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Title
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying sele...
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying sele...
Waterston, Robert H.;Lindblad-Toh, Kerstin;Birney, Ewan;Rogers, Jane;Abril, Josep F.;Agarwal, Pankaj;Agarwala, Richa;Ainscough, Rachel;Alexandersson, Marina;An, Peter;Antonarakis, Stylianos E.;Attwood, John;Baertsch, Robert;Bailey, Jonathon;Barlow, Karen;Beck, Stephan;Berry, Eric;Birren, Bruce;Bloom, Toby;Bork, Peer;Botcherby, Marc;Bray, Nicolas;Brent, Michael R.;Brown, Daniel G.;Brown, Stephen D.;Bult, Carol;Burton, John;Butler, Jonathan;Campbell, Robert D.;Carninci, Piero;Cawley, Simon;Chiaromonte, Francesca;Chinwalla, Asif T.;Church, Deanna M.;Clamp, Michele;Clee, Christopher;Collins, Francis S.;Cook, Lisa L.;Copley, Richard R.;Coulson, Alan;Couronne, Olivier;Cuff, James;Curwen, Val;Cutts, Tim;Daly, Mark;David, Robert;Davies, Joy;Delehaunty, Kimberly D.;Deri, Justin;Dermitzakis, Emmanouil T.;Dewey, Colin;Dickens, Nicholas J.;Diekhans, Mark;Dodge, Sheila;Dubchak, Inna;Dunn, Diane M.;Eddy, Sean R.;Elnitski, Laura;Emes, Richard D.;Eswara, Pallavi;Eyras, Eduardo;Felsenfeld, Adam;Fewell, Ginger A.;Flicek, Paul;Foley, Karen;Frankel, Wayne N.;Fulton, Lucinda A.;Fulton, Robert S.;Furey, Terrence S.;Gage, Diane;Gibbs, Richard A.;Glusman, Gustavo;Gnerre, Sante;Goldman, Nick;Goodstadt, Leo;Grafham, Darren;Graves, Tina A.;Green, Eric D.;Gregory, Simon;Guigó, Roderic;Guyer, Mark;Hardison, Ross C.;Haussler, David;Hayashizaki, Yoshihide;LaHillier, Deana W.;Hinrichs, Angela;Hlavina, Wratko;Holzer, Timothy;Hsu, Fan;Hua, Axin;Hubbard, Tim;Hunt, Adrienne;Jackson, Ian;Jaffe, David B.;Johnson, L. Steven;Jones, Matthew;Jones, Thomas A.;Joy, Ann;Kamal, Michael;Karlsson, Elinor K.;Karolchik, Donna;Kasprzyk, Arkadiusz;Kawai, Jun;Keibler, Evan;Kells, Cristyn;Kent, W. James;Kirby, Andrew;Kolbe, Diana L.;Korf, Ian;Kucherlapati, Raju S.;Kulbokas, Edward J.;Kulp, David;Landers, Tom;Leger, J. P.;Leonard, Steven;Letunic, Ivica;Levine, Rosie;Li, Jia;Li, Ming;Lloyd, Christine;Lucas, Susan;Ma, Bin;Maglott, Donna R.;Mardis, Elaine R.;Matthews, Lucy;Mauceli, Evan;Mayer, John H.;McCarthy, Megan;McCombie, W. Richard;McLaren, Stuart;McLay, Kirsten;McPherson, John D.;Meldrim, Jim;Meredith, Beverley;Mesirov, Jill P.;Miller, Webb;Miner, Tracie L.;Mongin, Emmanuel;Montgomery, Kate T.;Morgan, Michael;Mott, Richard;Mullikin, James C.;Muzny, Donna M.;Nash, William E.;Nelson, Joanne O.;Nhan, Michael N.;Nicol, Robert;Ning, Zemin;Nusbaum, Chad;O'Connor, Michael J.;Okazaki, Yasushi;Oliver, Karen;Overton-Larty, Emma;Pachter, Lior;Parra, Genís;Pepin, Kymberlie H.;Peterson, Jane;Pevzner, Pavel;Plumb, Robert;Pohl, Craig S.;Poliakov, Alex;Ponce, Tracy C.;Ponting, Chris P.;Potter, Simon;Quail, Michael;Reymond, Alexandre;Roe, Bruce A.;Roskin, Krishna M.;Rubin, Edward M.;Rust, Alistair G.;Santos, Ralph;Sapojnikov, Victor;Schultz, Brian;Schultz, Jorg;Schwartz, Matthias S.;Schwartz, Scott;Scott, Carol;Seaman, Steven;Searle, Steve;Sharpe, Ted;Sheridan, Andrew;Shownkeen, Ratna;Sims, Sarah;Singer, Jonathan B.;Slater, Guy;Smit, Arian;Smith, Douglas R.;Spencer, Brian;Stabenau, Arne;Stange-Thomann, Nicole;Sugnet, Charles;Suyama, Mikita;Tesler, Glenn;Thompson, Johanna;Torrents, David;Trevaskis, Evanne;Tromp, John;Ucla, Catherine;Ureta-Vidal, Abel;Vinson, Jade P.;von Niederhausern, Andrew C.;Wade, Claire M.;Wall, Melanie;Weber, Ryan J.;Weiss, Robert B.;Wendl, Michael C.;West, Anthony P.;Wetterstrand, Kris;Wheeler, Raymond;Whelan, Simon;Wierzbowski, Jamey;Willey, David;Williams, Sophie;Wilson, Richard K.;Winter, Eitan;Worley, Kim C.;Wyman, Dudley;Yang, Shan;Yang, Shiaw Pyng;Zdobnov, Evgeny M.;Zody, Michael C.;Lander, Eric S.
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quali...
Birney, Ewan;Stamatoyannopoulos, John A.;Dutta, Anindya;Guigó, Roderic;Gingeras, Thomas R.;Margulies, Elliott H.;Weng, Zhiping;Snyder, Michael;Dermitzakis, Emmanouil T.;Thurman, Robert E.;Kuehn, Michael S.;Taylor, Christopher M.;Neph, Shane;Koch, Christoph M.;Asthana, Saurabh;Malhotra, Ankit;Adzhubei, Ivan;Greenbaum, Jason A.;Andrews, Robert M.;Flicek, Paul;Boyle, Patrick J.;Cao, Hua;Carter, Nigel P.;Clelland, Gayle K.;Davis, Sean;Day, Nathan;Dhami, Pawandeep;Dillon, Shane C.;Dorschner, Michael O.;Fiegler, Heike;Giresi, Paul G.;Goldy, Jeff;Hawrylycz, Michael;Haydock, Andrew;Humbert, Richard;James, Keith D.;Johnson, Brett E.;Johnson, Ericka M.;Frum, Tristan T.;Rosenzweig, Elizabeth R.;Karnani, Neerja;Lee, Kirsten;Lefebvre, Gregory C.;Navas, Patrick A.;Neri, Fidencio;Parker, Stephen C J;Sabo, Peter J.;Sandstrom, Richard;Shafer, Anthony;Vetrie, David;Weaver, Molly;Wilcox, Sarah;Yu, Man;Collins, Francis S.;Dekker, Job;Lieb, Jason D.;Tullius, Thomas D.;Crawford, Gregory E.;Sunyaev, Shamil;Noble, William S.;Dunham, Ian;Denoeud, France;Reymond, Alexandre;Kapranov, Philipp;Rozowsky, Joel;Zheng, Deyou;Castelo, Robert;Frankish, Adam;Harrow, Jennifer;Ghosh, Srinka;Sandelin, Albin;Hofacker, Ivo L.;Baertsch, Robert;Keefe, Damian;Dike, Sujit;Cheng, Jill;Hirsch, Heather A.;Sekinger, Edward A.;Lagarde, Julien;Abril, Josep F.;Shahab, Atif;Flamm, Christoph;Fried, Claudia;Hackermüller, Jörg;Hertel, Jana;Lindemeyer, Manja;Missal, Kristin;Tanzer, Andrea;Washietl, Stefan;Korbel, Jan;Emanuelsson, Olof;Pedersen, Jakob S.;Holroyd, Nancy;Taylor, Ruth;Swarbreck, David;Matthews, Nicholas;Dickson, Mark C.;Thomas, Daryl J.;Weirauch, Matthew T.;Gilbert, James;Drenkow, Jorg;Bell, Ian;Zhao, Xiaodong;Srinivasan, K. G.;Sung, Wing Kin;Ooi, Hong Sain;Chiu, Kuo Ping;Foissac, Sylvain;Alioto, Tyler;Brent, Michael;Pachter, Lior;Tress, Michael L.;Valencia, Alfonso;Choo, Siew Woh;Choo, Chiou Yu;Ucla, Catherine;Manzano, Caroline;Wyss, Carine;Cheung, Evelyn;Clark, Taane G.;Brown, James B.;Ganesh, Madhavan;Patel, Sandeep;Tammana, Hari;Chrast, Jacqueline;Henrichsen, Charlotte N.;Kai, Chikatoshi;Kawai, Jun;Nagalakshmi, Ugrappa;Wu, Jiaqian;Lian, Zheng;Lian, Jin;Newburger, Peter;Zhang, Xueqing;Bickel, Peter;Mattick, John S.;Carninci, Piero;Hayashizaki, Yoshihide;Weissman, Sherman;Hubbard, Tim;Myers, Richard M.;Rogers, Jane;Stadler, Peter F.;Lowe, Todd M.;Wei, Chia Lin;Ruan, Yijun;Struhl, Kevin;Gerstein, Mark;Antonarakis, Stylianos E.;Fu, Yutao;Green, Eric D.;Karaöz, Ulaş;Siepel, Adam;Taylor, James;Liefer, Laura A.;Wetterstrand, Kris A.;Good, Peter J.;Feingold, Elise A.;Guyer, Mark S.;Cooper, Gregory M.;Asimenos, George;Dewey, Colin N.;Hou, Minmei;Nikolaev, Sergey;Montoya-Burgos, Juan I.;Löytynoja, Ari;Whelan, Simon;Pardi, Fabio;Massingham, Tim;Huang, Haiyan;Zhang, Nancy R.;Holmes, Ian;Mullikin, James C.;Ureta-Vidal, Abel;Paten, Benedict;Seringhaus, Michael;Church, Deanna;Rosenbloom, Kate;Kent, W. James;Stone, Eric A.;Batzoglou, Serafim;Goldman, Nick;Hardison, Ross C.;Haussler, David;Miller, Webb;Sidow, Arend;Trinklein, Nathan D.;Zhang, Zhengdong D.;Barrera, Leah;Stuart, Rhona;King, David C.;Ameur, Adam;Enroth, Stefan;Bieda, Mark C.;Kim, Jonghwan;Bhinge, Akshay A.;Jiang, Nan;Liu, Jun;Yao, Fei;Vega, Vinsensius B.;Lee, Charlie W H;Ng, Patrick;Yang, Annie;Moqtaderi, Zarmik;Zhu, Zhou;Xu, Xiaoqin;Squazzo, Sharon;Oberley, Matthew J.;Inman, David;Singer, Michael A.;Richmond, Todd A.;Munn, Kyle J.;Rada-Iglesias, Alvaro;Wallerman, Ola;Komorowski, Jan;Fowler, Joanna C.;Couttet, Phillippe;Bruce, Alexander W.;Dovey, Oliver M.;Ellis, Peter D.;Langford, Cordelia F.;Nix, David A.;Euskirchen, Ghia;Hartman, Stephen;Urban, Alexander E.;Kraus, Peter;Van Calcar, Sara;Heintzman, Nate;Hoon Kim, Tae;Wang, Kun;Qu, Chunxu;Hon, Gary;Luna, Rosa;Glass, Christopher K.;Rosenfeld, M. Geoff;Aldred, Shelley Force;Cooper, Sara J.;Halees, Anason;Lin, Jane M.;Shulha, Hennady P.;Zhang, Xiaoling;Xu, Mousheng;Haidar, Jaafar N S;Yu, Yong;Iyer, Vishwanath R.;Green, Roland D.;Wadelius, Claes;Farnham, Peggy J.;Ren, Bing;Harte, Rachel A.;Hinrichs, Angie S.;Trumbower, Heather;Clawson, Hiram;Hillman-Jackson, Jennifer;Zweig, Ann S.;Smith, Kayla;Thakkapallayil, Archana;Barber, Galt;Kuhn, Robert M.;Karolchik, Donna;Armengol, Lluis;Bird, Christine P.;De Bakker, Paul I W;Kern, Andrew D.;Lopez-Bigas, Nuria;Martin, Joel D.;Stranger, Barbara E.;Woodroffe, Abigail;Davydov, Eugene;Dimas, Antigone;Eyras, Eduardo;Hallgrímsdóttir, Ingileif B.;Huppert, Julian;Zody, Michael C.;Abecasis, Gonçalo R.;Estivill, Xavier;Bouffard, Gerard G.;Guan, Xiaobin;Hansen, Nancy F.;Idol, Jacquelyn R.;Maduro, Valerie V B;Maskeri, Baishali;McDowell, Jennifer C.;Park, Morgan;Thomas, Pamela J.;Young, Alice C.;Blakesley, Robert W.;Muzny, Donna M.;Sodergren, Erica;Wheeler, David A.;Worley, Kim C.;Jiang, Huaiyang;Weinstock, George M.;Gibbs, Richard A.;Graves, Tina;Fulton, Robert;Mardis, Elaine R.;Wilson, Richard K.;Clamp, Michele;Cuff, James;Gnerre, Sante;Jaffe, David B.;Chang, Jean L.;Lindblad-Toh, Kerstin;Lander, Eric S.;Koriabine, Maxim;Nefedov, Mikhail;Osoegawa, Kazutoyo;Yoshinaga, Yuko;Zhu, Baoli;De Jong, Pieter J.
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a nu...
Clark, Andrew G.;Eisen, Michael B.;Smith, Douglas R.;Bergman, Casey M.;Oliver, Brian;Markow, Therese A.;Kaufman, Thomas C.;Kellis, Manolis;Gelbart, William;Iyer, Venky N.;Pollard, Daniel A.;Sackton, Timothy B.;Larracuente, Amanda M.;Singh, Nadia D.;Abad, Jose P.;Abt, Dawn N.;Adryan, Boris;Aguade, Montserrat;Akashi, Hiroshi;Anderson, Wyatt W.;Aquadro, Charles F.;Ardell, David H.;Arguello, Roman;Artieri, Carlo G.;Barbash, Daniel A.;Barker, Daniel;Barsanti, Paolo;Batterham, Phil;Batzoglou, Serafim;Begun, Dave;Bhutkar, Arjun;Blanco, Enrico;Bosak, Stephanie A.;Bradley, Robert K.;Brand, Adrianne D.;Brent, Michael R.;Brooks, Angela N.;Brown, Randall H.;Butlin, Roger K.;Caggese, Corrado;Calvi, Brian R.;Bernardo De Carvalho, A.;Caspi, Anat;Castrezana, Sergio;Celniker, Susan E.;Chang, Jean L.;Chapple, Charles;Chatterji, Sourav;Chinwalla, Asif;Civetta, Alberto;Clifton, Sandra W.;Comeron, Josep M.;Costello, James C.;Coyne, Jerry A.;Daub, Jennifer;David, Robert G.;Delcher, Arthur L.;Delehaunty, Kim;Do, Chuong B.;Ebling, Heather;Edwards, Kevin;Eickbush, Thomas;Evans, Jay D.;Filipski, Alan;Findeiß, Sven;Freyhult, Eva;Fulton, Lucinda;Fulton, Robert;Garcia, Ana C L;Gardiner, Anastasia;Garfield, David A.;Garvin, Barry E.;Gibson, Greg;Gilbert, Don;Gnerre, Sante;Godfrey, Jennifer;Good, Robert;Gotea, Valer;Gravely, Brenton;Greenberg, Anthony J.;Griffiths-Jones, Sam;Gross, Samuel;Guigo, Roderic;Gustafson, Erik A.;Haerty, Wilfried;Hahn, Matthew W.;Halligan, Daniel L.;Halpern, Aaron L.;Halter, Gillian M.;Han, Mira V.;Heger, Andreas;Hillier, LaDeana;Hinrichs, Angie S.;Holmes, Ian;Hoskins, Roger A.;Hubisz, Melissa J.;Hultmark, Dan;Huntley, Melanie A.;Jaffe, David B.;Jagadeeshan, Santosh;Jeck, William R.;Johnson, Justin;Jones, Corbin D.;Jordan, William C.;Karpen, Gary H.;Kataoka, Eiko;Keightley, Peter D.;Kheradpour, Pouya;Kirkness, Ewen F.;Koerich, Leonardo B.;Kristiansen, Karsten;Kudrna, Dave;Kulathinal, Rob J.;Kumar, Sudhir;Kwok, Roberta;Lander, Eric;Langley, Charles H.;Lapoint, Richard;Lazzaro, Brian P.;Lee, So Jeong;Levesque, Lisa;Li, Ruiqiang;Lin, Chiao Feng;Lin, Michael F.;Lindblad-Toh, Kerstin;Llopart, Ana;Long, Manyuan;Low, Lloyd;Lozovsky, Elena;Lu, Jian;Luo, Meizhong;Machado, Carlos A.;Makalowski, Wojciech;Marzo, Mar;Matsuda, Muneo;Matzkin, Luciano;McAllister, Bryant;McBride, Carolyn S.;McKernan, Brendan;McKernan, Kevin;Mendez-Lago, Maria;Minx, Patrick;Mollenhauer, Michael U.;Montooth, Kristi;Mount, Stephen M.;Mu, Xu;Myers, Eugene;Negre, Barbara;Newfeld, Stuart;Nielsen, Rasmus;Noor, Mohamed A F;O'Grady, Patrick;Pachter, Lior;Papaceit, Montserrat;Parisi, Matthew J.;Parisi, Michael;Parts, Leopold;Pedersen, Jakob S.;Pesole, Graziano;Phillippy, Adam M.;Ponting, Chris P.;Pop, Mihai;Porcelli, Damiano;Powell, Jeffrey R.;Prohaska, Sonja;Pruitt, Kim;Puig, Marta;Quesneville, Hadi;Ravi Ram, Kristipati;Rand, David;Rasmussen, Matthew D.;Reed, Laura K.;Reenan, Robert;Reily, Amy;Remington, Karin A.;Rieger, Tania T.;Ritchie, Michael G.;Robin, Charles;Rogers, Yu Hui;Rohde, Claudia;Rozas, Julio;Rubenfield, Marc J.;Ruiz, Alfredo;Russo, Susan;Salzberg, Steven L.;Sanchez-Gracia, Alejandro;Saranga, David J.;Sato, Hajime;Schaeffer, Stephen W.;Schatz, Michael C.;Schlenke, Todd;Schwartz, Russell;Segarra, Carmen;Singh, Rama S.;Sirot, Laura;Sirota, Marina;Sisneros, Nicholas B.;Smith, Chris D.;Smith, Temple F.;Spieth, John;Stage, Deborah E.;Stark, Alexander;Stephan, Wolfgang;Strausberg, Robert L.;Strempel, Sebastian;Sturgill, David;Sutton, Granger;Sutton, Granger G.;Tao, Wei;Teichmann, Sarah;Tobari, Yoshiko N.;Tomimura, Yoshihiko;Tsolas, Jason M.;Valente, Vera L S;Venter, Eli;Craig Venter, J.;Vicario, Saverio;Vieira, Filipe G.;Vilella, Albert J.;Villasante, Alfredo;Walenz, Brian;Wang, Jun;Wasserman, Marvin;Watts, Thomas;Wilson, Derek;Wilson, Richard K.;Wing, Rod A.;Wolfner, Mariana F.;Wong, Alex;Ka-Shu Wong, Gane;Wu, Chung I.;Wu, Gabriel;Yamamoto, Daisuke;Yang, Hsiao Pei;Yang, Shiaw Pyng;Yorke, James A.;Yoshida, Kiyohito;Zdobnov, Evgeny;Zhang, Peili;Zhang, Yu;Zimin, Aleksey V.;Baldwin, Jennifer;Abdouelleil, Amr;Abdulkadir, Jamal;Abebe, Adal;Abera, Brikti;Abreu, Justin;Christophe Acer, St;Aftuck, Lynne;Alexander, Allen;An, Peter;Anderson, Erica;Anderson, Scott;Arachi, Harindra;Azer, Marc;Bachantsang, Pasang;Barry, Andrew;Bayul, Tashi;Berlin, Aaron;Bessette, Daniel;Bloom, Toby;Blye, Jason;Boguslavskiy, Leonid;Bonnet, Claude;Boukhgalter, Boris;Bourzgui, Imane;Brown, Adam;Cahill, Patrick;Channer, Sheridon;Cheshatsang, Yama;Chuda, Lisa;Citroen, Mieke;Collymore, Alville;Cooke, Patrick;Costello, Maura;D'Aco, Katie;Daza, Riza;De Haan, Georgius;Degray, Stuart;Demaso, Christina;Dhargay, Norbu;Dooley, Kimberly;Dooley, Erin;Doricent, Missole;Dorje, Passang;Dorjee, Kunsang;Dupes, Alan;Elong, Richard;Falk, Jill;Farina, Abderrahim;Faro, Susan;Ferguson, Diallo;Fisher, Sheila;Foley, Chelsea D.;Franke, Alicia;Friedrich, Dennis;Gadbois, Loryn;Gearin, Gary;Gearin, Christina R.;Giannoukos, Georgia;Goode, Tina;Graham, Joseph;Grandbois, Edward;Grewal, Sharleen;Gyaltsen, Kunsang;Hafez, Nabil;Hagos, Birhane;Hall, Jennifer;Henson, Charlotte;Hollinger, Andrew;Honan, Tracey;Huard, Monika D.;Hughes, Leanne;Hurhula, Brian;Erii Husby, M.;Kamat, Asha;Kanga, Ben;Kashin, Seva;Khazanovich, Dmitry;Kisner, Peter;Lance, Krista;Lara, Marcia;Lee, William;Lennon, Niall;Letendre, Frances;Levine, Rosie;Lipovsky, Alex;Liu, Xiaohong;Liu, Jinlei;Liu, Shangtao;Lokyitsang, Tashi;Lokyitsang, Yeshi;Lubonja, Rakela;Lui, Annie;MacDonald, Pen;Magnisalis, Vasilia;Maru, Kebede;Matthews, Charles;McCusker, William;McDonough, Susan;Mehta, Teena;Meldrim, James;Meneus, Louis;Mihai, Oana;Mihalev, Atanas;Mihova, Tanya;Mittelman, Rachel;Mlenga, Valentine;Montmayeur, Anna;Mulrain, Leonidas;Navidi, Adam;Naylor, Jerome;Negash, Tamrat;Nguyen, Thu;Nguyen, Nga;Nicol, Robert;Norbu, Choe;Norbu, Nyima;Novod, Nathaniel;O'Neill, Barry;Osman, Sahal;Markiewicz, Eva;Oyono, Otero L.;Patti, Christopher;Phunkhang, Pema;Pierre, Fritz;Priest, Margaret;Raghuraman, Sujaa;Rege, Filip;Reyes, Rebecca;Rise, Cecil;Rogov, Peter;Ross, Keenan;Ryan, Elizabeth;Settipalli, Sampath;Shea, Terry;Sherpa, Ngawang;Shi, Lu;Shih, Diana;Sparrow, Todd;Spaulding, Jessica;Stalker, John;Stange-Thomann, Nicole;Stavropoulos, Sharon;Stone, Catherine;Strader, Christopher;Tesfaye, Senait;Thomson, Talene;Thoulutsang, Yama;Thoulutsang, Dawa;Topham, Kerri;Topping, Ira;Tsamla, Tsamla;Vassiliev, Helen;Vo, Andy;Wangchuk, Tsering;Wangdi, Tsering;Weiand, Michael;Wilkinson, Jane;Wilson, Adam;Yadav, Shailendra;Young, Geneva;Yu, Qing;Zembek, Lisa;Zhong, Danni;Zimmer, Andrew;Zwirko, Zac;Alvarez, Pablo;Brockman, Will;Butler, Jonathan;Chin, Cheewhye;Grabherr, Manfred;Kleber, Michael;Mauceli, Evan;MacCallum, Iain
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila sp...
Birney, Ewan;Stamatoyannopoulos, John A.;Dutta, Anindya;Guigó, Roderic;Gingeras, Thomas R.;Margulies, Elliott H.;Weng, Zhiping;Snyder, Michael;Dermitzakis, Emmanouil T.;Thurman, Robert E.;Kuehn, Michael S.;Taylor, Christopher M.;Neph, Shane;Koch, Christoph M.;Asthana, Saurabh;Malhotra, Ankit;Adzhubei, Ivan;Greenbaum, Jason A.;Andrews, Robert M.;Flicek, Paul;Boyle, Patrick J.;Cao, Hua;Carter, Nigel P.;Clelland, Gayle K.;Davis, Sean;Day, Nathan;Dhami, Pawandeep;Dillon, Shane C.;Dorschner, Michael O.;Fiegler, Heike;Giresi, Paul G.;Goldy, Jeff;Hawrylycz, Michael;Haydock, Andrew;Humbert, Richard;James, Keith D.;Johnson, Brett E.;Johnson, Ericka M.;Frum, Tristan T.;Rosenzweig, Elizabeth R.;Karnani, Neerja;Lee, Kirsten;Lefebvre, Gregory C.;Navas, Patrick A.;Neri, Fidencio;Parker, Stephen C J;Sabo, Peter J.;Sandstrom, Richard;Shafer, Anthony;Vetrie, David;Weaver, Molly;Wilcox, Sarah;Yu, Man;Collins, Francis S.;Dekker, Job;Lieb, Jason D.;Tullius, Thomas D.;Crawford, Gregory E.;Sunyaev, Shamil;Noble, William S.;Dunham, Ian;Denoeud, France;Reymond, Alexandre;Kapranov, Philipp;Rozowsky, Joel;Zheng, Deyou;Castelo, Robert;Frankish, Adam;Harrow, Jennifer;Ghosh, Srinka;Sandelin, Albin;Hofacker, Ivo L.;Baertsch, Robert;Keefe, Damian;Dike, Sujit;Cheng, Jill;Hirsch, Heather A.;Sekinger, Edward A.;Lagarde, Julien;Abril, Josep F.;Shahab, Atif;Flamm, Christoph;Fried, Claudia;Hackermüller, Jörg;Hertel, Jana;Lindemeyer, Manja;Missal, Kristin;Tanzer, Andrea;Washietl, Stefan;Korbel, Jan;Emanuelsson, Olof;Pedersen, Jakob S.;Holroyd, Nancy;Taylor, Ruth;Swarbreck, David;Matthews, Nicholas;Dickson, Mark C.;Thomas, Daryl J.;Weirauch, Matthew T.;Gilbert, James;Drenkow, Jorg;Bell, Ian;Zhao, Xiaodong;Srinivasan, K. G.;Sung, Wing Kin;Ooi, Hong Sain;Chiu, Kuo Ping;Foissac, Sylvain;Alioto, Tyler;Brent, Michael;Pachter, Lior;Tress, Michael L.;Valencia, Alfonso;Choo, Siew Woh;Choo, Chiou Yu;Ucla, Catherine;Manzano, Caroline;Wyss, Carine;Cheung, Evelyn;Clark, Taane G.;Brown, James B.;Ganesh, Madhavan;Patel, Sandeep;Tammana, Hari;Chrast, Jacqueline;Henrichsen, Charlotte N.;Kai, Chikatoshi;Kawai, Jun;Nagalakshmi, Ugrappa;Wu, Jiaqian;Lian, Zheng;Lian, Jin;Newburger, Peter;Zhang, Xueqing;Bickel, Peter;Mattick, John S.;Carninci, Piero;Hayashizaki, Yoshihide;Weissman, Sherman;Hubbard, Tim;Myers, Richard M.;Rogers, Jane;Stadler, Peter F.;Lowe, Todd M.;Wei, Chia Lin;Ruan, Yijun;Struhl, Kevin;Gerstein, Mark;Antonarakis, Stylianos E.;Fu, Yutao;Green, Eric D.;Karaöz, Ulaş;Siepel, Adam;Taylor, James;Liefer, Laura A.;Wetterstrand, Kris A.;Good, Peter J.;Feingold, Elise A.;Guyer, Mark S.;Cooper, Gregory M.;Asimenos, George;Dewey, Colin N.;Hou, Minmei;Nikolaev, Sergey;Montoya-Burgos, Juan I.;Löytynoja, Ari;Whelan, Simon;Pardi, Fabio;Massingham, Tim;Huang, Haiyan;Zhang, Nancy R.;Holmes, Ian;Mullikin, James C.;Ureta-Vidal, Abel;Paten, Benedict;Seringhaus, Michael;Church, Deanna;Rosenbloom, Kate;Kent, W. James;Stone, Eric A.;Batzoglou, Serafim;Goldman, Nick;Hardison, Ross C.;Haussler, David;Miller, Webb;Sidow, Arend;Trinklein, Nathan D.;Zhang, Zhengdong D.;Barrera, Leah;Stuart, Rhona;King, David C.;Ameur, Adam;Enroth, Stefan;Bieda, Mark C.;Kim, Jonghwan;Bhinge, Akshay A.;Jiang, Nan;Liu, Jun;Yao, Fei;Vega, Vinsensius B.;Lee, Charlie W H;Ng, Patrick;Yang, Annie;Moqtaderi, Zarmik;Zhu, Zhou;Xu, Xiaoqin;Squazzo, Sharon;Oberley, Matthew J.;Inman, David;Singer, Michael A.;Richmond, Todd A.;Munn, Kyle J.;Rada-Iglesias, Alvaro;Wallerman, Ola;Komorowski, Jan;Fowler, Joanna C.;Couttet, Phillippe;Bruce, Alexander W.;Dovey, Oliver M.;Ellis, Peter D.;Langford, Cordelia F.;Nix, David A.;Euskirchen, Ghia;Hartman, Stephen;Urban, Alexander E.;Kraus, Peter;Van Calcar, Sara;Heintzman, Nate;Hoon Kim, Tae;Wang, Kun;Qu, Chunxu;Hon, Gary;Luna, Rosa;Glass, Christopher K.;Rosenfeld, M. Geoff;Aldred, Shelley Force;Cooper, Sara J.;Halees, Anason;Lin, Jane M.;Shulha, Hennady P.;Zhang, Xiaoling;Xu, Mousheng;Haidar, Jaafar N S;Yu, Yong;Iyer, Vishwanath R.;Green, Roland D.;Wadelius, Claes;Farnham, Peggy J.;Ren, Bing;Harte, Rachel A.;Hinrichs, Angie S.;Trumbower, Heather;Clawson, Hiram;Hillman-Jackson, Jennifer;Zweig, Ann S.;Smith, Kayla;Thakkapallayil, Archana;Barber, Galt;Kuhn, Robert M.;Karolchik, Donna;Armengol, Lluis;Bird, Christine P.;De Bakker, Paul I W;Kern, Andrew D.;Lopez-Bigas, Nuria;Martin, Joel D.;Stranger, Barbara E.;Woodroffe, Abigail;Davydov, Eugene;Dimas, Antigone;Eyras, Eduardo;Hallgrímsdóttir, Ingileif B.;Huppert, Julian;Zody, Michael C.;Abecasis, Gonçalo R.;Estivill, Xavier;Bouffard, Gerard G.;Guan, Xiaobin;Hansen, Nancy F.;Idol, Jacquelyn R.;Maduro, Valerie V B;Maskeri, Baishali;McDowell, Jennifer C.;Park, Morgan;Thomas, Pamela J.;Young, Alice C.;Blakesley, Robert W.;Muzny, Donna M.;Sodergren, Erica;Wheeler, David A.;Worley, Kim C.;Jiang, Huaiyang;Weinstock, George M.;Gibbs, Richard A.;Graves, Tina;Fulton, Robert;Mardis, Elaine R.;Wilson, Richard K.;Clamp, Michele;Cuff, James;Gnerre, Sante;Jaffe, David B.;Chang, Jean L.;Lindblad-Toh, Kerstin;Lander, Eric S.;Koriabine, Maxim;Nefedov, Mikhail;Osoegawa, Kazutoyo;Yoshinaga, Yuko;Zhu, Baoli;De Jong, Pieter J.
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a nu...
Haas, Brian J.;Kamoun, Sophien;Zody, Michael C.;Jiang, Rays H. Y.;Handsaker, Robert E.;Cano, Liliana M.;Grabherr, Manfred;Kodira, Chinnappa D.;Raffaele, Sylvain;Torto-Alalibo, Trudy;Bozkurt, Tolga O.;Ah-Fong, Audrey M. V.;Alvarado, Lucia;Anderson, Vicky L.;Armstrong, Miles R.;Avrova, Anna;Baxter, Laura;Beynon, Jim;Boevink, Petra C.;Bollmann, Stephanie R.;Bos, Jorunn I. B.;Bulone, Vincent;Cai, Guohong;Cakir, Cahid;Carrington, James C.;Chawner, Megan;Conti, Lucio;Costanzo, Stefano;Ewan, Richard;Fahlgren, Noah;Fischbach, Michael A.;Fugelstad, Johanna;Gilroy, Eleanor M.;Gnerre, Sante;Green, Pamela J.;Grenville-Briggs, Laura J.;Griffith, John;Gruenwald, Niklaus J.;Horn, Karolyn;Horner, Neil R.;Hu, Chia-Hui;Huitema, Edgar;Jeong, Dong-Hoon;Jones, Alexandra M. E.;Jones, Jonathan D. G.;Jones, Richard W.;Karlsson, Elinor K.;Kunjeti, Sridhara G.;Lamour, Kurt;Liu, Zhenyu;Ma, LiJun;MacLean, Daniel;Chibucos, Marcus C.;McDonald, Hayes;McWalters, Jessica;Meijer, Harold J. G.;Morgan, William;Morris, Paul F.;Munro, Carol A.;O'Neill, Keith;Ospina-Giraldo, Manuel;Pinzon, Andres;Pritchard, Leighton;Ramsahoye, Bernard;Ren, Qinghu;Restrepo, Silvia;Roy, Sourav;Sadanandom, Ari;Savidor, Alon;Schornack, Sebastian;Schwartz, David C.;Schumann, Ulrike D.;Schwessinger, Ben;Seyer, Lauren;Sharpe, Ted;Silvar, Cristina;Song, Jing;Studholme, David J.;Sykes, Sean;Thines, Marco;van de Vondervoort, Peter J. I.;Phuntumart, Vipaporn;Wawra, Stephan;Weide, Rob;Win, Joe;Young, Carolyn;Zhou, Shiguo;Fry, William;Meyers, Blake C.;van West, Pieter;Ristaino, Jean;Govers, Francine;Birch, Paul R. J.;Whisson, Stephen C.;Judelson, Howard S.;Nusbaum, Chad
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Amemiya, Chris T;Alföldi, Jessica;Lee, Alison P;Fan, Shaohua;Philippe, Hervé;Maccallum, Iain;Braasch, Ingo;Manousaki, Tereza;Schneider, Igor;Rohner, Nicolas;Organ, Chris;Chalopin, Domitille;Smith, Jeramiah J;Robinson, Mark;Dorrington, Rosemary A;Gerdol, Marco;Aken, Bronwen;Biscotti, Maria Assunta;Barucca, Marco;Baurain, Denis;Berlin, Aaron M;Blatch, Gregory L;Buonocore, Francesco;Burmester, Thorsten;Campbell, Michael S;Canapa, Adriana;Cannon, John P;Christoffels, Alan;De Moro, Gianluca;Edkins, Adrienne L;Fan, Lin;Fausto, Anna Maria;Feiner, Nathalie;Forconi, Mariko;Gamieldien, Junaid;Gnerre, Sante;Gnirke, Andreas;Goldstone, Jared V;Haerty, Wilfried;Hahn, Mark E;Hesse, Uljana;Hoffmann, Steve;Johnson, Jeremy;Karchner, Sibel I;Kuraku, Shigehiro;Lara, Marcia;Levin, Joshua Z;Litman, Gary W;Mauceli, Evan;Miyake, Tsutomu;Mueller, M Gail;Nelson, David R;Nitsche, Anne;Olmo, Ettore;Ota, Tatsuya;Pallavicini, Alberto;Panji, Sumir;Picone, Barbara;Ponting, Chris P;Prohaska, Sonja J;Przybylski, Dariusz;Saha, Nil Ratan;Ravi, Vydianathan;Ribeiro, Filipe J;Sauka-Spengler, Tatjana;Scapigliati, Giuseppe;Searle, Stephen M J;Sharpe, Ted;Simakov, Oleg;Stadler, Peter F;Stegeman, John J;Sumiyama, Kenta;Tabbaa, Diana;Tafer, Hakim;Turner-Maier, Jason;van Heusden, Peter;White, Simon;Williams, Louise;Yandell, Mark;Brinkmann, Henner;Volff, Jean-Nicolas;Tabin, Clifford J;Shubin, Neil;Schartl, Manfred;Jaffe, David B;Postlethwait, John H;Venkatesh, Byrappa;Di Palma, Federica;Lander, Eric S;Meyer, Axel;Lindblad-Toh, Kerstin
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and it...
Clark, Andrew G;Eisen, Michael B;Smith, Douglas R;Bergman, Casey M;Oliver, Brian;Markow, Therese A;Kaufman, Thomas C;Kellis, Manolis;Gelbart, William;Iyer, Venky N;Pollard, Daniel A;Sackton, Timothy B;Larracuente, Amanda M;Singh, Nadia D;Abad, Jose P;Abt, Dawn N;Adryan, Boris;Aguade, Montserrat;Akashi, Hiroshi;Anderson, Wyatt W;Aquadro, Charles F;Ardell, David H;Arguello, Roman;Artieri, Carlo G;Barbash, Daniel A;Barker, Daniel;Barsanti, Paolo;Batterham, Phil;Batzoglou, Serafim;Begun, Dave;Bhutkar, Arjun;Blanco, Enrico;Bosak, Stephanie A;Bradley, Robert K;Brand, Adrianne D;Brent, Michael R;Brooks, Angela N;Brown, Randall H;Butlin, Roger K;Caggese, Corrado;Calvi, Brian R;Bernardo de Carvalho, A;Caspi, Anat;Castrezana, Sergio;Celniker, Susan E;Chang, Jean L;Chapple, Charles;Chatterji, Sourav;Chinwalla, Asif;Civetta, Alberto;Clifton, Sandra W;Comeron, Josep M;Costello, James C;Coyne, Jerry A;Daub, Jennifer;David, Robert G;Delcher, Arthur L;Delehaunty, Kim;Do, Chuong B;Ebling, Heather;Edwards, Kevin;Eickbush, Thomas;Evans, Jay D;Filipski, Alan;Findeiss, Sven;Freyhult, Eva;Fulton, Lucinda;Fulton, Robert;Garcia, Ana C L;Gardiner, Anastasia;Garfield, David A;Garvin, Barry E;Gibson, Greg;Gilbert, Don;Gnerre, Sante;Godfrey, Jennifer;Good, Robert;Gotea, Valer;Gravely, Brenton;Greenberg, Anthony J;Griffiths-Jones, Sam;Gross, Samuel;Guigo, Roderic;Gustafson, Erik A;Haerty, Wilfried;Hahn, Matthew W;Halligan, Daniel L;Halpern, Aaron L;Halter, Gillian M;Han, Mira V;Heger, Andreas;Hillier, LaDeana;Hinrichs, Angie S;Holmes, Ian;Hoskins, Roger A;Hubisz, Melissa J;Hultmark, Dan;Huntley, Melanie A;Jaffe, David B;Jagadeeshan, Santosh;Jeck, William R;Johnson, Justin;Jones, Corbin D;Jordan, William C;Karpen, Gary H;Kataoka, Eiko;Keightley, Peter D;Kheradpour, Pouya;Kirkness, Ewen F;Koerich, Leonardo B;Kristiansen, Karsten;Kudrna, Dave;Kulathinal, Rob J;Kumar, Sudhir;Kwok, Roberta;Lander, Eric;Langley, Charles H;Lapoint, Richard;Lazzaro, Brian P;Lee, So-Jeong;Levesque, Lisa;Li, Ruiqiang;Lin, Chiao-Feng;Lin, Michael F;Lindblad-Toh, Kerstin;Llopart, Ana;Long, Manyuan;Low, Lloyd;Lozovsky, Elena;Lu, Jian;Luo, Meizhong;Machado, Carlos A;Makalowski, Wojciech;Marzo, Mar;Matsuda, Muneo;Matzkin, Luciano;McAllister, Bryant;McBride, Carolyn S;McKernan, Brendan;McKernan, Kevin;Mendez-Lago, Maria;Minx, Patrick;Mollenhauer, Michael U;Montooth, Kristi;Mount, Stephen M;Mu, Xu;Myers, Eugene;Negre, Barbara;Newfeld, Stuart;Nielsen, Rasmus;Noor, Mohamed A F;O'Grady, Patrick;Pachter, Lior;Papaceit, Montserrat;Parisi, Matthew J;Parisi, Michael;Parts, Leopold;Pedersen, Jakob S;Pesole, Graziano;Phillippy, Adam M;Ponting, Chris P;Pop, Mihai;Porcelli, Damiano;Powell, Jeffrey R;Prohaska, Sonja;Pruitt, Kim;Puig, Marta;Quesneville, Hadi;Ram, Kristipati Ravi;Rand, David;Rasmussen, Matthew D;Reed, Laura K;Reenan, Robert;Reily, Amy;Remington, Karin A;Rieger, Tania T;Ritchie, Michael G;Robin, Charles;Rogers, Yu-Hui;Rohde, Claudia;Rozas, Julio;Rubenfield, Marc J;Ruiz, Alfredo;Russo, Susan;Salzberg, Steven L;Sanchez-Gracia, Alejandro;Saranga, David J;Sato, Hajime;Schaeffer, Stephen W;Schatz, Michael C;Schlenke, Todd;Schwartz, Russell;Segarra, Carmen;Singh, Rama S;Sirot, Laura;Sirota, Marina;Sisneros, Nicholas B;Smith, Chris D;Smith, Temple F;Spieth, John;Stage, Deborah E;Stark, Alexander;Stephan, Wolfgang;Strausberg, Robert L;Strempel, Sebastian;Sturgill, David;Sutton, Granger;Sutton, Granger G;Tao, Wei;Teichmann, Sarah;Tobari, Yoshiko N;Tomimura, Yoshihiko;Tsolas, Jason M;Valente, Vera L S;Venter, Eli;Venter, J Craig;