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Evolution. Uniting alignments and trees.

Löytynoja, Ari ; Goldman, Nick Löytynoja, Ari (correspondence author) ; Löytynoja, Ari (record owner)

Science (New York, N.Y.), June 19, 2009, Vol.324(5934), pp.1528-1529 [Peer Reviewed Journal]

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An algorithm for progressive multiple alignment of sequences with insertions

Loeytynoja, Ari ; Goldman, Nick Loeytynoja, Ari (correspondence author)

Proceedings of the National Academy of Sciences, USA, Jul 2005, Vol.102(30), pp.10557-10562 [Peer Reviewed Journal]

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webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja, Ari ; Goldman, Nick Löytynoja, Ari (correspondence author) ; Löytynoja, Ari (record owner)

BMC bioinformatics, November 26, 2010, Vol.11, p.579 [Peer Reviewed Journal]

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A model of evolution and structure for multiple sequence alignment

Löytynoja, Ari ; Goldman, Nick

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 27 December 2008, Vol.363(1512), pp.3913-9 [Peer Reviewed Journal]

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Crystallization and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry

Ora, Ari ; Oksanen, Esko ; Kajander, Tommi ; Goldman, Adrian ; Butcher, Sarah J.

Acta Crystallographica Section F, 01 March 2010, Vol.66(3), pp.357-360 [Peer Reviewed Journal]

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Determination and validation of principal gene products

Tress, Michael L ; Wesselink, Jan - Jaap ; Frankish, Adam ; López, Gonzalo ; Goldman, Nick ; Löytynoja, Ari ; Massingham, Tim ; Pardi, Fabio ; Whelan, Simon ; Harrow, Jennifer ; Valencia, Alfonso

Bioinformatics, 2008, Vol. 24(1), pp.11-17 [Peer Reviewed Journal]

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7
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The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

Brentani, Helena ; Caballero, Otávia L ; Camargo, Anamaria A ; Da Silva, Aline M ; Da Silva, Wilson Araújo ; Dias Neto, Emmanuel ; Grivet, Marco ; Gruber, Arthur ; Guimaraes, Pedro Edson Moreira ; Hide, Winston ; Iseli, Christian ; Jongeneel, C Victor ; Kelso, Janet ; Nagai, Maria Aparecida ; Ojopi, Elida Paula Benquique ; Osorio, Elisson C ; Reis, Eduardo M R ; Riggins, Gregory J ; Simpson, Andrew John George ; de Souza, Sandro ; Stevenson, Brian J ; Strausberg, Robert L ; Tajara, Eloiza H ; Verjovski-Almeida, Sergio ; Acencio, Marcio Luis ; Bengtson, Mário Henrique ; Bettoni, Fabiana ; Bodmer, Walter F ; Briones, Marcelo R S ; Camargo, Luiz Paulo ; Cavenee, Webster ; Cerutti, Janete M ; Coelho Andrade, Luis Eduardo ; Costa Dos Santos, Paulo César ; Ramos Costa, Maria Cristina ; Da Silva, Israel Tojal ; Estécio, Marcos Roberto H ; Sa Ferreira, Karine ; Furnari, Frank B ; Faria, Milton ; Galante, Pedro A F ; Guimaraes, Gustavo S ; Holanda, Adriano Jesus ; Kimura, Edna Teruko ; Leerkes, Maarten R ; Lu, Xin ; Maciel, Rui M B ; Martins, Elizabeth A L ; Massirer, Katlin Brauer ; Melo, Analy S A ; Mestriner, Carlos Alberto ; Miracca, Elisabete Cristina ; Miranda, Leandro Lorenco ; Nobrega, Francisco G ; Oliveira, Paulo S ; Paquola, Apua C M ; Pandolfi, José Rodrigo C ; Campos Pardini, Maria Ines de Moura ; Passetti, Fabio ; Quackenbush, John ; Schnabel, Beatriz ; Sogayar, Mari Cleide ; Souza, Jorge E ; Valentini, Sandro R ; Zaiats, Andre C ; Amaral, Elisabete Jorge ; Arnaldi, Liliane A T ; de Araújo, Amelia Goes ; de Bessa, Simone Aparecida ; Bicknell, David C ; Ribeiro de Camaro, Maria Eugenia ; Carraro, Dirce Maria ; Carrer, Helaine ; Carvalho, Alex F ; Colin, Christian ; Costa, Fernando ; Curcio, Cyntia ; Guerreiro Da Silva, Ismael Dale Cotrim ; Pereira Da Silva, Neusa ; Dellamano, Márcia ; El-Dorry, Hamza ; Espreafico, Enilza Maria ; Scattone Ferreira, Ari José ; Ayres Ferreira, Cristiane ; Fortes, Maria Angela H Z ; Gama, Angelita Habr ; Giannella-Neto, Daniel ; Giannella, Maria Lúcia C C ; Giorgi, Ricardo R ; Goldman, Gustavo Henrique ; Goldman, Maria Helena S ; Hackel, Christine ; Ho, Paulo Lee ; Kimura, Elza Myiuki ; Kowalski, Luiz Paulo ; Krieger, Jose E ; Leite, Luciana C C ; Lopes, Ademar ; Luna, Ana Mercedes S C ; Mackay, Alan ; Mari, Suely Kazue Nagahashi ; Marques, Adriana Aparecida ; Martins, Waleska K ; Montagnini, André ; Mourão Neto, Mario ; Nascimento, Ana Lucia T O ; Neville, A Munro ; Nobrega, Marina P ; O'Hare, Mike J ; Otsuka, Audrey Yumi ; Ruas de Melo, Anna Izabel ; Paco-Larson, Maria Luisa ; Guimarães Pereira, Gonçalo ; Pereira Da Silva, Neusa ; Pesquero, Joao Bosco ; Pessoa, Juliana Gilbert ; Rahal, Paula ; Rainho, Claudia Aparecida ; Rodrigues, Vanderlei ; Rogatto, Silvia Regina ; Romano, Camila Malta ; Romeiro, Janaina Gusmao ; Rossi, Benedito Mauro ; Rusticci, Monica ; Guerra de Sá, Renata ; Sant' Anna, Simone Cristina ; Sarmazo, Miriam L ; Silva, Teresa Cristina de Lima E ; Soares, Fernando Augusto ; Sonati, Maria de Fátima ; de Freitas Sousa, Josane ; Queiroz, Diana ; Valente, Valéria ; Vettore, André Luiz ; Villanova, Fabiola Elizabeth ; Zago, Marco Antonio ; Zalcberg, Heloisa ; Brentani, Helena Brentani, Helena (correspondence author) ; Brentani, Helena (record owner)

Proceedings of the National Academy of Sciences of the United States of America, November 11, 2003, Vol.100(23), pp.13418-13423 [Peer Reviewed Journal]

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8
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

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 ; Shahab, Atif ; 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 ; Kim, Tae Hoon ; 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 ; Ruan, Yijun ; Iyer, Vishwanath R ; Green, Roland D ; Wadelius, Claes ; Farnham, Peggy J

Nature, June 14, 2007, Vol.447(7146), pp.799-816 [Peer Reviewed Journal]

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The somatic genomic landscape of glioblastoma.

Brennan, Cameron W ; Verhaak, Roel G W ; Mckenna, Aaron ; Campos, Benito ; Noushmehr, Houtan ; Salama, Sofie R ; Zheng, Siyuan ; Chakravarty, Debyani ; Sanborn, J Zachary ; Berman, Samuel H ; Beroukhim, Rameen ; Bernard, Brady ; Wu, Chang-Jiun ; Genovese, Giannicola ; Shmulevich, Ilya ; Barnholtz-Sloan, Jill ; Zou, Lihua ; Vegesna, Rahulsimham ; Shukla, Sachet A ; Ciriello, Giovanni ; Yung, W K ; Zhang, Wei ; Sougnez, Carrie ; Mikkelsen, Tom ; Aldape, Kenneth ; Bigner, Darell D ; Van Meir, Erwin G ; Prados, Michael ; Sloan, Andrew ; Black, Keith L ; Eschbacher, Jennifer ; Finocchiaro, Gaetano ; Friedman, William ; Andrews, David W ; Guha, Abhijit ; Iacocca, Mary ; O'Neill, Brian P ; Foltz, Greg ; Myers, Jerome ; Weisenberger, Daniel J ; Penny, Robert ; Kucherlapati, Raju ; Perou, Charles M ; Hayes, D Neil ; Gibbs, Richard ; Marra, Marco ; Mills, Gordon B ; Lander, Eric ; Spellman, Paul ; Wilson, Richard ; Sander, Chris ; Weinstein, John ; Meyerson, Matthew ; Gabriel, Stacey ; Laird, Peter W ; Haussler, David ; Getz, Gad ; Chin, Lynda ; Brennan, Cameron W Benz, Christopher (correspondence author) ; Barnholtz-Sloan, Jill (record owner) ; Barrett, Wendi ; Ostrom, Quinn ; Wolinsky, Yingli ; Black, Keith L ; Bose, Bikash ; Boulos, Paul T ; Boulos, Madgy ; Brown, Jenn ; Czerinski, Christine ; Eppley, Matthew ; Iacocca, Mary ; Kempista, Thelma ; Kitko, Teresa ; Koyfman, Yakov ; Rabeno, Brenda ; Rastogi, Pawan ; Sugarman, Michael ; Swanson, Patricia ; Yalamanchii, Kennedy ; Otey, Ilana P ; Liu, Yingchun Spring ; Xiao, Yonghong ; Auman, J Todd ; Chen, Peng-Chieh ; Hadjipanayis, Angela ; Lee, Eunjung ; Lee, Semin ; Park, Peter J ; Seidman, Jonathan ; Yang, Lixing ; Kucherlapati, Raju ; Kalkanis, Steven ; Mikkelsen, Tom ; Poisson, Laila M ; Raghunathan, Aditya ; Scarpace, Lisa ; Bernard, Brady ; Bressler, Ryan ; Eakin, Andrea ; Iype, Lisa ; Kreisberg, Richard B ; Leinonen, Kalle ; Reynolds, Sheila ; Rovira, Hector ; Thorsson, Vesteinn ; Shmulevich, Ilya ; Annala, Matti J ; Penny, Robert ; Paulauskis, Joseph ; Curley, Erin ; Hatfield, Martha ; Mallery, David ; Morris, Scott ; Shelton, Troy ; Shelton, Candace ; Sherman, Mark ; Yena, Peggy ; Cuppini, Lucia ; Dimeco, Francesco ; Eoli, Marica ; Finocchiaro, Gaetano ; Maderna, Emanuela ; Pollo, Bianca ; Saini, Marco ; Balu, Saianand ; Hoadley, Katherine A ; Li, Ling ; Miller, C Ryan ; Shi, Yan ; Topal, Michael D ; Wu, Junyuan ; Dunn, Gavin ; Giannini, Caterina ; O'Neill, Brian P ; Aksoy, B Arman ; Antipin, Yevgeniy ; Borsu, Laetitia ; Berman, Samuel H ; Brennan, Cameron W ; Cerami, Ethan ; Chakravarty, Debyani ; Ciriello, Giovanni ; Gao, Jianjiong ; Gross, Benjamin ; Jacobsen, Anders ; Ladanyi, Marc ; Lash, Alex ; Liang, Yupu ; Reva, Boris ; Sander, Chris ; Schultz, Nikolaus ; Shen, Ronglai ; Socci, Nicholas D ; Viale, Agnes ; Ferguson, Martin L ; Chen, Qing-Rong ; Demchok, John A ; Dillon, Laura A L ; Shaw, Kenna R Mills ; Sheth, Margi ; Tarnuzzer, Roy ; Wang, Zhining ; Yang, Liming ; Davidsen, Tanja ; Guyer, Mark S ; Ozenberger, Bradley A ; Sofia, Heidi J ; Bergsten, Julie ; Eckman, John ; Harr, Jodi ; Myers, Jerome ; Smith, Christine ; Tucker, Kelly ; Winemiller, Cindy ; Zach, Leigh Anne ; Ljubimova, Julia Y ; Eley, Greg ; Ayala, Brenda ; Jensen, Mark A ; Kahn, Ari ; Pihl, Todd D ; Pot, David A ; Wan, Yunhu ; Eschbacher, Jennifer ; Foltz, Greg ; Hansen, Nathan ; Hothi, Parvi ; Lin, Biaoyang ; Shah, Nameeta ; Yoon, Jae-Geun ; Lau, Ching ; Berens, Michael ; Ardlie, Kristin ; Beroukhim, Rameen ; Carter, Scott L ; Cherniack, Andrew D ; Noble, Mike ; Cho, Juok ; Cibulskis, Kristian ; Dicara, Daniel ; Frazer, Scott ; Gabriel, Stacey B ; Gehlenborg, Nils ; Gentry, Jeff ; Heiman, David ; Kim, Jaegil ; Jing, Rui ; Lander, Eric S ; Lawrence, Michael ; Lin, Pei ; Mallard, Will ; Meyerson, Matthew ; Onofrio, Robert C ; Saksena, Gordon ; Schumacher, Steve ; Sougnez, Carrie ; Stojanov, Petar ; Tabak, Barbara ; Voet, Doug ; Zhang, Hailei ; Zou, Lihua ; Getz, Gad ; Dees, Nathan N ; Ding, Li ; Fulton, Lucinda L ; Fulton, Robert S ; Kanchi, Krishna-Latha ; Mardis, Elaine R ; Wilson, Richard K ; Baylin, Stephen B ; Andrews, David W ; Harshyne, Larry ; Cohen, Mark L ; Devine, Karen ; Sloan, Andrew E ; Vandenberg, Scott R ; Berger, Mitchel S ; Prados, Michael ; Carlin, Daniel ; Craft, Brian ; Ellrott, Kyle ; Goldman, Mary ; Goldstein, Theodore ; Grifford, Mia ; Haussler, David ; Ma, Singer ; Ng, Sam ; Salama, Sofie R ; Sanborn, J Zachary

Cell, October 10, 2013, Vol.155(2), pp.462-477 [Peer Reviewed Journal]

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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Margulies, Elliott H ; Cooper, Gregory M ; Asimenos, George ; Thomas, Daryl J ; Dewey, Colin N ; Siepel, Adam ; Birney, Ewan ; Keefe, Damian ; Schwartz, Ariel S ; Hou, Minmei ; Taylor, James ; Nikolaev, Sergey ; Montoya-Burgos, Juan I ; Löytynoja, Ari ; Whelan, Simon ; Pardi, Fabio ; Massingham, Tim ; Brown, James B ; Bickel

Genome research, June 2007, Vol.17(6), pp.760-74 [Peer Reviewed Journal]

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