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Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.(Report)

Kellis, Manolis ; Bansal, Mukul S. ; Rasmussen, Matthew D. ; Yi - Chieh Wu

Genome Research, March, 2014, Vol.24(3), p.475-486 [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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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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Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast

Chan, Clara ; Jungreis, Irwin ; Kellis, Manolis

PLoS One, Mar 2013, p.e59450 [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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An Epigenetic Signature for Monoallelic Olfactory Receptor Expression.(Report)

Magklara, Angeliki ; Yen, Angela ; Colquitt, Bradley m ; Clowney, E. josephine ; Allen, William ; Markenscoff-Papadimitriou, Eirene ; Evans, Zoe a ; Kheradpour, Pouya ; Mountoufaris, George ; Carey, Catriona ; Barnea, Gilad ; Kellis, Manolis ; Lomvardas, Stavros;

Cell, May 13, 2011, Vol.145(4), p.555(16) [Peer Reviewed Journal]

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Distinguishing protein-coding and noncoding genes in the human genome.(GENETICS)(Author abstract)

Clamp, Michele ; Fry, Ben ; Kamal, Mike ; Xie, Xiaohui ; Cuff, James ; Lin, Michael F. ; Kellis, Manolis ; Lindblad - Toh, Kerstin ; Lander, Eric S.

Proceedings of the National Academy of Sciences of the United States, Dec 4, 2007, Vol.104(49), p.19428(6) [Peer Reviewed Journal]

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8
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RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

Zeitlinger, Julia ; Stark, Alexander ; Kellis, Manolis ; Hong, Joung-Woo ; Nechaev, Sergei ; Adelman, Karen ; Levine, Michael ; Young, Richard

Nature Genetics, Dec 2007, pp.1512-6 [Peer Reviewed Journal]

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The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse.(Report)

Grote, Phillip ; Wittler, Lars ; Hendrix, David ; Koch, Frederic ; Währisch, Sandra ; Beisaw, Arica ; Macura, Karol ; Bläss, Gaby ; Kellis, Manolis ; Werber, Martin ; Herrmann, Bernhard g;

Developmental Cell, Jan 28, 2013, Vol.24(2), p.206(9) [Peer Reviewed Journal]

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A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

Rasmussen, Matthew D ; Kellis, Manolis

Molecular Biology and Evolution, 2011, Vol.28(1), p.273-290 [Peer Reviewed Journal]

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