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ORCIDDavid T. Jones
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- affiliation: University College London, UK
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2020 – today
- 2024
[i5]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 abs/2402.01796 (2024)- 2023
- [c9]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: 1-7 - [c8]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: 1-6 - [i4]Leland Barnard, Farwa Ali, Hugo Botha, David T. Jones:
SparCA: Sparse Compressed Agglomeration for Feature Extraction and Dimensionality Reduction. CoRR abs/2302.10776 (2023) - [i3]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 abs/2310.13010 (2023) - 2022
- [j53]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: 119020 (2022) - [i2]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 abs/2210.09975 (2022) - 2021
- [j52]Lewis Moffat, David T. Jones:
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinform. 37(21): 3744-3751 (2021) - [j51]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: 117433 (2021) - [j50]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: 117899 (2021) - [j49]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: 118440 (2021) - [c7]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: 130-142 - [c6]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: 20903-20915 - [i1]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 abs/2106.16187 (2021) - 2020
- [j48]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): D314-D319 (2020) - [j47]Cen Wan, David T. Jones:
Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks. Nat. Mach. Intell. 2(9): 540-550 (2020) - [j46]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): 706-710 (2020)
2010 – 2019
- 2019
- [j45]Daniel W. A. Buchan, David T. Jones:
The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res. 47(Webserver-Issue): W402-W407 (2019) - 2018
- [j44]David T. Jones, Shaun M. Kandathil:
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinform. 34(19): 3308-3315 (2018) - 2017
- [j43]Daniel W. A. Buchan, David T. Jones:
EigenTHREADER: analogous protein fold recognition by efficient contact map threading. Bioinform. 33(17): 2684-2690 (2017) - [j42]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) - 2015
- [j41]David T. Jones, Domenico Cozzetto:
DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinform. 31(6): 857-863 (2015) - [j40]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): 999-1006 (2015) - [j39]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): 382-386 (2015) - [j38]Serguei V. S. Pakhomov, David T. Jones, David S. Knopman:
Language networks associated with computerized semantic indices. NeuroImage 104: 125-137 (2015) - 2014
- [j37]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): 243-254 (2014) - 2013
- [j36]Timothy Nugent, David T. Jones:
Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinform. 14: 276 (2013) - [j35]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): S1 (2013) - [j34]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): 499-507 (2013) - [j33]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): 349-357 (2013) - 2012
- [j32]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): 184-190 (2012) - [j31]Timothy Nugent, David T. Jones:
Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinform. 13: 169 (2012) - 2011
- [j30]Timothy Nugent, Sean Ward, David T. Jones:
The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinform. 27(10): 1438-1439 (2011) - [j29]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): 420-426 (2011) - 2010
- [j28]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): 563-568 (2010) - [j27]Timothy Nugent, David T. Jones:
Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. PLoS Comput. Biol. 6(3) (2010) - [p1]Melissa M. Pentony, Jonathan J. Ward, David T. Jones:
Computational Resources for the Prediction and Analysis of Native Disorder in Proteins. Proteome Bioinformatics 2010: 369-393
2000 – 2009
- 2009
- [j26]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): 1761-1767 (2009) - [j25]Antonis Koussounadis, Oliver Redfern, David T. Jones:
Improving classification in protein structure databases using text mining. BMC Bioinform. 10 (2009) - [j24]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: 365 (2009) - [j23]Timothy Nugent, David T. Jones:
Transmembrane protein topology prediction using support vector machines. BMC Bioinform. 10 (2009) - 2008
- [j22]Ching-Wai Tan, David T. Jones:
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinform. 9 (2008) - [j21]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): 297-302 (2008) - [j20]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): 485-490 (2008) - 2007
- [j19]David T. Jones:
Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinform. 23(5): 538-544 (2007) - [j18]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) - 2006
- [j17]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: 288 (2006) - [j16]Stefano Lise, Alice Walker-Taylor, David T. Jones:
Docking protein domains in contact space. BMC Bioinform. 7: 310 (2006) - [c5]Stefano Lise, David T. Jones:
Invited Talk: Docking Protein Domains Using a Contact Map Representation. German Conference on Bioinformatics 2006: 74 - [c4]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 - 2005
- [j15]Chris Steven Pettitt, Liam J. McGuffin, David T. Jones:
Improving sequence-based fold recognition by using 3D model quality assessment. Bioinform. 21(17): 3509-3515 (2005) - [j14]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): 36-38 (2005) - 2004
- [j13]Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones:
The Genomic Threading Database. Bioinform. 20(1): 131-132 (2004) - [j12]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): 2138-2139 (2004) - [j11]David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones:
BioRAT: extracting biological information from full-length papers. Bioinform. 20(17): 3206-3213 (2004) - [j10]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): 196-199 (2004) - [c3]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 - [c2]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 - 2003
- [j9]Liam J. McGuffin, David T. Jones:
Improvement of the GenTHREADER Method for Genomic Fold Recognition. Bioinform. 19(7): 874-881 (2003) - [j8]Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones:
Secondary structure prediction with support vector machines. Bioinform. 19(13): 1650-1655 (2003) - 2001
- [j7]Kevin Bryson, Michael Luck, Mike Joy, David T. Jones:
Agent Interaction for Bioinformatics Data Management. Appl. Artif. Intell. 15(10): 917-947 (2001) - [j6]David T. Jones:
Protein Structure Prediction in Genomics. Briefings Bioinform. 2(2): 111-125 (2001) - [j5]Liam J. McGuffin, Kevin Bryson, David T. Jones:
What are the baselines for protein fold recognition? Bioinform. 17(1): 63-72 (2001) - 2000
- [j4]Liam J. McGuffin, Kevin Bryson, David T. Jones:
The PSIPRED protein structure prediction server. Bioinform. 16(4): 404-405 (2000) - [c1]Kevin Bryson, Michael Luck, Mike Joy, David T. Jones:
Applying Agents to Bioinformatics in GeneWeaver. CIA 2000: 60-71
1990 – 1999
- 1998
- [j3]Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones:
PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinform. 14(8): 726-733 (1998) - 1993
- [j2]David T. Jones, Janet M. Thornton:
Protein fold recognition. J. Comput. Aided Mol. Des. 7(4): 439-456 (1993) - 1992
- [j1]David T. Jones, William R. Taylor, Janet M. Thornton:
The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8(3): 275-282 (1992)
Coauthor Index
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