AuthorProfile for Tim J. Hubbard

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

France Denoeud Philipp Kapranov Catherine Ucla Adam Frankish Robert Castelo Jorg Drenkow Julien Lagarde Tyler Alioto Jacqueline Chrast Carine Wyss Ruth Taylor Zahra Hance Sylvain Foissac Jane Rogers Tim Hubbard Jennifer Harrow Roderic Guigó Alexandre Reymond

SCOP: a Structural Classification of Proteins database.

T. J. Hubbard

New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.

Andriy Kryshtafovych Andreas Prlic Pawel Daniluk Maciej Milostan Tim Hubbard Krzysztof Fidelis

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Karen Eilbeck Michele Magrane Sandra Orchard Andreas Prlic Tim J. P. Hubbard Henning Hermjakob

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

Tim J. P. Hubbard

SCOP database in 2002: refinements accommodate structural genomics.

Loredana Lo Conte Tim J. P. Hubbard Cyrus Chothia

Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach.

Jenny Mattison Jaap Kool Jeroen de Ridder Lodewyk Wessels Jos Jonkers Adam Butler Markus Brosch Louise van der Weyden Maarten van Lohuizen Anton Berns Tim Hubbard

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Jennifer Harrow Craig Wallin Mark Diekhans Steve Searle Elizabeth Hart Bronwen Aken Sarah Ayling Robert Baertsch Val Curwen Michael Dicuccio Manolis Kellis Jennifer Lee Michael Schuster Andrew Shkeda Clara Amid Garth Brown Oksana Dukhanina Adam Frankish Jennifer Hart Jonathan Mudge Terence Murphy Jeena Rajan Bhanu Rajput Catherine Snow Charles Steward David Webb Laurens Wilming Wenyu Wu Ewan Birney David Haussler Tim Hubbard James Ostell Richard Durbin David Lipman

Protein folds in the all-beta and all-alpha classes.

T. Hubbard

International network of cancer genome projects.

Warwick Anderson Fabien Calvo Mark Guyer David Kerr Peter Klatt Patrik Kolar Frank Laplace Jane Peterson Tatsuhiro Shibata Koichi Watanabe Huanming Yang Martin Bobrow Yann Joly Kazuto Kato Pilar Nicolás Susan Wallace Nikolajs Zeps Peter Lichter Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Peter Geary Arek Kasprzyk Hidewaki Nakagawa Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver Hiroyuki Aburatani Xavier Estivill Ivo Gut Martin Hirst Partha Majumder Marco Marra Hidewaki Nakagawa Zemin Ning Yijun Ruan Tatsuhiro Shibata Harold Swerdlow Liu Yang Paul Flicek Gad Getz Roderic Guigó David Haussler Simon Heath Tim J. Hubbard Tao Jiang Qibin Li Ruibang Luo Victor Quesada Chris Sander Tatsuhiro Shibata Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia Honglong Wu Shancen Zhao Guangyu Zhou Roderic Guigó Yann Joly Arek Kasprzyk Mark Lathrop Gilles Thomas Alfonso Valencia Teruhiko Yoshida Myles Axton Chris Gunter Mark Guyer Arek Kasprzyk Junjun Zhang Jianxin Wang Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jack Hsu Martin Bobrow Yann Joly Pilar Nicolás Catherine Vergely Teruhiko Yoshida Nicole Cloonan Anna deFazio Dariush Etemadmoghadam Aldo Scarpa Steve Gallinger Debabrata Mukhopadhyay Lynda Chin Sarah Thayer Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Egor Prokhortchouk Mathias Uhlén Juris Viksna Fredrik Ponten Ewan Birney Ake Borg Carlos Caldas Christos Sotiriou Marc van de Vijver Fabien Calvo Daniel Birnbaum Hélène Blanche Sandrine Boyault Christian Chabannon Ivo Gut Mark Lathrop Xavier Pivot Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Peter Lichter Roland Eils Benedikt Brors Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Christof von Kalle Rajiv Sarin Aldo Scarpa Paolo Pederzoli Massimo Delledonne Alberto Bardelli Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Xavier Estivill Roderic Guigó Silvia de Sanjosé Emili Montserrat Pedro Jares Alfonso Valencia Victor Quesada Silvia Bea Marc van de Vijver Gilles Thomas Samuel Aparicio Ake Borg Carlos Caldas Lynda Chin Gad Getz Chris Gunter Mark Guyer Jane Peterson Chris Sander Lynda Chin Peter Lichter Warwick Anderson Martin Bobrow Wylie Burke Mark Guyer Youyong Lu Partha Majumder Marco Marra Jane Peterson Huanming Yang

SPEM: a parser for EMBL style flat file database entries.

T. Hubbard

RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.

T. J. Hubbard

SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data.

T. J. Hubbard

Relevance Vector Machines for classifying points and regions in biological sequences

Hubbard, Tim J. P.

Petabyte-scale innovations at the European Nucleotide Archive.

Guy Cochrane Ruth Akhtar 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

Population statistics of protein structures: lessons from structural classifications.

T. J. Hubbard

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

Antonina Andreeva Dave Howorth Tim J. P. Hubbard Cyrus Chothia

Numerical criteria for the evaluation of ab initio predictions of protein structure.

T. J. Hubbard

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

Antonina Andreeva Dave Howorth Tim J. P. Hubbard Cyrus Chothia

The DNA sequence and analysis of human chromosome 6.

T. Hubbard

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

Guy Cochrane Ruth Akhtar Philippe Aldebert Nicola Althorpe Alastair Baldwin Kirsty Bates Sumit Bhattacharyya James 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 Hubbard Ewan Birney

Prepublication data sharing.

Ewan Birney Chris Gunter Sean Eddy Jane Rogers Rolf Apweiler Lisa Berglund Martin Bobrow Chas Bountra Ken Dewar Richard Durbin Khaled El Emam Lars Feuk John Gallacher Antoni Granell Francisco Guarner Tim Hubbard Yann Joly Jane Kaye Bartha Maria Knoppers Jingchu Luo Linda Miller Webb Miller Don Moerman Vincent Mooser Julian Parkhill Christopher Rawlings Toshihiro Tanaka Janet Thornton Tatsuhiko Tsunoda David Valle Susan Wallace George Weinstock Cathy Wu Jiayan Wu Jun Yu

Large-scale discovery of promoter motifs in Drosophila melanogaster.

Jing Su Tim J. P. Hubbard

SISYPHUS—structural alignments for proteins with non-trivial

Antonina Andreeva Andreas Prlić Tim J. P. Hubbard

The Ensembl genome database project.

Tim J. P. Hubbard Daniel Barker Ewan Birney Graham Cameron Yuan Chen Laura Clarke Tony Cox 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 Alastair Rust Esther Schmidt Guy Slater James Smith William Spooner Arne Stabenau Jim Stalker Elia Stupka Imre Vastrik

The DNA sequence and comparative analysis of human chromosome 20.

T. Hubbard

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

John Moult Krzysztof Fidelis Adam Zemla Tim Hubbard Anna Tramontano

SCOP: a Structural Classification of Proteins database

Tim J. P. Hubbard Bart Ailey Cyrus Chothia

Using neural networks for prediction of the subcellular location of proteins.

T. Hubbard

Prediction of the structure of GroES and its interaction with GroEL.

T. J. Hubbard

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.

Mario Caccamo Tim Hubbard Jane Rogers

Use of beta-strand Interaction Pseudo-Potentials in Protein Structure Prediction and Modeling.

Tim J. P. Hubbard

Update on protein structure prediction: results of the 1995 IRBM workshop.

T. Hubbard

The vertebrate genome annotation (Vega) database.

Tim J. P. Hubbard

Petabyte-scale innovations at the European Nucleotide Archive.

Guy Cochrane Ruth Akhtar James Bonfield Lawrence Bower Fehmi Demiralp Nadeem Faruque Richard Gibson Gemma Hoad Tim 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

SCOP: a Structural Classification of Proteins database.

Loredana Lo Conte Bart Ailey Tim J. P. Hubbard Cyrus Chothia

Understanding protein structure: using scop for fold interpretation.

T. J. Hubbard

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Karen Eilbeck Michele Magrane Andreas Prlic Tim J. P. Hubbard Henning Hermjakob

statistics of protein structures. Current Opinion in

Hubbard T.

The Ensembl genome database project.

T. Hubbard

SCOP: a Structural Classification of Proteins database

Tim J. P. Hubbard Cyrus Chothia

MaxBench: evaluation of sequence and structure comparison methods.

Raphaël Leplae Tim J. P. Hubbard

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

Tim J. P. Hubbard

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

Matias Piipari Tim J. P. Hubbard

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

Antonina Andreeva Andreas Prlić Tim J. P. Hubbard

Mining the draft human genome.

T. J. Hubbard

The Vertebrate Genome Annotation (Vega) database.

Patrick Meidl Jim Stalker Tim J. P. Hubbard

SCOP: a structural classification of proteins database.

T. J. Hubbard

SCOP: a structural classification of proteins database.

T. J. Hubbard

New horizons in sequence analysis.

T. J. Hubbard

The DNA sequence and biological annotation of human chromosome 1.

T. Hubbard

The DNA sequence and analysis of human chromosome 13

Hubbard, T.

The vertebrate genome annotation (Vega) database.

T. Hubbard

The Vertebrate Genome Annotation (Vega) database.

T. Hubbard

The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.

T. J. Hubbard

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

Hubbard, Tim J. P.

The DNA sequence and analysis of human chromosome 13.

T. Hubbard

The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms.

T. J. Hubbard

Protein engineering and design.

T. Hubbard

The Vertebrate Genome Annotation (Vega) database

T. Hubbard

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

Jaap Kool Konstantin Matentzoglu Jeroen de Ridder Jenny Mattison Miranda van Uitert Wendy Lagcher Daoud Sie Tony Cox Marcel Reinders Tim J. Hubbard Jane Rogers Jos Jonkers Lodewyk Wessels Maarten van Lohuizen Anton Berns

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

Tim J. P. Hubbard

SCOP: a structural classification of proteins database.

Tim J. P. Hubbard Cyrus Chothia

SCOP database in 2002: refinements accommodate structural genomics

Loredana Lo Conte Tim J. P. Hubbard Cyrus Chothia

SPEM: a parser for EMBL style flat file database entries.

Tim J. P. Hubbard Ewan Birney

The DNA sequence of the human X chromosome.

Kirsten McLay Donna Muzny Matthias Platzer Adam Frankish Ralf Sudbrak Gaiping Wen Stephen Searle Juliane Ramser Rui Chen Preethi Gunaratne Paul Havlak Stephen Richards Graham Scott David Steffen Erica Sodergren Swaroop Aradhya Andrea Ballabio Ruby Banerjee Helen Beasley Alfred Beck Christian Buhay Joanne Burgess John Burton Dean Chavez Guan Chen Yuan Chen Zhijian Chen Craig Chinault Alfredo Ciccodicola Graham Clarke Karen Clifford Robert David Joy Davies Clay Davis John Davis Oliver Delgado Pawandeep Dhami Yan Ding Huyen Dinh Heather Draper Matthew Dunn Fiona Francis John Frankland James Gilbert Gernot Glöckner Susan Gribble Rhian Gwilliam Cerissa Hamilton Steffen Hennig Bernd Hinzmann Sarah Ho Jennifer Hume David Johnson Sally Jones Stephen Keenan Susan Kelly Petra Kioschis Sven Klages Cordelia Langford Wen Liu Jing Lu Jie Ma Jennifer McDowall Patrick Meidl Thomas Meitinger Sarah Milne George Miner Margaret Morgan Sidney Morris Ines Müller Ngoc Nguyen David Parker Julia Parrish Shiran Pasternak Dina Patel Kathrin Reichwald Susan Rhodes David Schlessinger Hua Shen David Swarbreck Stefan Taudien Brian Teague Karen Thomas Alan Tracey Daniel Verduzco Melanie Wall Qiaoyan Wang James Warren Xuehong Wei Anthony West Gabrielle Williams Helen Williamson Laurens Wilming Jingkun Zhang David Buck Richard Reinhardt Annemarie Poustka André Rosenthal Hans Lehrach Alfons Meindl Mark Vaudin George Weinstock Richard Durbin Tim Hubbard Stephan Beck Jane Rogers

MaxBench: evaluation of sequence and structure comparison methods.

Tim J. P. Hubbard

NestedMICA as an ab initio protein motif discovery tool.

Mutlu Dogruel Tim J. P. Hubbard

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.

T. Hubbard

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

Hubbard, Tim J.

The Distributed Annotation System for Integration of Biological Data.

Andreas Prlic Ewan Birney Tony Cox Stefan Gräf Andreas Kähäri Eugene Kulesha Roger Pettett James Smith Jim Stalker Tim J. P. Hubbard

Prediction targets of CASP4.

T. J. Hubbard

18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design.

T. Hubbard

SCOP: a structural classification of proteins database for the investigation of sequences and structures.

T. Hubbard

Open annotation offers a democratic solution to genome sequencing.

T. Hubbard

SCOP: a Structural Classification of Proteins database

Loredana Lo Conte Bart Ailey Tim J. P. Hubbard Cyrus Chothia

The DNA sequence and comparative analysis of human chromosome 10.

T. Hubbard

Protein structure prediction: playing the fold.

T. Hubbard

SCOP: a Structural Classification of Proteins database.

Tim J. P. Hubbard Bart Ailey Cyrus Chothia

Intermediate sequences increase the detection of homology between sequences.

T. Hubbard

Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote . . .

Jong Park Kevin Karplus Christian Barrett Richard Hughey David Haussler Tim Hubbard Cyrus Chothia

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

Guy Cochrane Ruth Akhtar Philippe Aldebert Nicola Althorpe Alastair Baldwin Kirsty Bates Sumit Bhattacharyya 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

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

Antonina Andreeva Andreas Prlic Tim J. P. Hubbard

SCOP database in 2002: refinements accommodate structural genomics.

Loredana Lo Conte Tim J. P. Hubbard Cyrus Chothia