Tim Hubbard

Tim Hubbard

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Tim Hubbard

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Scientists on the Spot: Sequencing the human genome to influence patient healthcare.

Cardiovasc Res 2018 07;114(9):e66-e67

Department of Medical & Molecular Genetics, King's College London.

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http://dx.doi.org/10.1093/cvr/cvy133DOI Listing
July 2018

Analysis of diagnoses extracted from electronic health records in a large mental health case register.

PLoS One 2017 16;12(2):e0171526. Epub 2017 Feb 16.

NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171526PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312950PMC
August 2017

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease.

Database (Oxford) 2017 01;2017(1)

Department of Biostatistics and Health Informatics, King's College London, De Crespigny Park, Denmark Hill London SE5 8AF, UK.

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http://dx.doi.org/10.1093/database/bax027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467557PMC
January 2017

An interactive genome browser of association results from the UK10K cohorts project.

Bioinformatics 2015 Dec 26;31(24):4029-31. Epub 2015 Aug 26.

Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK, Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673976PMC
December 2015

A comparison of peak callers used for DNase-Seq data.

PLoS One 2014 8;9(5):e96303. Epub 2014 May 8.

The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096303PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014496PMC
October 2015

Comparative analysis of pseudogenes across three phyla.

Proc Natl Acad Sci U S A 2014 Sep 25;111(37):13361-6. Epub 2014 Aug 25.

Program in Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Department of Computer Science, Yale University, New Haven, CT 06511

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http://dx.doi.org/10.1073/pnas.1407293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169933PMC
September 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

PLoS One 2013 26;8(7):e69853. Epub 2013 Jul 26.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069853PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724795PMC
April 2014

Current status and new features of the Consensus Coding Sequence database.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D865-72. Epub 2013 Nov 11.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965069PMC
January 2014

Systematic evaluation of spliced alignment programs for RNA-seq data.

Nat Methods 2013 Dec 3;10(12):1185-91. Epub 2013 Nov 3.

1] European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK. [2].

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http://dx.doi.org/10.1038/nmeth.2722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018468PMC
December 2013

Assessment of transcript reconstruction methods for RNA-seq.

Nat Methods 2013 Dec 3;10(12):1177-84. Epub 2013 Nov 3.

European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.2714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851240PMC
December 2013

The zebrafish reference genome sequence and its relationship to the human genome.

Authors:
Kerstin Howe Matthew D Clark Carlos F Torroja James Torrance Camille Berthelot Matthieu Muffato John E Collins Sean Humphray Karen McLaren Lucy Matthews Stuart McLaren Ian Sealy Mario Caccamo Carol Churcher Carol Scott Jeffrey C Barrett Romke Koch Gerd-Jörg Rauch Simon White William Chow Britt Kilian Leonor T Quintais José A Guerra-Assunção Yi Zhou Yong Gu Jennifer Yen Jan-Hinnerk Vogel Tina Eyre Seth Redmond Ruby Banerjee Jianxiang Chi Beiyuan Fu Elizabeth Langley Sean F Maguire Gavin K Laird David Lloyd Emma Kenyon Sarah Donaldson Harminder Sehra Jeff Almeida-King Jane Loveland Stephen Trevanion Matt Jones Mike Quail Dave Willey Adrienne Hunt John Burton Sarah Sims Kirsten McLay Bob Plumb Joy Davis Chris Clee Karen Oliver Richard Clark Clare Riddle David Elliot David Eliott Glen Threadgold Glenn Harden Darren Ware Sharmin Begum Beverley Mortimore Beverly Mortimer Giselle Kerry Paul Heath Benjamin Phillimore Alan Tracey Nicole Corby Matthew Dunn Christopher Johnson Jonathan Wood Susan Clark Sarah Pelan Guy Griffiths Michelle Smith Rebecca Glithero Philip Howden Nicholas Barker Christine Lloyd Christopher Stevens Joanna Harley Karen Holt Georgios Panagiotidis Jamieson Lovell Helen Beasley Carl Henderson Daria Gordon Katherine Auger Deborah Wright Joanna Collins Claire Raisen Lauren Dyer Kenric Leung Lauren Robertson Kirsty Ambridge Daniel Leongamornlert Sarah McGuire Ruth Gilderthorp Coline Griffiths Deepa Manthravadi Sarah Nichol Gary Barker Siobhan Whitehead Michael Kay Jacqueline Brown Clare Murnane Emma Gray Matthew Humphries Neil Sycamore Darren Barker David Saunders Justene Wallis Anne Babbage Sian Hammond Maryam Mashreghi-Mohammadi Lucy Barr Sancha Martin Paul Wray Andrew Ellington Nicholas Matthews Matthew Ellwood Rebecca Woodmansey Graham Clark James D Cooper James Cooper Anthony Tromans Darren Grafham Carl Skuce Richard Pandian Robert Andrews Elliot Harrison Andrew Kimberley Jane Garnett Nigel Fosker Rebekah Hall Patrick Garner Daniel Kelly Christine Bird Sophie Palmer Ines Gehring Andrea Berger Christopher M Dooley Zübeyde Ersan-Ürün Cigdem Eser Horst Geiger Maria Geisler Lena Karotki Anette Kirn Judith Konantz Martina Konantz Martina Oberländer Silke Rudolph-Geiger Mathias Teucke Christa Lanz Günter Raddatz Kazutoyo Osoegawa Baoli Zhu Amanda Rapp Sara Widaa Cordelia Langford Fengtang Yang Stephan C Schuster Nigel P Carter Jennifer Harrow Zemin Ning Javier Herrero Steve M J Searle Anton Enright Robert Geisler Ronald H A Plasterk Charles Lee Monte Westerfield Pieter J de Jong Leonard I Zon John H Postlethwait Christiane Nüsslein-Volhard Tim J P Hubbard Hugues Roest Crollius Jane Rogers Derek L Stemple

Nature 2013 Apr 17;496(7446):498-503. Epub 2013 Apr 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature12111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927PMC
April 2013

The GENCODE pseudogene resource.

Genome Biol 2012 Sep 26;13(9):R51. Epub 2012 Sep 26.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395PMC
September 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Prizes for innovation of new medicines and vaccines.

Ann Health Law 2009 ;18(2):155-86, 8 p. preceding i

Knowledge Ecology International.

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November 2011

Developing and implementing an institute-wide data sharing policy.

Genome Med 2011 Sep 28;3(9):60. Epub 2011 Sep 28.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1186/gm276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239235PMC
September 2011

Dalliance: interactive genome viewing on the web.

Bioinformatics 2011 Mar 19;27(6):889-90. Epub 2011 Jan 19.

Wellcome Trust/CRUK Gurdon Institute, Cambridge CB2 1QN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051325PMC
March 2011

AnnoTrack--a tracking system for genome annotation.

BMC Genomics 2010 Oct 5;11:538. Epub 2010 Oct 5.

Vertebrate Genome Analysis, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK.

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http://dx.doi.org/10.1186/1471-2164-11-538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091687PMC
October 2010

Metamotifs--a generative model for building families of nucleotide position weight matrices.

BMC Bioinformatics 2010 Jun 25;11:348. Epub 2010 Jun 25.

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1186/1471-2105-11-348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906491PMC
June 2010

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

iMotifs: an integrated sequence motif visualization and analysis environment.

Bioinformatics 2010 Mar 26;26(6):843-4. Epub 2010 Jan 26.

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832821PMC
March 2010

Cancer gene discovery in mouse and man.

Biochim Biophys Acta 2009 Dec 12;1796(2):140-61. Epub 2009 Mar 12.

Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.

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http://dx.doi.org/10.1016/j.bbcan.2009.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756404PMC
December 2009

Accurate and sensitive peptide identification with Mascot Percolator.

J Proteome Res 2009 Jun;8(6):3176-81

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1021/pr800982sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734080PMC
June 2009

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.

Mol Cell Proteomics 2008 May 23;7(5):962-70. Epub 2008 Jan 23.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1074/mcp.M700293-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656932PMC
May 2008

Critical assessment of methods of protein structure prediction-Round VII.

Proteins 2007 ;69 Suppl 8:3-9

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1002/prot.21767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653632PMC
January 2008

Data growth and its impact on the SCOP database: new developments.

Nucleic Acids Res 2008 Jan 13;36(Database issue):D419-25. Epub 2007 Nov 13.

MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238974PMC
January 2008

NestedMICA as an ab initio protein motif discovery tool.

BMC Bioinformatics 2008 Jan 14;9:19. Epub 2008 Jan 14.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

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http://dx.doi.org/10.1186/1471-2105-9-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267705PMC
January 2008

Integrating sequence and structural biology with DAS.

BMC Bioinformatics 2007 Sep 12;8:333. Epub 2007 Sep 12.

The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2105-8-333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031907PMC
September 2007

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

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

SISYPHUS--structural alignments for proteins with non-trivial relationships.

Nucleic Acids Res 2007 Jan 26;35(Database issue):D253-9. Epub 2006 Oct 26.

MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635320PMC
January 2007

Large-scale discovery of promoter motifs in Drosophila melanogaster.

PLoS Comput Biol 2007 Jan 5;3(1):e7. Epub 2006 Dec 5.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.0030007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779301PMC
January 2007

A machine learning strategy to identify candidate binding sites in human protein-coding sequence.

BMC Bioinformatics 2006 Sep 26;7:419. Epub 2006 Sep 26.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1186/1471-2105-7-419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592515PMC
September 2006

Critical assessment of methods of protein structure prediction (CASP)--round 6.

Proteins 2005 ;61 Suppl 7:3-7

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1002/prot.20716DOI Listing
May 2006

Biological information: making it accessible and integrated (and trying to make sense of it).

Authors:
Tim Hubbard

Bioinformatics 2002 ;18 Suppl 2:S140

Sanger Institute, Cambridgeshire, UK.

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September 2005

Adding some SPICE to DAS.

Bioinformatics 2005 Sep;21 Suppl 2:ii40-1

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti1106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656757PMC
September 2005

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.

Nucleic Acids Res 2005 10;33(5):1445-53. Epub 2005 Mar 10.

Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gki282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1064142PMC
March 2005

The DNA sequence of the human X chromosome.

Authors:
Mark T Ross Darren V Grafham Alison J Coffey Steven Scherer Kirsten McLay Donna Muzny Matthias Platzer Gareth R Howell Christine Burrows Christine P Bird Adam Frankish Frances L Lovell Kevin L Howe Jennifer L Ashurst Robert S Fulton Ralf Sudbrak Gaiping Wen Matthew C Jones Matthew E Hurles T Daniel Andrews Carol E Scott Stephen Searle Juliane Ramser Adam Whittaker Rebecca Deadman Nigel P Carter Sarah E Hunt Rui Chen Andrew Cree Preethi Gunaratne Paul Havlak Anne Hodgson Michael L Metzker Stephen Richards Graham Scott David Steffen Erica Sodergren David A Wheeler Kim C Worley Rachael Ainscough Kerrie D Ambrose M Ali Ansari-Lari Swaroop Aradhya Robert I S Ashwell Anne K Babbage Claire L Bagguley Andrea Ballabio Ruby Banerjee Gary E Barker Karen F Barlow Ian P Barrett Karen N Bates David M Beare Helen Beasley Oliver Beasley Alfred Beck Graeme Bethel Karin Blechschmidt Nicola Brady Sarah Bray-Allen Anne M Bridgeman Andrew J Brown Mary J Brown David Bonnin Elspeth A Bruford Christian Buhay Paula Burch Deborah Burford Joanne Burgess Wayne Burrill John Burton Jackie M Bye Carol Carder Laura Carrel Joseph Chako Joanne C Chapman Dean Chavez Ellson Chen Guan Chen Yuan Chen Zhijian Chen Craig Chinault Alfredo Ciccodicola Sue Y Clark Graham Clarke Chris M Clee Sheila Clegg Kerstin Clerc-Blankenburg Karen Clifford Vicky Cobley Charlotte G Cole Jen S Conquer Nicole Corby Richard E Connor Robert David Joy Davies Clay Davis John Davis Oliver Delgado Denise Deshazo Pawandeep Dhami Yan Ding Huyen Dinh Steve Dodsworth Heather Draper Shannon Dugan-Rocha Andrew Dunham Matthew Dunn K James Durbin Ireena Dutta Tamsin Eades Matthew Ellwood Alexandra Emery-Cohen Helen Errington Kathryn L Evans Louisa Faulkner Fiona Francis John Frankland Audrey E Fraser Petra Galgoczy James Gilbert Rachel Gill Gernot Glöckner Simon G Gregory Susan Gribble Coline Griffiths Russell Grocock Yanghong Gu Rhian Gwilliam Cerissa Hamilton Elizabeth A Hart Alicia Hawes Paul D Heath Katja Heitmann Steffen Hennig Judith Hernandez Bernd Hinzmann Sarah Ho Michael Hoffs Phillip J Howden Elizabeth J Huckle Jennifer Hume Paul J Hunt Adrienne R Hunt Judith Isherwood Leni Jacob David Johnson Sally Jones Pieter J de Jong Shirin S Joseph Stephen Keenan Susan Kelly Joanne K Kershaw Ziad Khan Petra Kioschis Sven Klages Andrew J Knights Anna Kosiura Christie Kovar-Smith Gavin K Laird Cordelia Langford Stephanie Lawlor Margaret Leversha Lora Lewis Wen Liu Christine Lloyd David M Lloyd Hermela Loulseged Jane E Loveland Jamieson D Lovell Ryan Lozado Jing Lu Rachael Lyne Jie Ma Manjula Maheshwari Lucy H Matthews Jennifer McDowall Stuart McLaren Amanda McMurray Patrick Meidl Thomas Meitinger Sarah Milne George Miner Shailesh L Mistry Margaret Morgan Sidney Morris Ines Müller James C Mullikin Ngoc Nguyen Gabriele Nordsiek Gerald Nyakatura Christopher N O'Dell Geoffery Okwuonu Sophie Palmer Richard Pandian David Parker Julia Parrish Shiran Pasternak Dina Patel Alex V Pearce Danita M Pearson Sarah E Pelan Lesette Perez Keith M Porter Yvonne Ramsey Kathrin Reichwald Susan Rhodes Kerry A Ridler David Schlessinger Mary G Schueler Harminder K Sehra Charles Shaw-Smith Hua Shen Elizabeth M Sheridan Ratna Shownkeen Carl D Skuce Michelle L Smith Elizabeth C Sotheran Helen E Steingruber Charles A Steward Roy Storey R Mark Swann David Swarbreck Paul E Tabor Stefan Taudien Tineace Taylor Brian Teague Karen Thomas Andrea Thorpe Kirsten Timms Alan Tracey Steve Trevanion Anthony C Tromans Michele d'Urso Daniel Verduzco Donna Villasana Lenee Waldron Melanie Wall Qiaoyan Wang James Warren Georgina L Warry Xuehong Wei Anthony West Siobhan L Whitehead Mathew N Whiteley Jane E Wilkinson David L Willey Gabrielle Williams Leanne Williams Angela Williamson Helen Williamson Laurens Wilming Rebecca L Woodmansey Paul W Wray Jennifer Yen Jingkun Zhang Jianling Zhou Huda Zoghbi Sara Zorilla David Buck Richard Reinhardt Annemarie Poustka André Rosenthal Hans Lehrach Alfons Meindl Patrick J Minx Ladeana W Hillier Huntington F Willard Richard K Wilson Robert H Waterston Catherine M Rice Mark Vaudin Alan Coulson David L Nelson George Weinstock John E Sulston Richard Durbin Tim Hubbard Richard A Gibbs Stephan Beck Jane Rogers David R Bentley

Nature 2005 Mar;434(7031):325-37

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665286PMC
March 2005

What can we learn from noncoding regions of similarity between genomes?

BMC Bioinformatics 2004 Sep 15;5:131. Epub 2004 Sep 15.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1186/1471-2105-5-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523850PMC
September 2004

Domain insertions in protein structures.

J Mol Biol 2004 May;338(4):633-41

The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1016/j.jmb.2004.03.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665287PMC
May 2004

A new trade framework for global healthcare R&D.

PLoS Biol 2004 Feb 17;2(2):E52. Epub 2004 Feb 17.

Wellcome Trust Sanger Institute in Hinxton, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.0020052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC340954PMC
February 2004

Critical assessment of methods of protein structure prediction (CASP)-round V.

Proteins 2003 ;53 Suppl 6:334-9

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1002/prot.10556DOI Listing
January 2004

CASP5 target classification.

Proteins 2003 ;53 Suppl 6:340-51

Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75390-9050, USA.

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http://dx.doi.org/10.1002/prot.10555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656935PMC
January 2004

SCOP database in 2004: refinements integrate structure and sequence family data.

Nucleic Acids Res 2004 Jan;32(Database issue):D226-9

MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1093/nar/gkh039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308773PMC
January 2004

ddbRNA: detection of conserved secondary structures in multiple alignments.

Bioinformatics 2003 Sep;19(13):1606-11

Telethon Institute of Genetics and Medicine, Via P Castellino 111, 80133 Naples, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btg229DOI Listing
September 2003

Databases and tools for browsing genomes.

Annu Rev Genomics Hum Genet 2002 15;3:293-310. Epub 2002 Apr 15.

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.

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December 2002

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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December 2002

A physical map of the mouse genome.

Nature 2002 Aug 4;418(6899):743-50. Epub 2002 Aug 4.

The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature00957DOI Listing
August 2002

Computational detection and location of transcription start sites in mammalian genomic DNA.

Genome Res 2002 Mar;12(3):458-61

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.216102
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155284PMC
March 2002

MaxBench: evaluation of sequence and structure comparison methods.

Bioinformatics 2002 Mar;18(3):494-5

Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/18.3.494DOI Listing
March 2002

The significance of performance ranking in CASP--response to Marti-Renom et al.

Structure 2002 Mar;10(3):291-2; discussion 292-3

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.

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http://dx.doi.org/10.1016/s0969-2126(02)00728-1DOI Listing
March 2002

SCOP database in 2002: refinements accommodate structural genomics.

Nucleic Acids Res 2002 Jan;30(1):264-7

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

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http://dx.doi.org/10.1093/nar/30.1.264DOI Listing
January 2002