Tim J. P. Hubbard

Paul Flicek, Ikhlak Ahmed, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Monika Komorowska, Eugene Kulesha, Ian Longden, Thomas Maurel, William M. McLaren, Matthieu Muffato, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sheppard, Daniel Sobral, Kieron Taylor, Anja Thormann, Stephen Trevanion, Simon White, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Jennifer Harrow, Javier Herrero, Tim J. P. Hubbard, Nathan Johnson, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates, Amonida Zadissa, Stephen M. J. Searle: Ensembl 2013. Nucleic Acids Research 41(Database-Issue): 48-55 (2013)

Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron Taylor, Stephen Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Jennifer Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle: Ensembl 2012. Nucleic Acids Research 40(Database-Issue): 84-90 (2012)

Thomas A. Down, Matias Piipari, Tim J. P. Hubbard: Dalliance: interactive genome viewing on the web. Bioinformatics 27(6): 889-890 (2011)

Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Bert Overduin, Bethan Pritchard, Harpreet Singh Riat, Daniel Rios, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Jana Vandrovcova, Albert J. Vilella, Simon White, Steven P. Wilder, Amonida Zadissa, Jorge Zamora, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Jan Vogel, Stephen M. J. Searle: Ensembl 2011. Nucleic Acids Research 39(Database-Issue): 800-806 (2011)

Matias Piipari, Thomas A. Down, Harpreet Kaur Saini, Anton J. Enright, Tim J. P. Hubbard: iMotifs: an integrated sequence motif visualization and analysis environment. Bioinformatics 26(6): 843-844 (2010)

Matias Piipari, Thomas A. Down, Tim J. P. Hubbard: Metamotifs - a generative model for building families of nucleotide position weight matrices. BMC Bioinformatics 11: 348 (2010)

Paul Flicek, Bronwen L. Aken, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William M. McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James Smith, Stephen M. J. Searle: Ensembl's 10th year. Nucleic Acids Research 38(Database-Issue): 557-562 (2010)

Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. Hubbard, Christopher Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra Ten Hoopen, Robert Vaughan, Vadim Zalunin, Ewan Birney: Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Research 37(Database-Issue): 19-25 (2009)

Tim J. P. Hubbard, Bronwen L. Aken, Sarah C. Ayling, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Laura Clarke, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Daniel Rios, Michael Schuster, Guy Slater, Damian Smedley, William Spooner, Giulietta Spudich, S. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Arek Zadissa, Ewan Birney, Fiona Cunningham, Val Curwen, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Arek Kasprzyk, Glenn Proctor, James Smith, Stephen M. J. Searle, Paul Flicek: Ensembl 2009. Nucleic Acids Research 37(Database-Issue): 690-697 (2009)

Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton: The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics 24(23): 2767-2772 (2008)

Mutlu Dogruel, Thomas A. Down, Tim J. P. Hubbard: NestedMICA as an ab initio protein motif discovery tool. BMC Bioinformatics 9 (2008)

Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic: Integrating biological data - the Distributed Annotation System. BMC Bioinformatics 9(S-8) (2008)

Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Research 36(Database-Issue): 5-12 (2008)

Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin: Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research 36(Database-Issue): 419-425 (2008)

Paul Flicek, Bronwen L. Aken, Kathryn Beal, Benoit Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andrew M. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, I. Sealy, Guy Slater, Damian Smedley, Giulietta Spudich, S. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James Smith, Abel Ureta-Vidal, Stephen M. J. Searle: Ensembl 2008. Nucleic Acids Research 36(Database-Issue): 707-714 (2008)

L. G. Wilming, J. G. R. Gilbert, Kerstin Howe, S. Trevanion, Tim J. P. Hubbard, J. L. Harrow: The vertebrate genome annotation (Vega) database. Nucleic Acids Research 36(Database-Issue): 753-760 (2008)

Andreas Prlic, Thomas A. Down, Eugene Kulesha, Robert D. Finn, Andreas Kähäri, Tim J. P. Hubbard: Integrating sequence and structural biology with DAS. BMC Bioinformatics 8 (2007)

Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin: SISYPHUS - structural alignments for proteins with non-trivial relationships. Nucleic Acids Research 35(Database-Issue): 253-259 (2007)

Tim J. P. Hubbard, Bronwen L. Aken, Kathryn Beal, Benoit Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas Down, S. C. Dyer, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Javier Herrero, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Craig Melsopp, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, I. Sealy, Jessica Severin, Guy Slater, Damian Smedley, Giulietta Spudich, S. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suarez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James Smith, Abel Ureta-Vidal, Ewan Birney: Ensembl 2007. Nucleic Acids Research 35(Database-Issue): 610-617 (2007)

Thomas A. Down, Casey M. Bergman, Jing Su, Tim J. P. Hubbard: Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster. PLoS Computational Biology 3(1) (2007)

Thomas Down, Bernard Leong, Tim J. P. Hubbard: A machine learning strategy to identify candidate binding sites in human protein-coding sequence. BMC Bioinformatics 7: 419 (2006)

Ewan Birney, T. Daniel Andrews, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, Xosé M. Fernández-Suarez, Paul Flicek, Stefan Gräf, Martin Hammond, Javier Herrero, Kevin L. Howe, Vivek Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Felix Kokocinski, Eugene Kulesha, D. London, Ian Longden, Craig Melsopp, Patrick Meidl, Bert Overduin, Anne Parker, Glenn Proctor, Andreas Prlic, Mark Rae, Daniel Rios, Seth Redmond, Michael Schuster, I. Sealy, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James Smith, Arne Stabenau, Jim Stalker, S. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Tim J. P. Hubbard: Ensembl 2006. Nucleic Acids Research 34(Database-Issue): 556-561 (2006)

Andreas Prlic, Ewan Birney, Tony Cox, Thomas A. Down, Robert D. Finn, Stefan Gräf, David K. Jackson, Andreas Kähäri, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker, Tim J. P. Hubbard: The Distributed Annotation System for Integration of Biological Data. DILS 2006: 195-203

Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, Xosé M. Fernández-Suarez, James Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, Vivek Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Felix Kokocinski, D. London, Ian Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, Daniel Rios, Michael Schuster, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, S. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Ewan Birney: Ensembl 2005. Nucleic Acids Research 33(Database-Issue): 447-453 (2005)

J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, Stephen Keenan, Patrick Meidl, Stephen M. J. Searle, Jim Stalker, R. Storey, S. Trevanion, L. G. Wilming, Tim J. P. Hubbard: The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Research 33(Database-Issue): 459-465 (2005)

Andreas Prlic, Thomas A. Down, Tim J. P. Hubbard: Adding Some SPICE to DAS. ECCB/JBI 2005: 41

Thomas A. Down, Tim J. P. Hubbard: What can we learn from noncoding regions of similarity between genomes? BMC Bioinformatics 5: 131 (2004)

Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 32(Database-Issue): 226-229 (2004)

Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Cáccamo, Graham Cameron, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, James A. Cuff, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, Eduardo Eyras, Xosé M. Fernández-Suarez, P. Gane, B. Gibbins, James Gilbert, Martin Hammond, H. Hotz, Vivek Iyer, Andreas Kähäri, K. Jekosch, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehväslaiho, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Glenn Proctor, Mark Rae, Stephen M. J. Searle, Guy Slater, Damian Smedley, James Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Abel Ureta-Vidal, Cara Woodwark, Michele E. Clamp, Tim J. P. Hubbard: Ensembl 2004. Nucleic Acids Research 32(Database-Issue): 468-470 (2004)

Diego di Bernardo, Thomas Down, Tim J. P. Hubbard: ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinformatics 19(13): 1606-1611 (2003)

Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas Down, Richard Durbin, Eduardo Eyras, James Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, Vivek Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alastair Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Ewan Birney: Ensembl 2002: accommodating comparative genomics. Nucleic Acids Research 31(1): 38-42 (2003)

Raphaël Leplae, Tim J. P. Hubbard: MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics 18(3): 494-495 (2002)

Tim J. P. Hubbard, Daniel Barker, Ewan Birney, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas Down, Richard Durbin, Eduardo Eyras, James Gilbert, Martin Hammond, Lukasz Huminiecki, Arek Kasprzyk, Heikki Lehväslaiho, Philip Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Matthew R. Pocock, Simon C. Potter, Alastair Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Michele E. Clamp: The Ensembl genome database project. Nucleic Acids Research 30(1): 38-41 (2002)

Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin: SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research 30(1): 264-267 (2002)

Tim J. P. Hubbard: Biological information: making it accessible and integrated (and trying to make sense of it). ECCB 2002: 140-140

Matthew R. Pocock, Tim J. P. Hubbard: A browser for expression data. Bioinformatics 16(4): 402-403 (2000)

Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia: SCOP: a Structural Classification of Proteins database. Nucleic Acids Research 28(1): 257-259 (2000)

Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia: SCOP: a Structural Classification of Proteins database. Nucleic Acids Research 27(1): 254-256 (1999)

Matthew R. Pocock, Tim J. P. Hubbard, Ewan Birney: SPEM: a parser for EMBL style flat file database entries. Bioinformatics 14(9): 823-824 (1998)

Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia: SCOP: a structural classification of proteins database. Nucleic Acids Research 25(1): 236-239 (1997)

Steven E. Brenner, Tim J. P. Hubbard: A Specification for Defining and Annotating Regions of Macromolecular Structures. ISMB 1995: 66-74

Tim J. P. Hubbard: Use of beta-strand Interaction Pseudo-Potentials in Protein Structure Prediction and Modeling. HICSS (5) 1994: 336-344