David T. Jones

Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo: Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Research 41(Database-Issue): 499-507 (2013)

David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto, Massimiliano Pontil: PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2): 184-190 (2012)

Timothy Nugent, David T. Jones: Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinformatics 13: 169 (2012)

Timothy Nugent, Sean Ward, David T. Jones: The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics 27(10): 1438-1439 (2011)

Alison L. Cuff, Ian Sillitoe, Tony Lewis, Andrew B. Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David T. Jones, Janet M. Thornton, Christine A. Orengo: Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Research 39(Database-Issue): 420-426 (2011)

Daniel W. A. Buchan, S. M. Ward, Anna E. Lobley, Timothy Nugent, Kevin Bryson, David T. Jones: Protein annotation and modelling servers at University College London. Nucleic Acids Research 38(Web-Server-Issue): 563-568 (2010)

Timothy Nugent, David T. Jones: Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. PLoS Computational Biology 6(3) (2010)

Anna E. Lobley, Michael I. Sadowski, David T. Jones: pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 25(14): 1761-1767 (2009)

Antonis Koussounadis, Oliver Redfern, David T. Jones: Improving classification in protein structure databases using text mining. BMC Bioinformatics 10 (2009)

Stefano Lise, Cédric Archambeau, Massimiliano Pontil, David T. Jones: Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics 10: 365 (2009)

Timothy Nugent, David T. Jones: Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 10 (2009)

Ching-Wai Tan, David T. Jones: Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics 9 (2008)

Anna E. Lobley, Timothy Nugent, Christine A. Orengo, David T. Jones: FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Research 36(Web-Server-Issue): 297-302 (2008)

Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel J. Martin, Alexandra Poulovassilis, Philip Jones, Richard G. Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo, Simon J. Hubbard: ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Research 36(Web-Server-Issue): 485-490 (2008)

David T. Jones: Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23(5): 538-544 (2007)

Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones: Inferring Function Using Patterns of Native Disorder in Proteins. PLoS Computational Biology 3(8) (2007)

Liam J. McGuffin, Richard T. Smith, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones: High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics 7: 288 (2006)

Stefano Lise, Alice Walker-Taylor, David T. Jones: Docking protein domains in contact space. BMC Bioinformatics 7: 310 (2006)

Stefano Lise, David T. Jones: Invited Talk: Docking Protein Domains Using a Contact Map Representation. German Conference on Bioinformatics 2006: 74

Timothy M. D. Ebbels, Bernard F. Buxton, David T. Jones: springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an "information landscape". ISMB (Supplement of Bioinformatics) 2006: 99-107

Chris S. Pettitt, Liam J. McGuffin, David T. Jones: Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21(17): 3509-3515 (2005)

Kevin Bryson, Liam J. McGuffin, Russell L. Marsden, Jonathan J. Ward, Jaspreet Singh Sodhi, David T. Jones: Protein structure prediction servers at University College London. Nucleic Acids Research 33(Web-Server-Issue): 36-38 (2005)

Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones: The Genomic Threading Database. Bioinformatics 20(1): 131-132 (2004)

Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones: The DISOPRED server for the prediction of protein disorder. Bioinformatics 20(13): 2138-2139 (2004)

David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones: BioRAT: extracting biological information from full-length papers. Bioinformatics 20(17): 3206-3213 (2004)

Liam J. McGuffin, Stefano A. Street, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones: The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Research 32(Database-Issue): 196-199 (2004)

Jonathan J. Ward, Jaspreet Singh Sodhi, Bernard F. Buxton, David T. Jones: Predicting Gene Ontology Annotations from Sequence Data Using Kernel-Based Machine Learning Algorithms. CSB 2004: 529-530

Jaspreet Singh Sodhi, Liam J. McGuffin, Kevin Bryson, Jonathan J. Ward, Lorenz Wernisch, David T. Jones: Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures. CSB 2004: 702-703

Liam J. McGuffin, David T. Jones: Improvement of the GenTHREADER Method for Genomic Fold Recognition. Bioinformatics 19(7): 874-881 (2003)

Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones: Secondary structure prediction with support vector machines. Bioinformatics 19(13): 1650-1655 (2003)

Kevin Bryson, Michael Luck, Mike Joy, David T. Jones: Agent Interaction for Bioinformatics Data Management. Applied Artificial Intelligence 15(10): 917-947 (2001)

David T. Jones: Protein Structure Prediction in Genomics. Briefings in Bioinformatics 2(2): 111-125 (2001)

Liam J. McGuffin, Kevin Bryson, David T. Jones: What are the baselines for protein fold recognition? Bioinformatics 17(1): 63-72 (2001)

Liam J. McGuffin, Kevin Bryson, David T. Jones: The PSIPRED protein structure prediction server. Bioinformatics 16(4): 404-405 (2000)

Kevin Bryson, Michael Luck, Mike Joy, David T. Jones: Applying Agents to Bioinformatics in GeneWeaver. CIA 2000: 60-71

Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones: PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14(8): 726-733 (1998)

David T. Jones, Janet M. Thornton: Protein fold recognition. Journal of Computer-Aided Molecular Design 7(4): 439-456 (1993)

David T. Jones, William R. Taylor, Janet M. Thornton: The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8(3): 275-282 (1992)