David T. Jones

69 papers A* 1A 1C 2Journal 59Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning. Bioinform. Shaun M. Kandathil, Andy M. Lau, Daniel W. A. Buchan, David T. Jones
2024	J	`jnl`	Exploring transfer learning for pathological speech feature prediction: Impact of layer selection. CoRR Daniela A. Wiepert, Rene L. Utianski, Joseph R. Duffy, John L. Stricker, Leland R. Barnard, David T. Jones, Hugo Botha
2024	A	`conf`	Speech foundation models in healthcare: Effect of layer selection on pathological speech feature prediction. INTERSPEECH Daniela A. Wiepert, Rene L. Utianski, Joseph R. Duffy, John L. Stricker, Leland R. Barnard, David T. Jones, Hugo Botha
2023	C	`conf`	Detecting Speech Abnormalities With a Perceiver-Based Sequence Classifier that Leverages a Universal Speech Model. ASRU Hagen Soltau, Izhak Shafran, Alex Ottenwess, Joseph R. Duffy, Rene L. Utianski, Leland R. Barnard, John L. Stricker, Daniela A. Wiepert, David T. Jones, Hugo Botha
2023	J	`jnl`	Detecting Speech Abnormalities with a Perceiver-based Sequence Classifier that Leverages a Universal Speech Model. CoRR Hagen Soltau, Izhak Shafran, Alex Ottenwess, Joseph R. Duffy, Rene L. Utianski, Leland R. Barnard, John L. Stricker, Daniela A. Wiepert, David T. Jones, Hugo Botha
2023	C	`conf`	Not All Errors Are Created Equal: Evaluating The Impact of Model and Speaker Factors on ASR Outcomes in Clinical Populations. ASRU Daniela A. Wiepert, Rene L. Utianski, Joseph R. Duffy, John L. Stricker, Leland Barnard, Keith A. Josephs, Jennifer L. Whitwell, David T. Jones, Hugo Botha
2023	J	`jnl`	SparCA: Sparse Compressed Agglomeration for Feature Extraction and Dimensionality Reduction. CoRR Leland Barnard, Farwa Ali, Hugo Botha, David T. Jones
2022	J	`jnl`	Deep learning identifies brain structures that predict cognition and explain heterogeneity in cognitive aging. NeuroImage Krishnakant V. Saboo, Chang Hu, Yogatheesan Varatharajah, Scott A. Przybelski, Robert I. Reid, Christopher G. Schwarz, Jonathan Graff-Radford, David S. Knopman, Mary M. Machulda, Michelle M. Mielke, Ronald C. Petersen, Paul M. Arnold, Gregory A. Worrell, David T. Jones, Clifford R. Jack Jr., Ravishankar K. Iyer, Prashanthi Vemuri
2022	J	`jnl`	Risk of re-identification for shared clinical speech recordings. CoRR Daniela A. Wiepert, Bradley A. Malin, Joseph R. Duffy, Rene L. Utianski, John L. Stricker, David T. Jones, Hugo Botha
2021	J	`jnl`	Associations of quantitative susceptibility mapping with Alzheimer's disease clinical and imaging markers. NeuroImage Petrice M. Cogswell, Heather J. Wiste, Matthew L. Senjem, Jeffrey L. Gunter, Stephen D. Weigand, Christopher G. Schwarz, Arvin Arani, Terry M. Therneau, Val J. Lowe, David S. Knopman, Hugo Botha, Jonathan Graff-Radford, David T. Jones, Kejal Kantarci, Prashanthi Vemuri, Bradley F. Boeve, Michelle M. Mielke, Ronald C. Petersen, Clifford R. Jack Jr.
2021	J	`jnl`	CSF dynamics as a predictor of cognitive progression. NeuroImage Petrice M. Cogswell, Stephen D. Weigand, Heather J. Wiste, Jeffrey L. Gunter, Jonathan Graff-Radford, David T. Jones, Christopher G. Schwarz, Matthew L. Senjem, David S. Knopman, Ronald C. Petersen, Clifford R. Jack Jr.
2021	—	`conf`	Domain-guided Self-supervision of EEG Data Improves Downstream Classification Performance and Generalizability. ML4H@NeurIPS Neeraj Wagh, Jionghao Wei, Samarth Rawal, Brent M. Berry, Leland Barnard, Benjamin H. Brinkmann, Gregory A. Worrell, David T. Jones, Yogatheesan Varatharajah
2021	J	`jnl`	Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinform. Lewis Moffat, David T. Jones
2021	A*	`conf`	Reinforcement Learning based Disease Progression Model for Alzheimer's Disease. NeurIPS Krishnakant V. Saboo, Anirudh Choudhary, Yurui Cao, Gregory A. Worrell, David T. Jones, Ravishankar K. Iyer
2021	J	`jnl`	Reinforcement Learning based Disease Progression Model for Alzheimer's Disease. CoRR Krishnakant V. Saboo, Anirudh Choudhary, Yurui Cao, Gregory A. Worrell, David T. Jones, Ravishankar K. Iyer
2021	J	`jnl`	Relationships between β-amyloid and tau in an elderly population: An accelerated failure time modelww. NeuroImage Terry M. Therneau, David S. Knopman, Val J. Lowe, Hugo Botha, Jonathan Graff-Radford, David T. Jones, Prashanthi Vemuri, Michelle M. Mielke, Christopher G. Schwarz, Matthew L. Senjem, Jeffrey L. Gunter, Ronald C. Petersen, Clifford R. Jack Jr.
2020	J	`jnl`	Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
2020	J	`jnl`	Improved protein structure prediction using potentials from deep learning. Nat. Andrew W. Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Zídek, Alexander W. R. Nelson, Alex Bridgland, Hugo Penedones, Stig Petersen, Karen Simonyan, Steve Crossan, Pushmeet Kohli, David T. Jones, David Silver, Koray Kavukcuoglu, Demis Hassabis
2020	J	`jnl`	Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks. Nat. Mach. Intell. Cen Wan, David T. Jones
2019	J	`jnl`	The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res. Daniel W. A. Buchan, David T. Jones
2018	J	`jnl`	High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinform. David T. Jones, Shaun M. Kandathil
2017	J	`jnl`	Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS Comput. Biol. Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones
2017	J	`jnl`	EigenTHREADER: analogous protein fold recognition by efficient contact map threading. Bioinform. Daniel W. A. Buchan, David T. Jones
2015	J	`jnl`	DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinform. David T. Jones, Domenico Cozzetto
2015	J	`jnl`	Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
2015	J	`jnl`	Language networks associated with computerized semantic indices. NeuroImage Serguei V. S. Pakhomov, David T. Jones, David S. Knopman
2015	J	`jnl`	MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinform. David T. Jones, Tanya Singh, Tomasz Kosciólek, Stuart J. Tetchner
2014	J	`jnl`	Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction. Bio Algorithms Med Syst. Stuart J. Tetchner, Tomasz Kosciólek, David T. Jones
2013	J	`jnl`	Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 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 L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo
2013	J	`jnl`	Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinform. Timothy Nugent, David T. Jones
2013	J	`jnl`	Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinform. Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones
2013	J	`jnl`	Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res. Daniel W. A. Buchan, Federico Minneci, Tim C. O. Nugent, Kevin Bryson, David T. Jones
2012	J	`jnl`	Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinform. Timothy Nugent, David T. Jones
2012	J	`jnl`	PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinform. David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto, Massimiliano Pontil
2011	J	`jnl`	Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res. Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Andrew B. Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David T. Jones, Janet M. Thornton, Christine A. Orengo
2011	J	`jnl`	The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinform. Timothy Nugent, Sean Ward, David T. Jones
2010	—	`ch.`	Computational Resources for the Prediction and Analysis of Native Disorder in Proteins. Proteome Bioinformatics Melissa M. Pentony, Jonathan J. Ward, David T. Jones
2010	J	`jnl`	Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. PLoS Comput. Biol. Timothy Nugent, David T. Jones
2010	J	`jnl`	Protein annotation and modelling servers at University College London. Nucleic Acids Res. Daniel W. A. Buchan, S. M. Ward, Anna E. Lobley, Timothy Nugent, Kevin Bryson, David T. Jones
2009	J	`jnl`	Improving classification in protein structure databases using text mining. BMC Bioinform. Antonis Koussounadis, Oliver Redfern, David T. Jones
2009	J	`jnl`	Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinform. Stefano Lise, Cédric Archambeau, Massimiliano Pontil, David T. Jones
2009	J	`jnl`	Transmembrane protein topology prediction using support vector machines. BMC Bioinform. Timothy Nugent, David T. Jones
2009	J	`jnl`	pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinform. Anna E. Lobley, Michael I. Sadowski, David T. Jones
2008	J	`jnl`	FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res. Anna E. Lobley, Timothy Nugent, Christine A. Orengo, David T. Jones
2008	J	`jnl`	ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 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
2008	J	`jnl`	Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinform. Ching-Wai Tan, David T. Jones
2007	J	`jnl`	Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinform. David T. Jones
2007	J	`jnl`	Inferring Function Using Patterns of Native Disorder in Proteins. PLoS Comput. Biol. Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones
2006	J	`jnl`	Docking protein domains in contact space. BMC Bioinform. Stefano Lise, Alice Walker-Taylor, David T. Jones
2006	J	`jnl`	High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinform. Liam J. McGuffin, Richard T. Smith, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones
2006	—	`conf`	Invited Talk: Docking Protein Domains Using a Contact Map Representation. German Conference on Bioinformatics Stefano Lise, David T. Jones
2005	J	`jnl`	Improving sequence-based fold recognition by using 3D model quality assessment. Bioinform. Chris Steven Pettitt, Liam J. McGuffin, David T. Jones
2005	J	`jnl`	Protein structure prediction servers at University College London. Nucleic Acids Res. Kevin Bryson, Liam J. McGuffin, Russell L. Marsden, Jonathan J. Ward, Jaspreet Singh Sodhi, David T. Jones
2004	—	`conf`	Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures. CSB Jaspreet Singh Sodhi, Liam J. McGuffin, Kevin Bryson, Jonathan J. Ward, Lorenz Wernisch, David T. Jones
2004	J	`jnl`	BioRAT: extracting biological information from full-length papers. Bioinform. David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones
2004	—	`conf`	Predicting Gene Ontology Annotations from Sequence Data Using Kernel-Based Machine Learning Algorithms. CSB Jonathan J. Ward, Jaspreet Singh Sodhi, Bernard F. Buxton, David T. Jones
2004	J	`jnl`	The DISOPRED server for the prediction of protein disorder. Bioinform. Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones
2004	J	`jnl`	The Genomic Threading Database. Bioinform. Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones
2004	J	`jnl`	The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res. Liam J. McGuffin, Stefano A. Street, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones
2003	J	`jnl`	Improvement of the GenTHREADER Method for Genomic Fold Recognition. Bioinform. Liam J. McGuffin, David T. Jones
2003	J	`jnl`	Secondary structure prediction with support vector machines. Bioinform. Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones
2001	J	`jnl`	Agent Interaction for Bioinformatics Data Management. Appl. Artif. Intell. Kevin Bryson, Michael Luck, Mike Joy, David T. Jones
2001	J	`jnl`	Protein Structure Prediction in Genomics. Briefings Bioinform. David T. Jones
2001	J	`jnl`	What are the baselines for protein fold recognition? Bioinform. Liam J. McGuffin, Kevin Bryson, David T. Jones
2000	—	`conf`	Applying Agents to Bioinformatics in GeneWeaver. CIA Kevin Bryson, Michael Luck, Mike Joy, David T. Jones
2000	J	`jnl`	The PSIPRED protein structure prediction server. Bioinform. Liam J. McGuffin, Kevin Bryson, David T. Jones
1998	J	`jnl`	PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinform. Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones
1993	J	`jnl`	Protein fold recognition. J. Comput. Aided Mol. Des. David T. Jones, Janet M. Thornton
1992	J	`jnl`	The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. David T. Jones, William R. Taylor, Janet M. Thornton