David T. Jones

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 25

Top Topics

Physiological Processes

Protein Structure

Dimensionality Reduction

Top Venues

Nucleic Acids Res.

Publications

Daniela A. Wiepert, Rene L. Utianski, Joseph R. Duffy, John L. Stricker, Leland R. Barnard, David T. Jones, Hugo Botha
Exploring transfer learning for pathological speech feature prediction: Impact of layer selection. CoRR (2024)
Leland Barnard, Farwa Ali, Hugo Botha, David T. Jones
SparCA: Sparse Compressed Agglomeration for Feature Extraction and Dimensionality Reduction. CoRR (2023)
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
Detecting Speech Abnormalities with a Perceiver-based Sequence Classifier that Leverages a Universal Speech Model. CoRR (2023)
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
Not All Errors Are Created Equal: Evaluating The Impact of Model and Speaker Factors on ASR Outcomes in Clinical Populations. ASRU (2023)
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
Detecting Speech Abnormalities With a Perceiver-Based Sequence Classifier that Leverages a Universal Speech Model. ASRU (2023)
Daniela A. Wiepert, Bradley A. Malin, Joseph R. Duffy, Rene L. Utianski, John L. Stricker, David T. Jones, Hugo Botha
Risk of re-identification for shared clinical speech recordings. CoRR (2022)
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
Deep learning identifies brain structures that predict cognition and explain heterogeneity in cognitive aging. NeuroImage 251 (2022)
Neeraj Wagh, Jionghao Wei, Samarth Rawal, Brent M. Berry, Leland Barnard, Benjamin H. Brinkmann, Gregory A. Worrell, David T. Jones, Yogatheesan Varatharajah
Domain-guided Self-supervision of EEG Data Improves Downstream Classification Performance and Generalizability. ML4H@NeurIPS (2021)
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.
Relationships between β-amyloid and tau in an elderly population: An accelerated failure time modelww. NeuroImage 242 (2021)
Krishnakant V. Saboo, Anirudh Choudhary, Yurui Cao, Gregory A. Worrell, David T. Jones, Ravishankar K. Iyer
Reinforcement Learning based Disease Progression Model for Alzheimer's Disease. CoRR (2021)
Krishnakant V. Saboo, Anirudh Choudhary, Yurui Cao, Gregory A. Worrell, David T. Jones, Ravishankar K. Iyer
Reinforcement Learning based Disease Progression Model for Alzheimer's Disease. NeurIPS (2021)
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.
Associations of quantitative susceptibility mapping with Alzheimer's disease clinical and imaging markers. NeuroImage 224 (2021)
Lewis Moffat, David T. Jones
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinform. 37 (21) (2021)
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.
CSF dynamics as a predictor of cognitive progression. NeuroImage 232 (2021)
Cen Wan, David T. Jones
Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks. Nat. Mach. Intell. 2 (9) (2020)
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
Improved protein structure prediction using potentials from deep learning. Nat. 577 (7792) (2020)
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
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. 48 (Database-Issue) (2020)
Daniel W. A. Buchan, David T. Jones
The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
David T. Jones, Shaun M. Kandathil
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinform. 34 (19) (2018)
Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS Comput. Biol. 13 (10) (2017)
Daniel W. A. Buchan, David T. Jones
EigenTHREADER: analogous protein fold recognition by efficient contact map threading. Bioinform. 33 (17) (2017)
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
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43 (Database-Issue) (2015)
David T. Jones, Tanya Singh, Tomasz Kosciólek, Stuart J. Tetchner
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinform. 31 (7) (2015)
Serguei V. S. Pakhomov, David T. Jones, David S. Knopman
Language networks associated with computerized semantic indices. NeuroImage 104 (2015)
David T. Jones, Domenico Cozzetto
DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinform. 31 (6) (2015)
Stuart J. Tetchner, Tomasz Kosciólek, David T. Jones
Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction. Bio Algorithms Med Syst. 10 (4) (2014)
Daniel W. A. Buchan, Federico Minneci, Tim C. O. Nugent, Kevin Bryson, David T. Jones
Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Timothy Nugent, David T. Jones
Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinform. 14 (2013)
Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinform. 14 (S-3) (2013)
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
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 41 (Database-Issue) (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. Bioinform. 28 (2) (2012)
Timothy Nugent, David T. Jones
Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinform. 13 (2012)
Timothy Nugent, Sean Ward, David T. Jones
The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinform. 27 (10) (2011)
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
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res. 39 (Database-Issue) (2011)
Timothy Nugent, David T. Jones
Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. PLoS Comput. Biol. 6 (3) (2010)
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 Res. 38 (Web-Server-Issue) (2010)
Anna E. Lobley, Michael I. Sadowski, David T. Jones
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinform. 25 (14) (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 Bioinform. 10 (2009)
Antonis Koussounadis, Oliver Redfern, David T. Jones
Improving classification in protein structure databases using text mining. BMC Bioinform. 10 (2009)
Timothy Nugent, David T. Jones
Transmembrane protein topology prediction using support vector machines. BMC Bioinform. 10 (2009)
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 Res. 36 (Web-Server-Issue) (2008)
Ching-Wai Tan, David T. Jones
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinform. 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 Res. 36 (Web-Server-Issue) (2008)
David T. Jones
Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinform. 23 (5) (2007)
Anna E. Lobley, Mark B. Swindells, Christine A. Orengo, David T. Jones
Inferring Function Using Patterns of Native Disorder in Proteins. PLoS Comput. Biol. 3 (8) (2007)
Stefano Lise, David T. Jones
Invited Talk: Docking Protein Domains Using a Contact Map Representation. German Conference on Bioinformatics (2006)
Stefano Lise, Alice Walker-Taylor, David T. Jones
Docking protein domains in contact space. BMC Bioinform. 7 (2006)
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 Bioinform. 7 (2006)
Timothy M. D. Ebbels, Bernard F. Buxton, David T. Jones
: visualisation of microarray and contextual bioinformatic data using spring embedding and an "information landscape". ISMB (Supplement of Bioinformatics) (2006)
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 Res. 33 (Web-Server-Issue) (2005)
Chris S. Pettitt, Liam J. McGuffin, David T. Jones
Improving sequence-based fold recognition by using 3D model quality assessment. Bioinform. 21 (17) (2005)
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 Res. 32 (Database-Issue) (2004)
David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones
BioRAT: extracting biological information from full-length papers. Bioinform. 20 (17) (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)
Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones
The Genomic Threading Database. Bioinform. 20 (1) (2004)
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)
Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones
The DISOPRED server for the prediction of protein disorder. Bioinform. 20 (13) (2004)
Liam J. McGuffin, David T. Jones
Improvement of the GenTHREADER Method for Genomic Fold Recognition. Bioinform. 19 (7) (2003)
Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones
Secondary structure prediction with support vector machines. Bioinform. 19 (13) (2003)
Liam J. McGuffin, Kevin Bryson, David T. Jones
What are the baselines for protein fold recognition? Bioinform. 17 (1) (2001)
David T. Jones
Protein Structure Prediction in Genomics. Briefings Bioinform. 2 (2) (2001)
Kevin Bryson, Michael Luck, Mike Joy, David T. Jones
Agent Interaction for Bioinformatics Data Management. Appl. Artif. Intell. 15 (10) (2001)
Kevin Bryson, Michael Luck, Mike Joy, David T. Jones
Applying Agents to Bioinformatics in GeneWeaver. CIA (2000)
Liam J. McGuffin, Kevin Bryson, David T. Jones
The PSIPRED protein structure prediction server. Bioinform. 16 (4) (2000)
Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones
PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinform. 14 (8) (1998)
David T. Jones, Janet M. Thornton
Protein fold recognition. J. Comput. Aided Mol. Des. 7 (4) (1993)
David T. Jones, William R. Taylor, Janet M. Thornton
The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (3) (1992)