Implementation of a Comparative Gene Finder

Colin Dewey, Jia Qian Wu, Simon Cawley, Marina Alexandersson, Richard Gibbs, Lior Pachter, None, Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse and Rat Genome Research. ,vol. 14, pp. 661- 664 ,(2004) , 10.1101/GR.1939804

Marina Alexandersson, Simon Cawley, Lior Pachter, None, SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model Genome Research. ,vol. 13, pp. 496- 502 ,(2003) , 10.1101/GR.424203

University of Utah Weiss Robert B. 14 Dunn Diane M. 14, NISC Comparative Sequencing Program, NHGRI Green Eric D. 15 Blakesley Robert W. 15 Bouffard Gerard G. 15, Pieter J de Jong, Kazutoyo Osoegawa, Baoli Zhu, Marco Marra, Jacqueline Schein, Ian Bosdet, Chris Fjell, Steven Jones, Martin Krzywinski, Carrie Mathewson, Asim Siddiqui, Natasja Wye, Genome Sequencing Center, Washington University School of Medicine McPherson John 1 17, Shaying Zhao, Claire M Fraser, Jyoti Shetty, Sofiya Shatsman, Keita Geer, Yixin Chen, Sofyia Abramzon, William C Nierman, Richard A Gibbs, George M Weinstock, Paul H Havlak, Rui Chen, K James Durbin, Rain Simons, Yanru Ren, Xing-Zhi Song, Bingshan Li, Yue Liu, Xiang Qin, Simon Cawley, Case Western Reserve University Bailey Jeffrey A. 4 Eichler Evan E. 4 Tuzun Eray 4, EBI, Wellcome Trust Genome Campus Birney Ewan 21 Mongin Emmanuel 21 Ureta-Vidal Abel 21 Woodwark Cara 21, EMBL, Heidelberg Zdobnov Evgeny 22 Bork Peer 22 23 Suyama Mikita 22 Torrents David 22, Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg Alexandersson Marina 24, Fred Hutchinson Cancer Research Center Trask Barbara J. 25 Young Janet M. 25, Genome Therapeutics Smith Douglas 12 13 Huang Hui 12 Fechtel Kim 12 Wang Huajun 12 Xing Heming 12 Weinstock Keith 12, Incyte Corporation Daniels Sue 26 Gietzen Darryl 26 Schmidt Jeanette 26 Stevens Kristian 26 Vitt Ursula 26 Wingrove Jim 26, Institut Municipal d'Investigacio Medica, Barcelona> Camara Francisco 27 Mar Albà M. 27 Abril Josep F. 27 Guigo Roderic 27, Institute for Systems Biology Smit Arian 28, Lawrence Berkeley National Laboratory Dubchak Inna 29 30 Rubin Edward M. 29 30 Couronne Olivier 29 30 Poliakov Alexander 29, Max Delbrück Center for Molecular Medicine Hübner Norbert 23 Ganten Detlev 23 Goesele Claudia 23 31 Hummel Oliver 23 31 Kreitler Thomas 23 31 Lee Young-Ae 23 Monti Jan 23 Schulz Herbert 23 Zimdahl Heike 23, Max Planck Institute for Molecular Genetics, Berlin Himmelbauer Heinz 31 Lehrach Hans 31, Medical College of Wisconsin Jacob (Principal Investigator) Howard J. 32 Bromberg Susan 33 Gullings-Handley Jo 32 Jensen-Seaman Michael I. 32 Kwitek Anne E. 32 Lazar Jozef 32 Pasko Dean 33 Tonellato Peter J. 32 Twigger Simon 32, MRC Functional Genetics Unit, University of Oxford Ponting Chris P. 34 Duarte Jose M. 34 Rice Stephen 34 Goodstadt Leo 34 Beatson Scott A. 34 Emes Richard D. 34 Winter Eitan E. 34 Webber Caleb 34, MWG-Biotech Brandt Petra 35 Nyakatura Gerald 35, Roche Genetics and Roche Center for Medical Genomics Lindpaintner Klaus 37, Sanger Institute Andrews T. Dan 38 Caccamo Mario 38 Clamp Michele 38 Clarke Laura 38 Curwen Valerie 38 Durbin Richard 38 Eyras Eduardo 38 Searle Stephen M. 38, Stanford University Cooper Gregory M. 39 Batzoglou Serafim 40 Brudno Michael 40 Sidow Arend 39 Stone Eric A. 39, Center for the Advancement of Genomics Craig Venter J. 3 8, University of Arizona Payseur Bret A. 41, Université de Montréal Bourque Guillaume 42, Universidad de Oviedo López-Otín Carlos 43 Puente Xose S. 43, University of California, Berkeley Chakrabarti Kushal 44 Chatterji Sourav 44 Dewey Colin 44 Pachter Lior 45 Bray Nicolas 45 Yap Von Bing 45 Caspi Anat 46, University of California, San Diego Tesler Glenn 47 Pevzner Pavel A. 48, University of California, Santa Cruz Haussler David 49 Roskin Krishna M. 50 Baertsch Robert 50 Clawson Hiram 50 Furey Terrence S. 50 Hinrichs Angie S. 50 Karolchik Donna 50 Kent William J. 50 Rosenbloom Kate R. 50 Trumbower Heather 50 Weirauch Matt 36 50, University of Wales College of Medicine Cooper David N. 51 Stenson Peter D. 51, University of Western Ontario Ma Bin 52, Washington University Brent Michael 53 Arumugam Manimozhiyan 53 Shteynberg David 53, Wellcome Trust Centre for Human Genetics, University of Oxford Copley Richard R. 54 Taylor Martin S. 54, Wistar Institute Riethman Harold 55 Mudunuri Uma 55, Jane Peterson, Mark Guyer, Adam Felsenfeld, Susan Old, Stephen Mockrin, Francis Collins, None, Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature. ,vol. 428, pp. 493- 521 ,(2004) , 10.1038/NATURE02426

Nick Bray, Inna Dubchak, Lior Pachter, None, AVID: A Global Alignment Program Genome Research. ,vol. 13, pp. 97- 102 ,(2003) , 10.1101/GR.789803

European Bioinformatics Institute: Birney Ewan 3 Goldman Nick 3 Kasprzyk Arkadiusz 3 Mongin Emmanuel 3 Rust Alistair G. 3 Slater Guy 3 Stabenau Arne 3 Ureta-Vidal Abel 3 Whelan Simon 3, Research Group in Biomedical Informatics Abril Josep F. 5 Guigó Roderic 5 Parra Genís 5, Bioinformatics Agarwal Pankaj 6, National Center for Biotechnology Information Agarwala Richa 7 Church Deanna M. 7 Hlavina Wratko 7 Maglott Donna R. 7 Sapojnikov Victor 7, Department of Mathematics Alexandersson Marina 8 Pachter Lior 8, Division of Medical Genetics Antonarakis Stylianos E. 9 Dermitzakis Emmanouil T. 9 Reymond Alexandre 9 Ucla Catherine 9, Center for Biomolecular Science and Engineering Baertsch Robert 10 Diekhans Mark 10 Furey Terrence S. 10 Hinrichs Angela 10 Hsu Fan 10 Karolchik Donna 10 Kent W. James 10 Roskin Krishna M. 10 Schwartz Matthias S. 10 Sugnet Charles 10 Weber Ryan J. 10, EMBL Bork Peer 11 Letunic Ivica 11 Suyama Mikita 11 Torrents David 11 Zdobnov Evgeny M. 11, UK MRC Mouse Sequencing Consortium Botcherby Marc 12 Brown Stephen D. 12 Campbell Robert D. 12 Jackson Ian 12, Lawrence Berkeley National Laboratory Bray Nicolas 13 Couronne Olivier 13 Dubchak Inna 13 Poliakov Alex 13 Rubin Edward M. 13, Department of Computer Science Brent Michael R. 14 Flicek Paul 14 Keibler Evan 14 Korf Ian 14, School of Computer Science Batalov S. 15, Jackson Laboratory Bult Carol 16 Frankel Wayne N. 16, Laboratory for Genome Exploration Carninci Piero 17 Hayashizaki Yoshihide 17 Kawai Jun 17 Okazaki Yasushi 17, Affymetrix Inc. Cawley Simon 18 Kulp David 18 Wheeler Raymond 18, Departments of Statistics and Health Evaluation Sciences Chiaromonte Francesca 19, National Human Genome Research Institute Collins Francis S. 20 Felsenfeld Adam 20 Guyer Mark 20 Peterson Jane 20 Wetterstrand Kris 20, Wellcome Trust Centre for Human Genetics Copley Richard R. 21 Mott Richard 21, Department of Electrical Engineering Dewey Colin 22, Department of Human Anatomy and Genetics Dickens Nicholas J. 23 Emes Richard D. 23 Goodstadt Leo 23 Ponting Chris P. 23 Winter Eitan 23, Department of Human Genetics Dunn Diane M. 24 von Niederhausern Andrew C. 24 Weiss Robert B. 24, Howard Hughes Medical Institute and Department of Genetics Eddy Sean R. 25 Johnson L. Steven 25 Jones Thomas A. 25, Departments of Biochemistry and Molecular Biology and Computer Science and Engineering Elnitski Laura 26 Kolbe Diana L. 26, Department of Computer Science and Engineering Eswara Pallavi 27 Miller Webb 27 O'Connor Michael J. 27 Schwartz Scott 27, Baylor College of Medicine Gibbs Richard A. 28 Muzny Donna M. 28, Institute for Systems Biology Glusman Gustavo 29 Smit Arian 29, National Human Genome Research Institute Green Eric D. 30, Department of Biochemistry and Molecular Biology Hardison Ross C. 31 Yang Shan 31, Howard Hughes Medical Institute Haussler David 32, Department of Chemistry and Biochemistry Hua Axin 33 Roe Bruce A. 33, Departments of Genetics and Medicine and Harvard-Partners Center for Genetics and Genomics Kucherlapati Raju S. 34 Montgomery Kate T. 34, Department of Statistics Li Jia 35, Department of Computer Science Li Ming 36, US DOE Joint Genome Institute Lucas Susan 37, Department of Computer Science Ma Bin 38, Cold Spring Harbor Laboratory McCombie W. Richard 39, Wellcome Trust Morgan Michael 40, Department of Computer Science and Engineering Pevzner Pavel 41 Tesler Glenn 41, Max Planck Institute for Molecular Genetics Schultz Jörg 42, Genome Therapeutics Corporation Smith Douglas R. 43, Bioinformatics Solutions Inc. Tromp John 44, Department of Molecular and Human Genetics Worley Kim C. 45, Department of Biology Lander Eric S. lander@ genome. wi. mit. edu 2 46 b, None, Initial sequencing and comparative analysis of the mouse genome. Nature. ,vol. 420, pp. 520- 562 ,(2002) , 10.1038/NATURE01262

Chris Burge, Samuel Karlin, Prediction of Complete Gene Structures in Human Genomic DNA Journal of Molecular Biology. ,vol. 268, pp. 78- 94 ,(1997) , 10.1006/JMBI.1997.0951