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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)

Dunham, Ian ; Kundaje, Anshul ; Aldred, Shelley F. ; Collins, Patrick J. ; Davis, Carrie A. ; Doyle, Francis ; Epstein, Charles B. ; Frietze, Seth ; Harrow, Jennifer ; Kaul, Rajinder ; Khatun, Jainab ; Lajoie, Bryan R. ; Landt, Stephen G. ; Lee, Bum - Kyu ; Pauli, Florencia ; Rosenbloom, Kate R. ; Sabo, Peter ; Safi, Alexias ; Sanyal, Amartya ; Shoresh, Noam ; Simon, Jeremy M. ; Song, Lingyun ; Trinklein, Nathan D. ; Altshuler, Robert C. ; Birney, Ewan ; Brown, James B. ; Cheng, Chao ; Djebali, Sarah ; Dong, Xianjun ; Ernst, Jason ; Furey, Terrence S. ; Gerstein, Mark ; Giardine, Belinda ; Greven, Melissa ; Hardison, Ross C. ; Harris, Robert S. ; Herrero, Javier ; Hoffman, Michael M. ; Iyer, Sowmya ; Kellis, Manolis ; Kheradpour, Pouya ; Lassmann, Timo ; Li, Qunhua ; Lin, Xinying ; Marinov, Georgi K. ; Merkel, Angelika ; Mortazavi, Ali ; Parker, Stephen C. J. ; Reddy, Timothy E. ; Rozowsky, Joel ; Schlesinger, Felix ; Thurman, Robert E. ; Wang, Jie ; Ward, Lucas D. ; Whitfield, Troy W. ; Wilder, Steven P. ; Wu, Weisheng ; Xi, Hualin S. ; Yip, Kevin Y. ; Zhuang, Jiali ; Bernstein, Bradley E. ; Green, Eric D. ; Gunter, Chris ; Snyder, Michael ; Pazin, Michael J. ; Lowdon, Rebecca F. ; Dillon, Laura A. L. ; Adams, Leslie B. ; Kelly, Caroline J. ; Zhang, Julia ; Wexler, Judith R. ; Good, Peter J. ; Feingold, Elise A. ; Crawford, Gregory E. ; Dekker, Job ; Elnitski, Laura ; Farnham, Peggy J. ; Giddings, Morgan C. ; Gingeras, Thomas R. ; Guigo, Roderic ; Hubbard, Timothy J. ; Kent, W. James ; Lieb, Jason D. ; Margulies, Elliott H. ; Myers, Richard M. ; Stamatoyannopoulos, John A. ; Tenenbaum, Scott A. ; Weng, Zhiping ; White, Kevin P. ; Wold, Barbara ; Yu, Yanbao ; Wrobel, John ; Risk, Brian A. ; Gunawardena, Harsha P. ; Kuiper, Heather C. ; Maier, Christopher W. ; Xie, Ling ; Chen, Xian ; Mikkelsen, Tarjei S. ; Gillespie, Shawn ; Goren, Alon ; Ram, Oren ; Zhang, Xiaolan ; Wang, Li ; Issner, Robbyn ; Coyne, Michael J. ; Durham, Timothy ; Ku, Manching ; Truong, Thanh ; Eaton, Matthew L. ; Dobin, Alex ; Tanzer, Andrea ; Lagarde, Julien ; Lin, Wei ; Xue, Chenghai ; Williams, Brian A. ; Zaleski, Chris ; Roder, Maik ; Kokocinski, Felix ; Abdelhamid, Rehab F. ; Alioto, Tyler ; Antoshechkin, Igor ; Baer, Michael T. ; Batut, Philippe ; Bell, Ian ; Bell, Kimberly ; Chakrabortty, Sudipto ; Chrast, Jacqueline ; Curado, Joao ; Derrien, Thomas ; Drenkow, Jorg ; Dumais, Erica ; Dumais, Jackie ; Duttagupta, Radha ; Fastuca, Megan ; Fejes - Toth, Kata ; Ferreira, Pedro ; Foissac, Sylvain ; Fullwood, Melissa J. ; Gao, Hui ; Gonzalez, David ; Gordon, Assaf ; Howald, Cedric ; Jha, Sonali ; Johnson, Rory ; Kapranov, Philipp ; King, Brandon ; Kingswood, Colin ; Li, Guoliang ; Luo, Oscar J. ; Park, Eddie ; Preall, Jonathan B. ; Presaud, Kimberly ; Ribeca, Paolo ; Robyr, Daniel ; Ruan, Xiaoan ; Sammeth, Michael ; Sandhu, Kuljeet Singh ; Schaeffer, Lorain ; See, Lei - Hoon ; Shahab, Atif ; Skancke, Jorgen ; Suzuki, Ana Maria ; Takahashi, Hazuki ; Tilgner, Hagen ; Trout, Diane ; Walters, Nathalie ; Wang, Huaien ; Hayashizaki, Yoshihide ; Reymond, Alexandre ; Antonarakis, Stylianos E. ; Hannon, Gregory J. ; Ruan, Yijun ; Carninci, Piero ; Sloan, Cricket A. ; Learned, Katrina ; Malladi, Venkat S. ; Wong, Matthew C. ; Barber, Galt P. ; Cline, Melissa S. ; Dreszer, Timothy R. ; Heitner, Steven G. ; Karolchik, Donna ; Kirkup, Vanessa M. ; Meyer, Laurence R. ; Long, Jeffrey C. ; Maddren, Morgan ; Raney, Brian J. ; Grasfeder, Linda L. ; Giresi, Paul G. ; Battenhouse, Anna ; Sheffield, Nathan C. ; Showers, Kimberly A. ; London, Darin ; Bhinge, Akshay A. ; Shestak, Christopher ; Schaner, Matthew R. ; Ki Kim, Seul ; Zhang, Zhuzhu Z. ; Mieczkowski, Piotr A. ; Mieczkowska, Joanna O. ; Liu, Zheng ; Mcdaniell, Ryan M. ; Ni, Yunyun ; Rashid, Naim U. ; Kim, Min Jae ; Adar, Sheera ; Zhang, Zhancheng ; Wang, Tianyuan ; Winter, Deborah ; Keefe, Damian ; Iyer, Vishwanath R. ; Zheng, Meizhen ; Wang, Ping ; Gertz, Jason ; Vielmetter, Jost ; Partridge, E. ; Varley, Katherine E. ; Gasper, Clarke ; Bansal, Anita ; Pepke, Shirley ; Jain, Preti ; Amrhein, Henry ; Bowling, Kevin M. ; Anaya, Michael ; Cross, Marie K. ; Muratet, Michael A. ; Newberry, Kimberly M. ; Mccue, Kenneth ; Nesmith, Amy S. ; Fisher - Aylor, Katherine I. ; Pusey, Barbara ; Desalvo, Gilberto ; Parker, Stephanie L. ; Balasubramanian, Sreeram ; Davis, Nicholas S. ; Meadows, Sarah K. ; Eggleston, Tracy ; Newberry, J. Scott ; Levy, Shawn E. ; Absher, Devin M. ; Wong, Wing H. ; Blow, Matthew J. ; Visel, Axel ; Pennachio, Len A. ; Petrykowska, Hanna M. ; Abyzov, Alexej ; Aken, Bronwen ; Barrell, Daniel ; Barson, Gemma;

Nature, Sept 6, 2012, Vol.489(7414), p.57(18) [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 ; Alföldi, 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 ; Baldwin, Jen ; Bloom, Toby ; Chin, Chee Whye ; Heiman, Dave ; Nicol, Robert ; Nusbaum, Chad ; Young, Sarah ; Wilkinson, Jane ; Worley, Kim C ; Kovar, Christie L ; Muzny, Donna M ; Gibbs, Richard A ; Cree, Andrew ; Dihn, Huyen H ; Fowler, Gerald ; Jhangiani, Shalili ; Joshi, Vandita ; Lee, Sandra ; Lewis, Lora R ; Nazareth, Lynne V ; Okwuonu, Geoffrey ; Santibanez, Jireh ; Warren, Wesley C ; Mardis, Elaine R ; Weinstock, George M ; Wilson, Richard K ; Delehaunty, Kim ; Dooling, David ; Fronik, Catrina ; Fulton, Lucinda ; Fulton, Bob ; Graves, Tina ; Minx, Patrick ; Sodergren, Erica ; 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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Comprehensive analysis of the chromatin landscape in drosophila melanogaster.(Report)

Kharchenko, Peter V. ; Alekseyenko, Artyom A. ; Schwartzst, Yuri B. ; Minoda, Aki ; Riddle, Nicole C. ; Ernst, Jason ; Sabo, Peter J. ; Larschan, Erica ; Gorchakov, Andrey A. ; Gu, Tingting ; Linder - Bassos, Daniela ; Plachetka, Annette ; Shanowers, Gregory ; Tolstorukov, Michael Y. ; Luquette, Lovelace J. ; Xi, Ruibin ; Jung, Youngsook L. ; Park, Richard W. ; Bishop, Eric P. ; Canfield, Theresa K. ; Sandstrom, Richard ; Thurman, Robert E. ; Macalpine, David M. ; Stamatoyannopoulos, John A. ; Kellis, Manolis ; Elgin, Sarah C. R. ; Kuroda, Mitzi I. ; Pirrotta, Vincenzo ; Karpen, Gary H. ; Park, Peter J.

Nature, March 24, 2011, Vol.471(7339), p.480(7) [Peer Reviewed Journal]

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Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease.(RESEARCH: LETTER)(Report)

Gjoneska, Elizabeta ; Pfenning, Andreas R. ; Mathys, Hansruedi ; Quon, Gerald ; Kundaje, Anshul ; Tsai, Li-Huei ; Kellis, Manolis

Nature, Feb 19, 2015, Vol.518(7539), p.365(17) [Peer Reviewed Journal]

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Dynamic landscape and regulation of RNA editing in mammals.(Report)

Tan, Meng How ; Li, Qin ; Shanmugam, Raghuvaran ; Piskol, Robert ; Kohler, Jennefer ; Young, Amy N. ; Liu, Kaiwen Ivy ; Zhang, Rui ; Ramaswami, Gokul ; Ariyoshi, Kentaro ; Gupte, Ankita ; Keegan, Liam P. ; George, Cyril X. ; Ramu, Avinash ; Huang, Ni ; Pollina, Elizabeth A. ; Leeman, Dena S. ; Rustighi, Alessandra ; Goh, Y. P. Sharon ; Aguet, Franois ; Ardlie, Kristin G. ; Cummings, Beryl B. ; Gelfand, Ellen T. ; Getz, Gad ; Hadley, Kane ; Handsaker, Robert E. ; Huang, Katherine H. ; Kashin, Seva ; Karczewski, Konrad J. ; Lek, Monkol ; Li, Xiao ; Macarthur, Daniel G. ; Nedzel, Jared L. ; Nguyen, Duyen T. ; Noble, Michael S. ; Segr, Ayellet V. ; Trowbridge, Casandra A. ; Tukiainen, Taru ; Abell, Nathan S. ; Balliu, Brunilda ; Barshir, Ruth ; Basha, Omer ; Battle, Alexis ; Bogu, Gireesh K. ; Brown, Andrew ; Brown, Christopher D. ; Castel, Stephane E. ; Chen, Lin S. ; Chiang, Colby ; Conrad, Donald F. ; Cox, Nancy J. ; Damani, Farhan N. ; Davis, Joe R. ; Delaneau, Olivier ; Dermitzakis, Emmanouil T. ; Engelhardt, Barbara E. ; Eskin, Eleazar ; Ferreira, Pedro G. ; Frsard, Laure ; Gamazon, Eric R. ; Garrido-Martn, Diego ; Gewirtz, Ariel D. H. ; Gliner, Genna ; Gloudemans, Michael J. ; Guigo, Roderic ; Hall, Ira M. ; Han, Buhm ; He, Yuan ; Hormozdiari, Farhad ; Howald, Cedric ; Kyung Im, Hae ; Jo, Brian ; Yong Kang, Eun ; Kim, Yungil ; Kim-Hellmuth, Sarah ; Lappalainen, Tuuli ; Li, Gen ; Li, Xin ; Liu, Boxiang ; Mangul, Serghei ; Mccarthy, Mark I. ; Mcdowell, Ian C. ; Mohammadi, Pejman ; Monlong, Jean ; Montgomery, Stephen B. ; Muoz-Aguirre, Manuel ; Ndungu, Anne W. ; Nicolae, Dan L. ; Nobel, Andrew B. ; Oliva, Meritxell ; Ongen, Halit ; Palowitch, John J. ; Panousis, Nikolaos ; Papasaikas, Panagiotis ; Park, Yoson ; Parsana, Princy ; Payne, Anthony J. ; Peterson, Christine B. ; Quan, Jie ; Reverter, Ferran ; Sabatti, Chiara ; Saha, Ashis ; Sammeth, Michael ; Scott, Alexandra J. ; Shabalin, Andrey A. ; Sodaei, Reza ; Stephens, Matthew ; Stranger, Barbara E. ; Strober, Benjamin J. ; Sul, Jae Hoon ; Tsang, Emily K. ; Urbut, Sarah ; van de Bunt, Martijn ; Wang, Gao ; Wen, Xiaoquan ; Wright, Fred A. ; Xi, Hualin S. ; Yeger-Lotem, Esti ; Zappala, Zachary ; Zaugg, Judith B. ; Zhou, Yi-Hui ; Akey, Joshua M. ; Bates, Daniel ; Chan, Joanne ; Claussnitzer, Melina ; Demanelis, Kathryn ; Diegel, Morgan ; Doherty, Jennifer A. ; Feinberg, Andrew P. ; Fernando, Marian S. ; Halow, Jessica ; Hansen, Kasper D. ; Haugen, Eric ; Hickey, Peter F. ; Hou, Lei ; Jasmine, Farzana ; Jian, Ruiqi ; Jiang, Lihua ; Johnson, Audra ; Kaul, Rajinder ; Kellis, Manolis ; Kibriya, Muhammad G. ; Lee, Kristen ; Li, Jin Billy ; Lin, Jessica ; Lin, Shin ; Linder, Sandra ; Linke, Caroline ; Liu, Yaping ; Maurano, Matthew T. ; Molinie, Benoit ; Nelson, Jemma ; Neri, Fidencio J. ; Park, Yongjin ; Pierce, Brandon L. ; Rinaldi, Nicola J. ; Rizzardi, Lindsay F. ; Sandstrom, Richard ; Skol, Andrew ; Smith, Kevin S. ; Snyder, Michael P. ; Stamatoyannopoulos, John ; Tang, Hua ; Wang, Li ; Wang, Meng ; Van Wittenberghe, Nicholas ; Wu, Fan ; Nierras, Concepcion R. ; Branton, Philip A. ; Carithers, Latarsha J. ; Guan, Ping ; Moore, Helen M. ; Rao, Abhi ; Vaught, Jimmie B. ; Gould, Sarah E. ; Lockart, Nicole C. ; Martin, Casey ; Struewing, Jeffery P. ; Volpi, Simona ; Addington, Anjene M. ; Koester, Susan E. ; Little, A. Roger ; Brigham, Lori E. ; Hasz, Richard ; Hunter, Marcus ; Johns, Christopher ; Johnson, Mark ; Kopen, Gene ; Leinweber, William F. ; Lonsdale, John T. ; Mcdonald, Alisa ; Mestichelli, Bernadette ; Myer, Kevin ; Roe, Brian ; Salvatore, Michael ; Shad, Saboor ; Thomas, Jeffrey A. ; Walters, Gary ; Washington, Michael ; Wheeler, Joseph ; Bridge, Jason ; Foster, Barbara A. ; Gillard, Bryan M. ; Karasik, Ellen ; Kumar, Rachna ; Miklos, Mark ; Moser, Michael T. ; Jewell, Scott D. ; Montroy, Robert G. ; Rohrer, Daniel C. ; Valley, Dana R. ; Davis, David A. ; Mash, Deborah C. ; Undale, Anita H. ; Smith, Anna M. ; Tabor, David E. ; Roche, Nancy V. ; Mclean, Jeffrey A. ; Vatanian, Negin ; Robinson, Karna L. ; Sobin, Leslie ; Barcus, Mary E. ; Valentino, Kimberly M. ; Qi, Liqun ; Hunter, Steven ; Hariharan, Pushpa ; Singh, Shilpi ; Um, Ki Sung ; Matose, Takunda ; Tomaszewski, Maria M. ; Barker, Laura K. ; Mosavel, Maghboeba ; Siminoff, Laura A. ; Traino, Heather M. ; Flicek, Paul ; Juettemann, Thomas ; Ruffier, Magali ; Sheppard, Dan ; Taylor, Kieron ; Trevanion, Stephen J. ; Zerbino, Daniel R. ; Craft, Brian ; Goldman, Mary ; Haeussler, Maximilian ; Kent, W. James ; Lee, Christopher M. ; Paten, Benedict ; Rosenbloom, Kate R. ; Vivian, John ; Zhu, Jingchun

Nature, Oct 12, 2017, Vol.550(7675), p.249(6) [Peer Reviewed Journal]

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Landscape of X chromosome inactivation across human tissues

Tukiainen, Taru ; Guigó Serra, Roderic ; Macarthur, Daniel G. ; Genotype - Tissue Expression (Gtex) Consortium 2017

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A cis-regulatory map of the Drosophila genome.(RESEARCH: LETTER)(Report)

Nègre, Nicolas ; Brown, Christopher D ; Ma, Lijia ; Bristow, Christopher Aaron ; Miller, Steven W ; Wagner, Ulrich ; Kheradpour, Pouya ; Eaton, Matthew L ; Loriaux, Paul ; Sealfon, Rachel ; Li, Zirong ; Ishii, Haruhiko ; Spokony, Rebecca F ; Chen, Jia ; Hwang, Lindsay ; Cheng, Chao ; Auburn, Richard P ; Davis, Melissa B ; Domanus, Marc ; Shah, Parantu K ; Morrison, Carolyn A ; Zieba, Jennifer ; Suchy, Sarah ; Senderowicz, Lionel ; Victorsen, Alec ; Bild, Nicholas A ; Grundstad, A Jason ; Hanley, David ; Macalpine, David M ; Mannervik, Mattias ; Venken, Koen ; Bellen, Hugo ; White, Robert ; Gerstein, Mark ; Russell, Steven ; Grossman, Robert L ; Ren, Bing ; Posakony, James W ; Kellis, Manolis ; White, Kevin P;

Nature, March 24, 2011, Vol.471(7339), p.527(5) [Peer Reviewed Journal]

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Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.(LETTER)(Report)

Flot, Jean-François ; Hespeels, Boris ; Li, Xiang ; Noel, Benjamin ; Arkhipova, Irina ; Danchin, Etienne ; Hejnol, Andreas ; Henrissat, Bernard ; Koszul, Romain ; Aury, Jean-Marc ; Barbe, Valérie ; Barthélémy, Roxane-Marie ; Bast, Jens ; Bazykin, Georgii ; Chabrol, Olivier ; Couloux, Arnaud ; Da Rocha, Martine ; Da Silva, Corinne ; Gladyshev, Eugene ; Gouret, Philippe ; Hallatschek, Oskar ; Hecox-Lea, Bette ; Labadie, Karine ; Lejeune, Benjamin ; Piskurek, Oliver ; Poulain, Julie ; Rodriguez, Fernando ; Ryan, Joseph ; Vakhrusheva, Olga ; Wajnberg, Eric ; Wirth, Bénédicte ; Yushenova, Irina ; Kellis, Manolis ; Kondrashov, Alexey ; Welch, David ; Pontarotti, Pierre ; Weissenbach, Jean ; Wincker, Patrick ; Jaillon, Olivier ; Van Doninck, Karine;

Nature, August 22, 2013, Vol.500(7463), p.453(5) [Peer Reviewed Journal]

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