Publications

Jones Lab Publications

    2020


  1. Wan C & Jones DT (2020) Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks. Nature Machine Intelligence. doi: 10.1038/s42256-020-0222-1 Reprint
  2. Buchan DWA & Jones DT (2020) Learning a functional grammar of protein domains using natural language word embedding techniques. 88(4):616-624. doi: 10.1002/prot.25842 PubMed
  3. Senior AW, Evans R, Jumper J, ..., Jones DT, ..., Hassabis D (2020). Improved protein structure prediction using potentials from deep learning. Nature. 577(7792):706-710. doi: 10.1038/s41586-019-1923-7 Reprint

    2019


  4. Senior AW, Evans R, Jumper J, ..., Jones DT, ..., Hassabis D (2019). Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13). Proteins. 87(12):1141-1148. doi: 10.1002/prot.25834 Reprint
  5. Greener JG, Kandathil SM, Jones DT (2019). Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. Nature Communications 10 (1), 1-13. doi: 10.1038/s41467-019-11994-0 Reprint
  6. Kandathil SM, Greener JG, Jones DT (2019). Recent developments in deep learning applied to protein structure prediction. Proteins. doi: 10.1002/prot.25779 Reprint
  7. Jones DT (2019). Setting the standards for machine learning in biology. Nature Reviews Molecular Cell Biology. 20(11):659-660. doi: 10.1038/s41580-019-0176-5 Reprint
  8. Kandathil SM, Greener JG, Jones DT (2019). Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13. Proteins. doi: 10.1002/prot.25779 Reprint
  9. Clark WT, Kasak L, Bakolitsa C, ..., Jones DT, ..., LeBowitz JH (2019) Assessment of predicted enzymatic activity of ?-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human Mutation doi: 10.1002/humu.23875.Reprint
  10. Clark WT, Kasak L, Bakolitsa C, ..., Jones DT, ..., LeBowitz JH (2019) Assessment of predicted enzymatic activity of ?-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human Mutation doi: 10.1002/humu.23875.Reprint
  11. Wan C, Cozzetto D, Fa R, Jones DT (2019). Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks. PLoS One. 14(7):e0209958. doi: 10.1371/journal.pone.0209958 Reprint
  12. Buchan DWA, Jones DT (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz297 Reprint
  13. 2018


  14. Fa R, Cozzetto D, Wan C, Jones DT (2018). Predicting human protein function with multi-task deep neural networks. PLoS One. 2018 Jun 11;13(6):e0198216. doi: 10.1371/journal.pone.0198216. eCollection 2018. Reprint
  15. Greener, J.G. Moffat, L. Jones, D.T. (2018) Design of metalloproteins and novel protein folds using variational autoencoders. Sci Rep. 2018 Nov 1;8(1):16189. doi: 10.1038/s41598-018-34533-1. Reprint
  16. Jones, D.T. Kandathil, S.M. (2018) High precision in protein contact prediction using fully convolutional neural networks and minimal sequence feature. Bioinformatics. 2018 Oct 1;34(19):3308-3315. doi: 10.1093/bioinformatics/bty341. Reprint
  17. 2017


  18. Wan, C., Lees, J.G., Minneci, F., Orengo, C.A., Jones, D.T. (2017) Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS computational biology doi: 10.1371/journal.pcbi.1005791.Reprint
  19. Buchan, D.W., Jones, D.T. (2017) Improved protein contact predictions with the MetaPSICOV2 server in CASP12. Proteins: Structure, Function, and Bioinformatics doi: 10.1002/prot.25379.Reprint
  20. Daneshjou, R., Wan, Y., ... Jones, D.T., ... (2017) Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation doi: 10.1002/humu.23280.Reprint
  21. Chandonia, J.M., Adhikari, A., Carraro, M., Chhibber, A., Cutting, G.R., Fu, Y., Gasparini, A., Jones, D.T., ... (2017) 3Lessons from the CAGI?4 Hopkins clinical panel challenge. Human Mutation doi: 10.1002/humu.23225.Reprint
  22. Xu, Q., Tang, Q., Katsonis, P., Lichtarge, O., Jones, D., Bovo, S., Babbi, G., ... (2017) Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Human Mutation doi: 10.1002/humu.23222.Reprint
  23. Giollo, M., Jones, D.T., Carraro, M., Leonardi, E., Ferrari, C., Tosatto, S.C.E. (2017) Crohn Disease Risk Prediction-Best Practices and Pitfalls with Exome Data. Human Mutation doi: 10.1002/humu.23177.Reprint
  24. Kosciolek, T., Buchan, D.W.A., Jones, D.T. (2017) Predictions of backbone dynamics in Intrinsically disordered proteins using de novo fragment-based protein structure predictions. Scientific Reports doi: 10.1038/s41598-017-07156-1.Reprint
  25. Buchan, D.W., Jones, D.T. (2017) EigenTHREADER: Analogous protein fold recognition by efficient contact map threading. Bioinformatics doi: 10.1093/bioinformatics/btx217.Reprint
  26. Cozzetto, D., Jones, D.T. (2017) Computational methods for annotation transfers from sequence. The Gene Ontology Handbook doi: 10.1007/978-1-4939-3743-1.Reprint
  27. Nugent, T., Jones, D., Hayat, S. (2017) Advances in Computational Methods for Transmembrane Protein Structure Prediction. Protein Structure to Function with Bioinformatics doi: 10.1007/978-94-024-1069-3.Reprint
  28. 2016


  29. Jiang, Y. Oron, T.R., ... Bryson, K., Cozzetto, D., Minneci, F., Jones, D.T., ... (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. arXiv preprint arXiv:1601.00891.Reprint
  30. Cozzetto, D., Minneci, F., Currant, H., Jones, D.T. (2016) FFPred 3: feature-based function prediction for all Gene Ontology domains. Scientific Reports 6:31865.Reprint
  31. Drew,E., Jones, D.T., Wallace, B.A. (2016) Protein Design for Decreased Disorder: SHERP as an Exemplar Protein. Biophysical Journal 3 (110), 555a.Author Manuscript Reprint

    2015


  32. Jones, D.T., Cozzetto, D. (2015) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31 (6), 857-863.Reprint
  33. Jones, D.T., Singh, T., Kosciolek, T., Tetchner, S. (2015) MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics 31 (7), 999-1006.Reprint
  34. Kosciolek,T., Jones,D.T. (2015) Accurate contact predictions using covariation techniques and machine learning. Proteins: Structure, Function, and Bioinformatics 84(Suppl 1):145-151.Reprint

    2014


  35. Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L., Buchan, D.W.A., Chothia, C., Cozzetto, D., Dana, J.M., Filippis, I., Gough, J., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mistry, J., Murzin, A.G., Ochoa-Montaño, B., Oates, M.E., Punta, M., Rackham, O.J.L, Stahlhacke, J., Sternberg, M.J.E., Velankar, S., Orengo, C. (2014) Genome3D: exploiting structure to help users understand their sequences. Nucleic acids research, gku973.Reprint
  36. Tetchner, S., Kosciolek, T., Jones, D.T. (2014) Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction. Bio-Algorithms and Med-Systems 10 (4), 243-254.Reprint
  37. Kosciolek, T. & Jones, D.T. (2014) De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts. PloS one 9 (3), e92197A. Reprint
  38. van der Lee, R., Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T., Kim, P.M., Kriwacki, R.W., Oldfield, C.J., Pappu, R.V., Tompa, P., Uversky, V.N., Wright, P.E., Babu, M.M. (2014) Classification of Intrinsically Disordered Regions and Proteins. Chemical Reviews 114 (13) : 6589-66 31. PubMed
  39. Nugent, T. , Cozzetto, D. & Jones, D.T. (2014) Evaluation of predictions in the CASP10 model refinement category. Proteins. 82, 98-111. Reprint

    2013


  40. Nugent, T. & Jones, D.T. (2013) Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics. 14, 276. Reprint
  41. Cozzetto, D. & Jones, D.T. (2013) The contribution of intrinsic disorder prediction to the elucidation of protein function. Curr. Opin. Struct. Biol. 23, 467-472. PubMed
  42. Buchan DWA, Minneci F, Nugent TCO, Bryson K, Jones DT (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research 41 (W1): W340-W348. Reprint
  43. Minneci F, Piovesan D, Cozzetto D, Jones DT (2013) FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences. PLoS ONE 8(5): e63754. doi:10.1371/journal.pone.0063754 Reprint
  44. Radivojac, P., Clark, W.T., Oron, T., Schnoes, A.M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., Pandey, G., Yunes, J.M., Talwalkar, A.S., Repo, S., Souza, M.L., Piovesan, D., Casadio, R., Wang, Z. Cheng, J., Fang, H., Gough, J., Koskinen, P., Toronen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D.W.A., Bryson, K., Jones, D.T. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods. doi:10.1038/nmeth.2340. Reprint
  45. Cozzetto, D., Buchan, D.W.A, Bryson, K., & Jones, D.T. (2013) Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics. 14 (Suppl. 3), S1. Reprint
  46. Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L., Buchan, D.W.A., Chothia, C., Cuff, A., Dana, J.M., Filippis, I., Gough, J., Hunter, S., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mitchell, A., Murzin, A.G., Ochoa-Montaño, B., Rackham, O.J.L, Smith, J., Sternberg, M.J.E., Velankar, S., Yeats, Orengo, C.A. (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic. Acid. Res. 41, D499-D507. Reprint

    2012


  47. Nugent, T. & Jones, D.T. (2012) Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinformatics. 13, 169. PubMed
  48. Nugent, T. & Jones, D.T. (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A. 109, E1540-E1547. Reprint
  49. Jones, D.T., Buchan, D.W., Cozzetto, D. & Pontil, M. (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 28, 184-190. Reprint
  50. Taylor, W.R., Jones, D.T. & Sadowski, M.I. (2012) Protein topology from predicted residue contacts. Protein Sci. 21, 299-305. PubMed

    2011


  51. Nugent, T & Jones, D.T. (2011) Membrane protein structural bioinformatics. J. Struct. Biol. Epub ahead of print. PubMed
  52. Lise, S., Buchan, D., Pontil, M. & Jones, D.T. (2011) Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One. e16774. Reprint
  53. Nugent, T., Ward, S & Jones, D.T. (2011) The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics. 27, 1438-1439. Reprint
  54. Nan, R., Farabella, I., Schumacher, F.F., Miller, A., Gor, J., Martin. A.C., Jones, D.T., Lengyel, I. & Perkins, S.J. (2011) Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration. J. Mol. Biol. 408, 714-735. Reprint
  55. Cuff, A.L., Sillitoe, I., Lewis, T., Clegg, A.B., Rentzsch, R,, Furnham, N., Pellegrini-Calace, M., Jones, D., Thornton, J. & Orengo, C.A. (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucl. Acids Res. 39, D420-D426. Reprint
  56. 2010


  57. Buchan, D.W., Ward, S.M., Lobley, A.E., Nugent, T.C., Bryson, K. & Jones, D.T. (2010) Protein annotation and modelling servers at University College London. Nucl. Acids Res. 38 Suppl, W563-W568. Reprint
  58. Nugent, T. & Jones, D.T. (2010) Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. Plos Comput. Biol.l. Biol. 6, e1000714604. Reprint
  59. Pentony, M.M., Ward, J. & Jones, D.T. (2010) Computational resources for the prediction and analysis of native disorder in proteins. Methods Mol. Biol. 604, 369-393. PubMed
  60. Pentony, M. & Jones, D.T. (2010) Modularity of intrinsic disorder in the human proteome. Proteins. 78, 212-221. PubMed
  61. 2009


  62. Lise, S., Archambeau, C., Pontil, M. & Jones, D.T. (2009) Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics. 10, 365. Epub. Reprint BioMed Highly accessed
  63. Nugent, T. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10, 159. Epub. Reprint BioMed Highly accessed
  64. Edwards, Y.J., Lobley, A., Pentony, M.M. & Jones, D.T. (2009) Insights into the regulation of intrinsically disordered proteins in the human proteome by analysing sequence and gene expression data. Genome Biol. 10, R50. Epub. Reprint BioMed Highly accessed
  65. Lobley, A., Sadowski, M.I. & Jones, D.T. (2009) pGenTHREADER and pDomTHREADER: New Methods For Improved Protein Fold Recognition and Superfamily Discrimination. Bioinformatics. 25, 1761-1767. Reprint
  66. Koussounadis, A., Redfern, O.C. & Jones, D.T. (2009) Improving classification in protein structure databases using text mining. BMC Bioinformatics. 10, 129. Epub. PubMed BioMed Highly accessed
  67. Sadowski, M.I. & Jones, D.T. (2009) The sequence-structure relationship and protein function prediction. Curr. Opin. Struct. Biol. Apr 28. Epub. PubMed
  68. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack, R.L. Jr, Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek, S.R. Jr, Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., Wilson, I.A. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure, 17, 151-159. PubMed
  69. Sadowski, M.I. & Jones, D.T. (2009) An automatic method for assessing structural importance of amino acid positions. BMC Struct Biol. 9, 10. Epub. Reprint BioMed Highly accessed

    2008


  70. Edwards, Y.J., Bryson, K. & Jones, D.T. (2008) A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS ONE. 3, e2712. Reprint
  71. Lobley, A.E., Nugent, T., Orengo, C.A. & Jones, D.T. (2008) FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res. May 7. PubMed
  72. Siepen, J.A., Belhajjame, K., Selley, J.N., Embury, S.M., Paton, N.W., Goble, C.A., Oliver, S.G., Stevens, R., Zamboulis, L., Martin, N., Poulovassillis, A., Jones, P., Cote, R., Hermjakob, H., Pentony, M.M., Jones, D.T., Orengo, C.A., Hubbard, S.J. (2008) ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 2008 Apr 25. PubMed
  73. Nugent, T., Mole, S. & Jones, D.T. (2008) The transmembrane topology of Batten disease protein CLN3 determined by consensus computational prediction constrained by experimental data. FEBS Lett. 582, 1019-1024. PubMed
  74. Tan, C. & Jones, D.T. (2008) Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics. 9, 94. Reprint
  75. 2007


  76. Lobley, A., Swindells, M.B., Orengo, C.A. & Jones, D.T. (2007) Inferring function using patterns of native disorder in proteins. PLoS Comput. Biol. 3:e162. Reprint
  77. Sadowski, M.I. & Jones, D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins. 69, 476-485. PubMed
  78. Bryson, K., Cozzetto, D. & Jones, D.T. (2007) Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci., 8, 181-188. PubMed
  79. Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J., Yeats, C., Olason, P.L., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., Lopez, G., Sadowski, M.I., Watson, J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Storling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher C, Ramirez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R. , Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M, Tramontano, A. & Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A. 104, 5495-5500. PubMed
  80. Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544. Reprint
  81. 2006


  82. Ebbels, T.M., Buxton, B.F. & Jones, D.T. (2006) springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'. Bioinformatics, 22, e99-e107. PubMed
  83. Berman, H.M., Burley, S.K., Chiu, W., Sali, A., Adzhubei, A., Bourne, P.E., Bryant, S.H., Dunbrack, R.L. Jr, Fidelis, K., Frank, J., Godzik, A., Henrick, K., Joachimiak, A., Heymann, B., Jones, D., Markley, J.L., Moult, J., Montelione, G.T., Orengo, C., Rossmann, M.G., Rost, B., Saibil, H., Schwede, T., Standley, D.M. & Westbrook, J.D. (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure, 14, 1211-1217. PubMed
  84. Lise, S., Walker-Taylor, A. & Jones, D.T. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310. Reprint BioMed Highly accessed
  85. McGuffin, L.J., Smith R.T., Bryson, K., Sorensen, S.A., & Jones, D.T. (2006) High throughput profile-profile based fold recognition for the entire Human proteome. BMC Bioinformatics, 7, 288. Reprint
  86. Hurwitz, N., Pellegrini-Calace, M., Jones, D.T. (2006) Towards genome-scale structure prediction for transmembrane proteins. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:465-475. PubMed

    2005


  87. Jones D.T., Bryson K., Coleman A., McGuffin L.J., Sadowski M.I., Sodhi J.S., Ward J.J. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins. Suppl 7:143-51. PubMed
  88. Corney, D.P.A., Byrne, E.L., Buxton, B.F. & Jones, D.T. (2005) "A Logical Framework for Template Creation and Information Extraction", Foundations of Semantic Oriented Data and Web Mining workshop, part of ICDM2005 (the Fifth IEEE International Conference on Data Mining). Reprint
  89. Pettitt, C.S., McGuffin, L.J. & Jones, D.T. (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21(17):3509-3515. Reprint
  90. Bryson, K., McGuffin, L.J., Marsden, R.L., Ward, J.J., Sodhi, J.S. & Jones, D.T. (2005) Protein structure prediction servers at University College London. Nucl. Acids Res. 33(Web Server issue):W36-38. Reprint
  91. Lise, S., & Jones, D.T. (2005) Sequence patterns associated with disordered regions in proteins. Proteins. 58, 144-150. PubMed

    2004


  92. Corney, D. P., Buxton, B. F., Langdon, W. B. & Jones, D. T. (2004) BioRAT: extracting biological information from full-length papers. Bioinformatics. 20, 3206-3213. Reprint
  93. Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L. & Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models. J. Mol. Biol., 342, 307-320. Reprint
  94. Ward, J.J., McGuffin, L. J., Bryson K., Buxton, B. F. & Jones, D.T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20, 2138-2139. Reprint
  95. Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., Jones, D.T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645. Reprint
  96. McGuffin, L.J., Street, S., Bryson, K., Sorensen, S.A., Jones, D.T. (2004) The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucl. Acids Res. 32, D196-199. PubMed
  97. McGuffin, L.J., Street, S., Sorensen, S.A., Jones, D.T. (2004) The genomic threading database. Bioinformatics. 20, 131-132. PubMed

    2003


  98. Jones, D.T. (2003) Learning to speak the language of proteins. Science. 302, 1347-1348. PubMed
  99. Jones, D.T., & Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins. S6, 573-578. PubMed
  100. Jones, D.T., & McGuffin, L.J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins. S6, 480-485. PubMed
  101. Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N. & Thorne, J.L. (2003) Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20, 1692-1704. PubMed
  102. Ward, J.J., McGuffin, L.J., Buxton, B.F. & Jones, D.T. (2003) Secondary structure prediction using support vector machines. Bioinformatics, 19, 1650-1655. Reprint
  103. Tress, M.L., Jones, D.T., Valencia, A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 18, 705-718. PubMed
  104. McGuffin, L.J. & Jones, D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881. PubMed
  105. McGuffin, L.J. & Jones, D.T. (2003) Benchmarking protein secondary structure prediction for protein fold recognition. Proteins: Structure, Function and Genetics, 52, 166-175. PubMed
  106. Pellegrini-Calace, M., Carotti, A. & Jones, D.T. (2003) Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3-D structures. Proteins: Structure, Function and Genetics. 50, 537-545. Reprint

    2002


  107. Marsden, R.L., McGuffin, L.J. & Jones, D.T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science. 11, 2814-2824. PubMed
  108. McGuffin, L. J. & Jones, D.T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function and Genetics 48, 44-52. PubMed
  109. Jones, D.T. & Swindells M.B. (2002) Getting the most from PSI-BLAST. TRENDS BIOCHEM SCI. 27, 161-164. PubMed

    2001


  110. Bryson, K, Luck, M., Joy, M. & Jones, D.T. (2001) Agent interaction for bioinformatics data management. Appl. Artif. Intell. 15, 917-947.
  111. Jones, D.T. (2001) Protein structure prediction in genomics. Brief. Bioinformatics. 2, 111-125. PubMed
  112. Jones, D.T., Swindells, M.B. & Fagan, R. (2001) The role of protein structure prediction in drug discovery. Ann. Rep. Med. Chem. 36, 211-225.
  113. Jones, D.T. (2001) Predicting novel protein folds by using FRAGFOLD. PROTEINS. Suppl 5, 127-132. PubMed
  114. Jones, D.T. (2001) Evaluating the potential of using fold-recognition models for molecular replacement. ACTA CRYSTALLOGR D. 57, 1428-1434. PubMed
  115. Jones, D.T. (2001) Critically assessing the state-of-the-art in protein structure prediction. Pharmacogenomics J. 1, 126-134. PubMed
  116. McGuffin L.J., Bryson K, Jones, D.T. (2001) What are the baselines for fold recognition? Bioinformatics 17, 63-72. PubMed

    2000


  117. Bryson, K., Luck, M., Joy, M. & Jones, D.T. (2000) Applying agents to bioinformatics in GeneWeaver. Lect. Notes Artif. Intell. 1860, 60-71. SpringerLink
  118. Jones, D.T. & Hadley, C. (2000) Threading methods for protein structure prediction. (In) Bioinformatics: Sequence, structure and databanks. Higgins, D. & Taylor, W.R. Eds., pp1-13, Springer-Verlag, Heidelberg.
  119. Jones, D.T. (2000) Protein structure prediction in the postgenomic era. Curr. Opin. Struct. Biol. 10, 371-379. PubMed
  120. Jones, D.T. (2000) A practical guide to protein structure prediction. Methods Mol. Biol. 143, 131-154. PubMed
  121. McGuffin L.J., Bryson K., Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405. PubMed

    1999


  122. Fulop, V. & Jones, D.T. (1999) Beta propellers: structural rigidity and functional diversity. Curr. Opin. Struct. Biol. 9, 715-721. PubMed
  123. Jones, D.T. (1999) Bioinformatics and the Y2K problem. Bioinformatics. 15, 955-956. Reprint
  124. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. PubMed
  125. Hadley, C. & Jones, D.T. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure. 7, 1099-1112. PubMed
  126. Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D.T., Karplus, K.J., Kelley, L.A., MacCallum, R.M., Pawowski, K., Rost, B., Rychlewski, L., Sternberg, M. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. Suppl 3, 209-217. PubMed
  127. Jones, D.T., Tress, M., Bryson, K. & Hadley, C. (1999) Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins. S3, 104-111. PubMed
  128. Jones, D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815. PubMed

    1998


  129. Jones, D.T. (1998) THREADER : Protein Sequence Threading by Double Dynamic Programming. (in) Computational Methods in Molecular Biology. Steven Salzberg, David Searls, and Simon Kasif, Eds. Elsevier Science. Chapter 13.
  130. Swindells, M.B., Orengo, C.A., Jones, D.T., Hutchinson, E.G. & Thornton, J.M. (1998) Contemporary approaches to protein structure classification. Bioessays. 20, 884-891. PubMed
  131. Jones, D.T. & Taylor, W.R. (1998) Towards structural genomics for transmembrane proteins. Biochem. Soc. Trans. 26, 429-438. PubMed
  132. Orengo, C.A., Martin, A.M., Hutchinson, G., Jones, S., Jones, D.T., Michie, A.D., Swindells, M.B. & Thornton, J.M. (1998) Classifying a protein in the CATH database of domain structures. Acta Cryst. D. 54, 1155-1167. PubMed
  133. Lio, P., Goldman, N., Thorne, J.L. & Jones, D.T. (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics. 14, 726-733. PubMed
  134. Goldman, N., Thorne, J.L. & Jones, D.T. (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics. 149, 445-458. PubMed
  135. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285. PubMed

    1997


  136. Jones, D.T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7, 377-387.
  137. Jones, D.T. (1997) Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs. PROTEINS. Suppl. 1, 185-191.
  138. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. & Thornton. J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure. 5, 1093-1108.

    1996


  139. Jones, D.T. & Thornton, J.M. (1996) Potential-energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
  140. Hubbard, T., Tramontano, A., Barton, G., Jones, D., Sippl, M., Valencia, A., Lesk, A., Moult, J., Rost, B., Sander, C., Schneider, R., Lahm, A., Leplae, R., Buta, C., Eisenstein, M., Fjellstrom, O., Floeckner, H., Grossmann, JG., Hansen, J., Citterich, MH., Joergensen, F.S., Marchler-Bauer, A., Osuna, J., Park, J., Reinhardt, A., dePouplana, LR., Rojo-Dominguez, A., Saudek, V., Sinclair, J., Sturrock, S., Venclovas, C., Vinals, C. (1996) Update on protein structure prediction: Results of the 1995 IRBM workshop. Folding & Design. 1, R55-R63.
  141. Jones, D.T., Orengo, C.A. & Thornton, J.M. (1996) Protein folds and their recognition from sequence. (In) Prediction of Protein Structure. Practical Approach Series. Sternberg, M.J.E. Ed. IRL Press. pp 173-206.
  142. Goldman, N., Thorne, J.L., & Jones, D.T. (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol. 263, 196-208.
  143. Thorne, J.L., Goldman, N. & Jones, D.T. (1996) Combining protein evolution and secondary structure. Molecular biology and evolution. 13, 666-673.
  144. Jones, D.T., Moody, C.M., Uppenbrink, J., Viles, J.H., Doyle, P.M., Harris, C.J., Pearl, L.H., Sadler, P.J. & Thornton, J.M. (1996) Towards meeting the Paracelsus challenge - the design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50-percent sequence identity to an all-beta protein. Proteins. 24, 502-513.
  145. Miller, R.T., Jones, D.T. & Thornton, J.M. (1996) Protein fold recognition by sequence threading - tools and assessment techniques. FASEB J. 10, 171-178.

    1995


  146. Jones, D.T. (1995) Theoretical approaches to designing novel sequences to fit a given fold. Curr. Opin. Biotech. 6, 452-459.
  147. Thornton, J.M., Jones, D.T., MacArthur, M.W., Orengo, C.A. & Swindells, M.B. (1995) Protein folds - towards understanding folding from inspection of native structures. Phil. Trans. Royal Soc. Series B. 348, 71-79.
  148. Taylor, W.R. & Jones, D.T. (1995) Modelling and predicting alpha-helical transmembrane structures. (In) Protein folds - A Distance-Based Approach. Bohr, H. & Brunak, S. Eds. CRC Press. pp283-293.
  149. Jones, D.T., Miller, R.T. & Thornton, J.M. (1995) Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 23, 387-397.

    1994


  150. Thornton, J.M., Orengo, C.M., Jones, D.T. & Taylor, W.R. (1994) Protein motifs and folding recognition. Biophysical Journal. 66, 241.
  151. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994) Protein domain superfolds and superfamilies. Nature. 372, 631-634.
  152. Jones, D.T. (1994) De novo protein design using pairwise potentials and a genetic algorithm. Protein Science. 3, 567-574.
  153. Taylor, W.R., Jones, D.T. & Green, N.M. (1994) A method for alpha-helical integral membrane protein fold prediction. Proteins. 18, 281-294.
  154. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33, 3038-3048.

    1993


  155. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A mutation data matrix for transmembrane proteins. FEBS Letts. 339, 269-275. Supplementary Material
  156. Swindells, M.B., Orengo, C.A., Jones, D.T., Pearl, L.H. & Thornton, J.M. (1993) Recurrence of a binding motif. Nature. 362, 299.
  157. Orengo, C.A., Flores, T.P., Jones, D.T., Taylor, W.R. & Thornton, J.M. (1993) Recurring structural motifs in proteins with different functions. Current Biology 3, 131-139.
  158. Wilson, S.A., Wachira, S.J., Drew, R.E., Jones, D.T. & Pearl, L.H. (1993) EMBO J. 12, 3637-3642.
  159. Taylor, W.R. & Jones, D.T. (1993) Deriving an amino acid distance matrix. J. Theor. Biol. 164, 6583.
  160. Taylor, W.R., Jones, D.T. & Segal, A.W. (1993) A structural model for the nucleotide binding domains of the flavocytochrome b245 chain. Protein Science 2, 1675-1685.
  161. Jones, D.T. & Thornton, J.M. (1993) Protein fold recognition. J. Comput. Aided Mol. Des. 7:439-456.
  162. Thornton, J.M., MacArthur, M.W., McDonald, I.K., Jones, D.T., Mitchell, J.B.O., Nandi, C.L., Price, S.L. & Zvelebil, M.J.J.M. (1993) Protein structures and complexes what they reveal about the interactions that stabilize them. Phil. Trans. Royal Soc. Series A Physical Sciences and Engineering 345, 113-129.
  163. Jones, D.T. (1993) More protein talk. Nature. 361, 694.

    1992


  164. Jones, D.T., Orengo, C.A., Taylor, W.R., and Thornton, J.M. Progress towards Recognising Protein Folds from Amino Acid Sequences. Proceedings of Miami Bio/Technology Winter Symposium, p124.
  165. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature 358, 86-89. Reprint
  166. Jones, D.T. (1992) A brief review of protein sequence pattern matching. (In) Patterns in protein sequence and structure. Taylor, W.R. Ed., pp11-28, Springer-Verlag, Heidelberg.
  167. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci. 8, 275-282. PubMed Supplementary Material

    1991


  168. Thornton, J.M., Flores, T.P., Jones, D.T. & Swindells, M.B. (1991) Prediction of progress at last. Nature (News and Views). 354, 105-106.
  169. Jones, D.T. (1991) Identification of Protein Consensus Sequences - book review. Biotechnology and Applied Biochemistry. 14, 247.
  170. Taylor, W.R. & Jones, D.T. (1991) Templates, consensus patterns and motifs. Curr. Opin. Struct. Biol. 1, 327-333.
  171. Jones, D.T. (1991) The application of fractal clustering to efficient molecular ray-tracing on low-cost computers. J. Mol. Graphics. 9, 249-253.

Bryson lab Publications

    2010

    • Buchan, D. W., Ward, S. M., Lobley, A. E., Nugent, T. C., Bryson, K., Jones, D. T. (2010). Protein annotation and modelling servers at University College London. Nucleic Acids Res 38(Web Server issue), W563-W568 doi:10.1093/nar/gkq427.
    • Itan, Y., Bryson, K., Thomas, M. G. (2010). Detecting gene duplications in the human lineage. Ann Hum Genet 74(6), 555-565 doi:10.1111/j.1469-1809.2010.00609.x.

    2008

    • Edwards, Y. J., Bryson, K., Jones, D. T. (2008). A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS One 3, e2712- Author URL

    2007

    • Bryson, K., Cozzetto, D., Jones, D. T. (2007). Computer-assisted protein domain boundary prediction using the DomPred server. Current Protein and Peptide Science 8(2), 181-188 doi:10.2174/138920307780363415. Author URL

    2006

    • Bryson, K., Loux, V., Bossy, R., Nicolas, P., Chaillou, S., van de Guchte, M., Penaud, S., Maguin, E., Hoebeke, M., Bessieres, P., Gibrat, J. F. (2006). AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Research 34(12), 3533-3545 doi:10.1093/nar/gkl471. Author URL
    • McGuffin, L. J., Smith, R. T., Bryson, K., Sorensen, S. A., Jones, D. T. (2006). High throughput profile-profile based fold recognition for the entire Human proteome. BMC Bioinformatics 7(1), 288- doi:10.1186/1471-2105-7-288. Author URL
    • van de Guchte, M., Penaud, S., Grimaldi, C., Barbe, V., Bryson, K., Nicolas, P., Robert, C., Oztas, S., Mangenot, S., Couloux, A., Loux, V., Dervyn, R., Bossy, R., Bolotin, A., Batto, J. M., Walunas, T., Gibrat, J. F., Bessieres, P., Weissenbach, J., Ehrlich, S. D., Maguin, E. (2006). The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America 103(24), 9274-9279 doi:10.1073/pnas.0603024103. Author URL

    2005

    • Bryson, K., McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S., Jones, D. T. (2005). Protein structure prediction servers at University College London. Nucleic Acids Research 33(1), 36-38 doi:10.1093/nar/gki410. Author URL
    • Jones, D. T., Bryson, K., Coleman, A., McGuffin, L. J., Sadowski, M. I., Sodhi, J. S., Ward, J. J. (2005). Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins 61(7), 143-151 doi:10.1002/prot.20731. Author URL
    • Jones, D., Sodhi, J., Lise, S., McGuffin, L., Bryson, K. (2005). Prediction of protein-protein and protein-ligand interactions from protein structures. FEBS JOURNAL. ( Vol. 272 pp.397-398).

    2004

    • McGuffin, L. J., Street, S., Bryson, K., Sorensen, S. A., Jones, D. T. (Eds.) (2004). The Genomic Threading Database: a Comprehensive Resource for Structural Annotations of the Genomes from Key Organisms. Nucleic Acids Research (32), 196-199 Author URL
    • Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L., Jones, D. T. (2004). Predicting metal-binding site residues in low-resolution structural models. Journal of Molecular Biology 342(1), 307-320 doi:10.1016/j.jmb.2004.07.019. Author URL
    • Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F., Jones, D. T. (2004). The DISOPRED server for the prediction of protein disorder. Bioinformatics 20(13), 2138-2139

    2001

    • Bryson, K., Luck, M., Joy, M., Jones, D. T. (2001). Agent interaction for bioinformatics data management. Applied Artificial Intelligence 15(10), 917-947 Author URL
    • McGuffin, L. J., Bryson, K., Jones, D. T. (2001). What are the baselines for protein fold recognition? Bioinformatics 17(1), 63-72 Author URL

    2000

    • Bryson, K., Greenall, R. J. (2000). Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing. Journal of Biomolecular Structure and Dynamics 18(3), 393-412 Author URL
    • Bryson, K., Luck, M., Joy, M., Jones, D. T. (2000). Applying agents to bioinformatics in GeneWeaver. Lecture Notes in Computer Science 1860, 60-71 Author URL
    • McGuffin, L. J., Bryson, K., Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics 16(4), 404-405 Author URL

    1999

    • Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K. J., Kelley, L. A., MacCallum, R. M., Pawowski, K., Rost, B., Rychlewski, L., Sternberg, M. (1999). CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins Suppl 3, 209-217 Author URL
    • Jones, D. T., Tress, M., Bryson, K., Hadley, C. (1999). Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins Suppl 3, 104-111 Author URL

    1996

    • Bryson, K., Greenall, R. J. (1996). Molecular dynamics of putrescine. Journal of the Chemical Society, Faraday Transactions 92(6), 913-919 doi:10.1039/FT9969200913. Author URL