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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...
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...
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...
Context: Autoimmune polyendocrine syndrome type 1 (APS1) is a monogenic disorder that features autoimmune Addison disease as a major component. Although APS1 accounts for only a small fraction of all patients with Addison disease, early identificatio...
Systemic lupus erythematosus (SLE) is an autoimmune disorder with heterogeneous clinical presentation and complex etiology involving the interplay between genetic, epigenetic, environmental and hormonal factors. Many common SNPs identified by genome ...