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Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

Löytynoja, Ari ; Goldman, Nick

Science (New York, N.Y.), 20 June 2008, Vol.320(5883), pp.1632-5 [Peer Reviewed Journal]

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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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Second time around

Goldman, Ari

Columbia Journalism Review, Jan/Feb 2003, Vol.41(5), p.64 [Peer Reviewed Journal]

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An algorithm for progressive multiple alignment of sequences with insertions

Loytynoja, Ari ; Goldman, Nick

Proceedings of the National Academy of Sciences of the United States of America, Jul 26, 2005, pp.10557-10562 [Peer Reviewed Journal]

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Telling the Story, Inch by Inch

Goldman, Ari

The Jerusalem Report, Mar 7, 2005, p.39

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He Made Our World Universal

Goldman, Ari

The Jerusalem Report, Aug 26, 2002, p.72

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The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

Camargo, Anamaria A. ; Samaia, Helena P. B. ; Dias - Neto, Emmanuel ; Simao, Daniel F. ; Migotto, Italo A. ; Briones, Marcelo R. S. ; Costa, Fernando F. ; Nagai, Maria Aparecida ; Verjovski - Almeida, Sergio ; Zago, Marco A. ; Andrade, Luis Eduardo C. ; Carrer, Helaine ; El - Dorry, Hamza F. A. ; Espreafico, Enilza M. ; Habr - Gama, Angelita ; Giannella - Neto, Daniel ; Goldman, Gustavo H. ; Gruber, Arthur ; Hackel, Christine ; Kimura, Edna T. ; Maciel, Rui M. B. ; Marie, Suely K. N. ; Martins, Elizabeth A. L. ; Nobrega, Marina P. ; Paco - Larson, Maria Luisa ; Pardini, Maria Ines M. C. ; Pereira, Goncalo G. ; Pesquero, Joao Bosco ; Rodrigues, Vanderlei ; Rogatto, Silvia R. ; Da Silva, Ismael D. C. G. ; Sogayar, Mari C. ; Sonati, Maria De Fatima ; Tajara, Eloiza H. ; Valentini, Sandro R. ; Alberto, Fernando L. ; Amaral, Maria Elisabete J. ; Aneas, Ivy ; Arnaldi, Liliane A. T. ; De Assis, Angela M. ; Bengtson, Mario Henrique ; Bergamo, Nadia Aparecida ; Bombonato, Vanessa ; De Camargo, Maria E. R. ; Canevari, Renata A. ; Carraro, Dirce M. ; Cerutti, Janete M. ; Correa, Maria Lucia C. ; Correa, Rosana F. R. ; Costa, Maria Cristina R. ; Curcio, Cyntia ; Hokama, Paula O. M. ; Ferreira, Ari J. S. ; Furuzawa, Gilberto K. ; Gushiken, Tsieko ; Ho, Paulo L. ; Kimura, Elza ; Krieger, Jose E. ; Leite, Luciana C. C. ; Majumder, Paromita ; Marins, Mozart ; Marques, Everaldo R. ; Melo, Analy S. A. ; Melo, Monica ; Mestriner, Carlos Alberto ; Miracca, Elisabete C. ; Miranda, Daniela C. ; Nascimento, Ana Lucia T. O. ; Nobrega, Francisco G. ; Ojopi, Elida P. B. ; Pandolfi, Jose Rodrigo C. ; Pessoa, Luciana G. ; Prevedel, Aline C. ; Rahal, Paula ; Rainho, Claudia A. ; Reis, Eduardo M. R. ; Ribeiro, Marcelo L. ; Da Ros, Nancy ; De Sa, Renata G. ; Sales, Magaly M. ; Sant' Anna, Simone Cristina ; Dos Santos, Mariana L. ; Da Silva, Aline M. ; Da Silva, Neusa P. ; Silva, Wilson A. , Jr. ; Da Silveira, Rosana A. ; Sousa, Josane F. ; Stecconi, Daniella ; Tsukumo, Fernando ; Valente, Valeria ; Soares, Fernando ; Moreira, Eloisa S. ; Nunes, Diana N. ; Correa, Ricardo G. ; Zalcberg, Heloisa ; Carvalho, Alex F. ; Reis, Luis F. L. ; Brentani, Ricardo R. ; Simpson, Andrew J. G. ; De Souza, Sandro J.

Proceedings of the National Academy of Sciences of the United States, Oct 9, 2001, Vol.98(21), p.12103(1) [Peer Reviewed Journal]

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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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Refugee faces

Goldman, Ari

Commonweal, Jun 4, 1999, pp.10-11

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10
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Tuesdays With Morbid

Goldman, Ari Jan 2010

First Things, pp.43-45 [Peer Reviewed Journal]

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