David Jones: Publications

  • Buchan, DWA and Jones, DT (2017)
    EigenTHREADER: analogous protein fold recognition by efficient contact map threading.
    Bioinformatics 33, 2684-2690 PubMed abstract
  • Buchan, DWA and Jones, DT (2017)
    Improved protein contact predictions with the MetaPSICOV2 server in CASP12.
    Proteins [Epub ahead of print] PubMed abstract
  • Chandonia, J-M; Adhikari, A; Carraro, M; Chhibber, A; Cutting, GR; Fu, Y; Gasparini, A; Jones, DT; Kramer, A; Kundu, K; Lam, HYK; Leonardi, E; Moult, J; Pal, LR; Searls, DB; Shah, S; Sunyaev, S; Tosatto, SCE; Yin, Y and Buckley, BA (2017)
    Lessons from the CAGI-4 Hopkins clinical panel challenge.
    Human Mutation 38, 1155-1168 PubMed abstract
  • Cozzetto, D and Jones, DT (2017)
    Computational methods for annotation transfers from sequence.
    Methods in Molecular Biology 1446, 55-67 PubMed abstract
  • Daneshjou, R; Wang, Y; Bromberg, Y; Bovo, S; Martelli, PL; Babbi, G; Lena, PD; Casadio, R; Edwards, M; Gifford, D; Jones, DT; Sundaram, L; Bhat, RR; Li, X; Pal, LR; Kundu, K; Yin, Y; Moult, J; Jiang, Y; Pejaver, V; Pagel, KA; Li, B; Mooney, SD; Radivojac, P; Shah, S; Carraro, M; Gasparini, A; Leonardi, E; Giollo, M; Ferrari, C; Tosatto, SCE; Bachar, E; Azaria, JR; Ofran, Y; Unger, R; Niroula, A; Vihinen, M; Chang, B; Wang, MH; Franke, A; Petersen, B-S; Pirooznia, M; Zandi, P; McCombie, R; Potash, JB; Altman, RB; Klein, TE; Hoskins, RA; Repo, S; Brenner, SE and Morgan, AA (2017)
    Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
    Human Mutation 38, 1182-1192 PubMed abstract
  • Giollo, M; Jones, DT; Carraro, M; Leonardi, E; Ferrari, C and Tosatto, SCE (2017)
    Crohn disease risk prediction-Best practices and pitfalls with exome data.
    Human Mutation 38, 1193-1200 PubMed abstract
  • Kosciolek, T; Buchan, DWA and Jones, DT (2017)
    Predictions of backbone dynamics in intrinsically disordered proteins using de novo fragment-based protein structure predictions.
    Scientific Reports 7, 6999 PubMed abstract
  • Wan, C; Lees, JG; Minneci, F; Orengo, CA and Jones, DT (2017)
    Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.
    PLOS Computational Biology 13, e1005791 PubMed abstract
  • Cozzetto, D; Minneci, F; Currant, H and Jones, DT (2016)
    FFPred 3: feature-based function prediction for all Gene Ontology domains.
    Scientific Reports 6, 31865 PubMed abstract
  • Jiang, Y; Oron, TR; Clark, WT; Bankapur, AR; D'Andrea, D; Lepore, R; Funk, CS; Kahanda, I; Verspoor, KM; Ben-Hur, A; Koo, DCE; Penfold-Brown, D; Shasha, D; Youngs, N; Bonneau, R; Lin, A; Sahraeian, SME; Martelli, PL; Profiti, G; Casadio, R; Cao, R; Zhong, Z; Cheng, J; Altenhoff, A; Skunca, N; Dessimoz, C; Dogan, T; Hakala, K; Kaewphan, S; Mehryary, F; Salakoski, T; Ginter, F; Fang, H; Smithers, B; Oates, M; Gough, J; Törönen, P; Koskinen, P; Holm, L; Chen, C-T; Hsu, W-L; Bryson, K; Cozzetto, D; Minneci, F; Jones, DT; Chapman, S; BKC, D; Khan, IK; Kihara, D; Ofer, D; Rappoport, N; Stern, A; Cibrian-Uhalte, E; Denny, P; Foulger, RE; Hieta, R; Legge, D; Lovering, RC; Magrane, M; Melidoni, AN; Mutowo-Meullenet, P; Pichler, K; Shypitsyna, A; Li, B; Zakeri, P; ElShal, S; Tranchevent, L-C; Das, S; Dawson, NL; Lee, D; Lees, JG; Sillitoe, I; Bhat, P; Nepusz, T; Romero, AE; Sasidharan, R; Yang, H; Paccanaro, A; Gillis, J; Sedeño-Cortés, AE; Pavlidis, P; Feng, S; Cejuela, JM; Goldberg, T; Hamp, T; Richter, L; Salamov, A; Gabaldon, T; Marcet-Houben, M; Supek, F; Gong, Q; Ning, W; Zhou, Y; Tian, W; Falda, M; Fontana, P; Lavezzo, E; Toppo, S; Ferrari, C; Giollo, M; Piovesan, D; Tosatto, SCE; del Pozo, A; Fernández, JM; Maietta, P; Valencia, A; Tress, ML; Benso, A; Di Carlo, S; Politano, G; Savino, A; Rehman, HU; Re, M; Mesiti, M; Valentini, G; Bargsten, JW; van Dijk, ADJ; Gemovic, B; Glisic, S; Perovic, V; Veljkovic, V; Veljkovic, N; Almeida-e-Silva, DC; Vencio, RZN; Sharan, M; Vogel, J; Kansakar, L; Zhang, S; Vucetic, S; Wang, Z; Sternberg, MJE; Wass, MN; Huntley, RP; Martin, MJ; O'Donovan, C; Robinson, PN; Moreau, Y; Tramontano, A; Babbitt, PC; Brenner, SE; Linial, M; Orengo, CA; Rost, B; Greene, CS; Mooney, SD; Friedberg, I and Radivojac, P (2016)
    An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
    Genome Biology 17, 184 PubMed abstract
  • Jones, DT and Cozzetto, D (2015)
    DISOPRED3: precise disordered region predictions with annotated protein-binding activity.
    Bioinformatics 31, 857-863 PubMed abstract
  • Jones, DT; Singh, T; Kosciolek, T and Tetchner, S (2015)
    MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.
    Bioinformatics 31, 999-1006 PubMed abstract
  • Kosciolek, T and Jones, DT (2015)
    Accurate contact predictions using covariation techniques and machine learning.
    Proteins 84, 145-151 PubMed abstract
  • Lewis, TE; Sillitoe, I; Andreeva, A; Blundell, TL; Buchan, DWA; Chothia, C; Cozzetto, D; Dana, JM; Filippis, I; Gough, J; Jones, DT; Kelley, LA; Kleywegt, GJ; Minneci, F; Mistry, J; Murzin, AG; Ochoa-Montaño, B; Oates, ME; Punta, M; Rackham, OJL; Stahlhacke, J; Sternberg, MJE; Velankar, S and Orengo, C (2015)
    Genome3D: exploiting structure to help users understand their sequences.
    Nucleic Acids Research 43, D382-D386 PubMed abstract
  • Kosciolek, T and Jones, DT (2014)
    De novo structure prediction of globular proteins aided by sequence variation-derived contacts.
    PLOS ONE 9, e92197 PubMed abstract
  • Nugent, T; Cozzetto, D and Jones, DT (2014)
    Evaluation of predictions in the CASP10 model refinement category.
    Proteins 82, 98-111 PubMed abstract
  • van der Lee, R; Buljan, M; Lang, B; Weatheritt, RJ; Daughdrill, GW; Dunker, AK; Fuxreiter, M; Gough, J; Gsponer, J; Jones, DT; Kim, PM; Kriwacki, RW; Oldfield, CJ; Pappu, RV; Tompa, P; Uversky, VN; Wright, PE and Babu, MM (2014)
    Classification of intrinsically disordered regions and proteins.
    Chemical Reviews 114, 6589-6631 PubMed abstract
  • Buchan, DWA; Minneci, F; Nugent, TCO; Bryson, K and Jones, DT (2013)
    Scalable web services for the PSIPRED Protein Analysis Workbench.
    Nucleic Acids Research 41, W349-W357 PubMed abstract
  • Cozzetto, D; Buchan, DWA; Bryson, K and Jones, DT (2013)
    Protein function prediction by massive integration of evolutionary analyses and multiple data sources.
    BMC Bioinformatics 14, S1 PubMed abstract
  • Cozzetto, D and Jones, DT (2013)
    The contribution of intrinsic disorder prediction to the elucidation of protein function.
    Current Opinion in Structural Biology 23, 467-472 PubMed abstract
  • Dunker, AK; Babu, MM; Barbar, E; Blackledge, M; Bondos, SE; Dosztányi, Z; Dyson, HJ; Forman-Kay, J; Fuxreiter, M; Gsponer, J; Han, K-H; Jones, DT; Longhi, S; Metallo, SJ; Nishikawa, K; Nussinov, R; Obradovic, Z; Pappu, RV; Rost, B; Selenko, P; Subramaniam, V; Sussman, JL; Tompa, P and Uversky, VN (2013)
    What's in a name? Why these proteins are intrinsically disordered.
    Intrinsically Disordered Proteins 1, e24157 PubMed abstract
  • Lewis, TE; Sillitoe, I; Andreeva, A; Blundell, TL; Buchan, DWA; Chothia, C; Cuff, A; Dana, JM; Filippis, I; Gough, J; Hunter, S; Jones, DT; Kelley, LA; Kleywegt, GJ; Minneci, F; Mitchell, A; Murzin, AG; Ochoa-Montaño, B; Rackham, OJL; Smith, J; Sternberg, MJE; Velankar, S; Yeats, C and Orengo, C (2013)
    Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
    Nucleic Acids Research 41, D499-D507 PubMed abstract
  • Minneci, F; Piovesan, D; Cozzetto, D and Jones, DT (2013)
    FFPred 2.0: improved homology-independent prediction of Gene Ontology terms for eukaryotic protein sequences.
    PLOS ONE 8, e63754 PubMed abstract
  • Nugent, T and Jones, DT (2013)
    Membrane protein orientation and refinement using a knowledge-based statistical potential.
    BMC Bioinformatics 14, 276 PubMed abstract
  • Radivojac, P; Clark, WT; Oron, TR; Schnoes, AM; Wittkop, T; Sokolov, A; Graim, K; Funk, C; Verspoor, K; Ben-Hur, A; Pandey, G; Yunes, JM; Talwalkar, AS; Repo, S; Souza, ML; Piovesan, D; Casadio, R; Wang, Z; Cheng, J; Fang, H; Gough, J; Koskinen, P; Törönen, P; Nokso-Koivisto, J; Holm, L; Cozzetto, D; Buchan, DWA; Bryson, K; Jones, DT; Limaye, B; Inamdar, H; Datta, A; Manjari, SK; Joshi, R; Chitale, M; Kihara, D; Lisewski, AM; Erdin, S; Venner, E; Lichtarge, O; Rentzsch, R; Yang, H; Romero, AE; Bhat, P; Paccanaro, A; Hamp, T; Kaßner, R; Seemayer, S; Vicedo, E; Schaefer, C; Achten, D; Auer, F; Boehm, A; Braun, T; Hecht, M; Heron, M; Hönigschmid, P; Hopf, TA; Kaufmann, S; Kiening, M; Krompass, D; Landerer, C; Mahlich, Y; Roos, M; Björne, J; Salakoski, T; Wong, A; Shatkay, H; Gatzmann, F; Sommer, I; Wass, MN; Sternberg, MJE; Škunca, N; Supek, F; Bošnjak, M; Panov, P; Džeroski, S; Šmuc, T; Kourmpetis, YAI; van Dijk, ADJ; ter Braak, CJF; Zhou, Y; Gong, Q; Dong, X; Tian, W; Falda, M; Fontana, P; Lavezzo, E; Di Camillo, B; Toppo, S; Lan, L; Djuric, N; Guo, Y; Vucetic, S; Bairoch, A; Linial, M; Babbitt, PC; Brenner, SE; Orengo, C; Rost, B; Mooney, SD and Friedberg, I (2013)
    A large-scale evaluation of computational protein function prediction.
    Nature Methods 10, 221-227 PubMed abstract
  • Jones, DT; Buchan, DWA; Cozzetto, D and Pontil, M (2012)
    PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.
    Bioinformatics 28, 184-190 PubMed abstract
  • Nugent, T and Jones, DT (2012)
    Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis.
    Proceedings of the National Academy of Sciences of the United States of America 109, E1540-E1547 PubMed abstract
  • Nugent, T and Jones, DT (2012)
    Detecting pore-lining regions in transmembrane protein sequences.
    BMC Bioinformatics 13, 169 PubMed abstract
  • Nugent, T and Jones, DT (2012)
    Membrane protein structural bioinformatics.
    Journal of Structural Biology 179, 327-337 PubMed abstract
  • Taylor, WR; Jones, DT and Sadowski, MI (2012)
    Protein topology from predicted residue contacts.
    Protein Science 21, 299-305 PubMed abstract
  • Cuff, AL; Sillitoe, I; Lewis, T; Clegg, AB; Rentzsch, R; Furnham, N; Pellegrini-Calace, M; Jones, D; Thornton, J and Orengo, CA (2011)
    Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
    Nucleic Acids Research 39, D420-D426 PubMed abstract
  • Lise, S; Buchan, D; Pontil, M and Jones, DT (2011)
    Predictions of hot spot residues at protein-protein interfaces using support vector machines.
    PLOS ONE 6, e16774 PubMed abstract
  • Nan, R; Farabella, I; Schumacher, FF; Miller, A; Gor, J; Martin, ACR; Jones, DT; Lengyel, I and Perkins, SJ (2011)
    Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration.
    Journal of Molecular Biology 408, 714-735 PubMed abstract
  • Nugent, T; Ward, S and Jones, DT (2011)
    The MEMPACK alpha-helical transmembrane protein structure prediction server.
    Bioinformatics 27, 1438-1439 PubMed abstract
  • Buchan, DWA; Ward, SM; Lobley, AE; Nugent, TCO; Bryson, K and Jones, DT (2010)
    Protein annotation and modelling servers at University College London.
    Nucleic Acids Research 38, W563-W568 PubMed abstract
  • Nugent, T and Jones, DT (2010)
    Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.
    PLOS Computational Biology 6, e1000714 PubMed abstract
  • Pentony, MM and Jones, DT (2010)
    Modularity of intrinsic disorder in the human proteome.
    Proteins 78, 212-221 PubMed abstract
  • Pentony, MM; Ward, J and Jones, DT (2010)
    Computational resources for the prediction and analysis of native disorder in proteins.
    Methods in Molecular Biology 604, 369-393 PubMed abstract

[Page last updated 1 Nov 2017]

David Jones

david.t.jones@crick.ac.uk
+44 (0)20 379 63300