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Author Details

David T Jones
University College London
1977
265
86
PMIDPaper TitleJournal TitlePublished Year
37320955Machine learning methods for predicting protein structure from single sequences.Curr Opin Struct Biol2023
35074909Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins.Proc Natl Acad Sci U S A2022
34213528Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework.Bioinformatics2021
34473813Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins.PLoS One2021
31703152Learning a functional grammar of protein domains using natural language word embedding techniques.Proteins2020
31251384The PSIPRED Protein Analysis Workbench: 20 years on.Nucleic Acids Res2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31589782Recent developments in deep learning applied to protein structure prediction.Proteins2019
31298436Prediction of interresidue contacts with DeepMetaPSICOV in CASP13.Proteins2019
31602685Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13).Proteins2019
31484923Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints.Nat Commun2019
31335894Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks.PLoS One2019
28901583Improved protein contact predictions with the MetaPSICOV2 server in CASP12.Proteins2018
29889900Predicting human protein function with multi-task deep neural networks.PLoS One2018
30385875Design of metalloproteins and novel protein folds using variational autoencoders.Sci Rep2018
29718112High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features.Bioinformatics2018
27812935Computational Methods for Annotation Transfers from Sequence.Methods Mol Biol2017
28087895Crohn disease risk prediction-Best practices and pitfalls with exome data.Hum Mutat2017
28084535DNA methylation is dispensable for changes in global chromatin architecture but required for chromocentre formation in early stem cell differentiation.Chromosoma2017
28358373Myogenic differentiation triggers PML nuclear body loss and DAXX relocalization to chromocentres.Cell Death Dis2017
28397312Lessons from the CAGI-4 Hopkins clinical panel challenge.Hum Mutat2017
28419258EigenTHREADER: analogous protein fold recognition by efficient contact map threading.Bioinformatics2017
28370845Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.Hum Mutat2017
29153988Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.Stem Cell Reports2017
29045400Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.PLoS Comput Biol2017
28765603Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions.Sci Rep2017
28634997Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.Hum Mutat2017
26223534Coming to terms with chromatin structure.Chromosoma2016
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
27427384FANCD2 limits BLM-dependent telomere instability in the alternative lengthening of telomeres pathway.Hum Mol Genet2016
27561554FFPred 3: feature-based function prediction for all Gene Ontology domains.Sci Rep2016
27389808A novel single cell method to identify the genetic composition at a single nuclear body.Sci Rep2016
27125671The pluripotency factor Nanog regulates pericentromeric heterochromatin organization in mouse embryonic stem cells.Genes Dev2016
26205532Accurate contact predictions using covariation techniques and machine learning.Proteins2016
25391399DISOPRED3: precise disordered region predictions with annotated protein-binding activity.Bioinformatics2015
26626085MLL5 Orchestrates a Cancer Self-Renewal State by Repressing the Histone Variant H3.3 and Globally Reorganizing Chromatin.Cancer Cell2015
26500702The histone chaperone DAXX maintains the structural organization of heterochromatin domains.Epigenetics Chromatin2015
26107557Unfolding the story of chromatin organization in senescent cells.Nucleus2015
25747659Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles.Mol Cell2015
25431331MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.Bioinformatics2015
25348407Genome3D: exploiting structure to help users understand their sequences.Nucleic Acids Res2015
23900810Evaluation of predictions in the CASP10 model refinement category.Proteins2014
25522242Identification of c-MYC SUMOylation by mass spectrometry.PLoS One2014
24773235Classification of intrinsically disordered regions and proteins.Chem Rev2014
24799430Nano-dissection and sequencing of DNA at single sub-nuclear structures.Small2014
24637808De novo structure prediction of globular proteins aided by sequence variation-derived contacts.PLoS One2014
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
28516007What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.Intrinsically Disord Proteins2013
24047460Membrane protein orientation and refinement using a knowledge-based statistical potential.BMC Bioinformatics2013
23840764Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations.PLoS One2013
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Collaborators

Liam J McGuffin
University of Reading
Co-authored papers 18
Christine Orengo
University College London, Institute of Structural and Molecular Biology
Co-authored papers 18
Kevin Bryson
University of Glasgow
Co-authored papers 16
Domenico Cozzetto
Imperial College London
Co-authored papers 15
Kashif Ahmed
The Wright Center for Graduate Medical Education
Co-authored papers 10
Fran??ois-Michel Boisvert
Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS)
Co-authored papers 9
Reagan W Ching
Max Planck Institute of Immunobiology and Epigenetics
Co-authored papers 9
Federico Minneci
University College London
Co-authored papers 8
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 6
Julian Gough
Medical Research Council Laboratory of Molecular Biology
Co-authored papers 6
Pier Luigi Martelli
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 5
Silvio C E Tosatto
University of Padova
Co-authored papers 5
Nick Goldman
Co-authored papers 5
Michael J E Sternberg
Imperial College London
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Ian Sillitoe
University College London
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C David Allis
The Rockefeller University
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Cen Wan
University College London
Co-authored papers 4
Damiano Piovesan
University of Padova
Co-authored papers 4
Predrag Radivojac
Indiana University
Co-authored papers 4
Sean D Mooney
University of Washington
Co-authored papers 4
Michael L Tress
Spanish National Cancer Research Centre (CNIO)
Co-authored papers 4
Marco Carraro
Hematology and Clinical Immunology Unit, University of Padova
Co-authored papers 4
Steven E Brenner
University of California berkeley
Co-authored papers 4
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 4
Prajwal Bhat
Royal Holloway University of London
Co-authored papers 3
Daisuke Kihara
Purdue University
Co-authored papers 3
Iddo Friedberg
Iowa State University
Co-authored papers 3
Carlo Ferrari
University of Padua
Co-authored papers 3
Rui Fa
University College London
Co-authored papers 3
Olivier Lichtarge
Baylor College of Medicine
Co-authored papers 3
Release 1.2