic cells.(RESEARCH ARTICLE SUMMARY)(Author abstract)

Lee, Mark N. ; Ye, Chun ; Villani, Alexandra - Chloe ; Raj, Towfique ; Li, Weibo ; Eisenhaure, Thomas M. ; Imboywa, Selina H. ; Chipendo, Portia I. ; Ran, F. Ann ; Slowikowski, Kamil ; Ward, Lucas D. ; Raddassi, Khadir ; Mccabe, Cristin ; Lee, Michelle H. ; Frohlich, Irene Y. ; Hafler, David A. ; Kellis, Manolis ; Raychaudhuri, Soumya ; Zhang, Feng ; Stranger, Barbara E. ; Benoist, Christophe O. ; De Jager, Philip L. ; Regev, Aviv ; Hacohen, Nir

Science, March 7, 2014, Vol.343(6175), p.1119(1) [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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An integrated encyclopedia of DNA elements in the human genome: the ENCODE project consortium.(Report)

Anonymous;

Nature, Sept 6, 2012, Vol.489(7414), p.57(18) [Peer Reviewed Journal]

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Three periods of regulatory innovation during vertebrate evolution.(REPORTS)(Author abstract)

Lowe, Craig B. ; Kellis, Manolis ; Siepel, Adam ; Raney, Brian J. ; Clamp, Michele ; Salama, Sofie R. ; Kingsley, David M. ; Lindblad - Toh, Kerstin ; Haussler, David

Science, August 19, 2011, Vol.333(6045), p.1019(6) [Peer Reviewed Journal]

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Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.(RESEARCH: LETTER)(Report)

Rouskin, Silvi ; Zubradt, Meghan ; Washietl, Stefan ; Kellis, Manolis ; Weissman, Jonathan S.

Nature, Jan 30, 2014, Vol.505(7485), p.701(17) [Peer Reviewed Journal]

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A high-resolution map of human evolutionary constraint using 29 mammals.(Report)

Lindblad-Toh, Kerstin ; Garber, Manuel ; Zuk, Or ; Lin, Michael F. ; Parker, Brian J. ; Washietl, Stefan ; Kheradpour, Pouya ; Ernst, Jason ; Jordan, Gregory ; Mauceli, Evan ; Ward, Lucas D. ; Lowe, Craig B. ; Holloway, Alisha K. ; Clamp, Michele ; Gnerre, Sante ; Alfoeldi, Jessica ; Beal, Kathryn ; Chang, Jean ; Clawson, Hiram ; Cuff, James ; Di Palma, Federica ; Fitzgerald, Stephen ; Flicek, Paul ; Guttman, Mitchell ; Hubisz, Melissa J. ; Jaffe, David B. ; Jungreis, Irwin ; Kent, W. James ; Kostka, Dennis ; Lara, Marcia ; Martins, Andre L. ; Massingham, Tim ; Moltke, Ida ; Raney, Brian J. ; Rasmussen, Matthew D. ; Robinson, Jim ; Stark, Alexander ; Vilella, Albert J. ; Wen, Jiayu ; Xie, Xiaohui ; Zody, Michael C. ; Worley, Kim C. ; Kovar, Christie L. ; Muzny, Donna M. ; Gibbs, Richard A. ; Warren, Wesley C. ; Mardis, Elaine R. ; Weinstock, George M. ; Wilson, Richard K. ; Birney, Ewan ; Margulies, Elliott H. ; Herrero, Javier ; Green, Eric D. ; Haussler, David ; Siepel, Adam ; Goldman, Nick ; Pollard, Katherine S. ; Pedersen, Jakob S. ; Lander, Eric S. ; Kellis, Manolis;

Nature, Oct 27, 2011, Vol.478(7370), p.476(7) [Peer Reviewed Journal]

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