Tim J Hubbard

Tim J Hubbard

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Tim J Hubbard

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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

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

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

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

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

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

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

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

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

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

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

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://dx.doi.org/10.1101/gr.216102DOI Listing
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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https://pdfs.semanticscholar.org/3d10/f5899af735ca541a04ce85
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http://dx.doi.org/10.1093/bioinformatics/18.3.494DOI 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC99154PMC
http://dx.doi.org/10.1093/nar/30.1.264DOI Listing
January 2002