Publications

Jones Lab Publications

    2018


  1. 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
  2. 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
  3. 2017


  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Buchan, D.W., Jones, D.T. (2017) EigenTHREADER: Analogous protein fold recognition by efficient contact map threading. Bioinformatics doi: 10.1093/bioinformatics/btx217.Reprint
  12. 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
  13. 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
  14. 2016


  15. 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
  16. 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
  17. 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


  18. Jones, D.T., Cozzetto, D. (2015) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31 (6), 857-863.Reprint
  19. 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
  20. 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


  21. 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
  22. 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
  23. 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
  24. 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
  25. Nugent, T. , Cozzetto, D. & Jones, D.T. (2014) Evaluation of predictions in the CASP10 model refinement category. Proteins. 82, 98-111. Reprint

    2013


  26. Nugent, T. & Jones, D.T. (2013) Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics. 14, 276. Reprint
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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


  33. Nugent, T. & Jones, D.T. (2012) Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinformatics. 13, 169. PubMed
  34. 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
  35. 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
  36. Taylor, W.R., Jones, D.T. & Sadowski, M.I. (2012) Protein topology from predicted residue contacts. Protein Sci. 21, 299-305. PubMed

    2011


  37. Nugent, T & Jones, D.T. (2011) Membrane protein structural bioinformatics. J. Struct. Biol. Epub ahead of print. PubMed
  38. 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
  39. Nugent, T., Ward, S & Jones, D.T. (2011) The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics. 27, 1438-1439. Reprint
  40. 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
  41. 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
  42. 2010


  43. 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
  44. 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
  45. 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
  46. Pentony, M. & Jones, D.T. (2010) Modularity of intrinsic disorder in the human proteome. Proteins. 78, 212-221. PubMed
  47. 2009


  48. 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
  49. Nugent, T. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10, 159. Epub. Reprint BioMed Highly accessed
  50. 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
  51. 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
  52. 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
  53. Sadowski, M.I. & Jones, D.T. (2009) The sequence-structure relationship and protein function prediction. Curr. Opin. Struct. Biol. Apr 28. Epub. PubMed
  54. 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
  55. 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


  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 2007


  62. 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
  63. Sadowski, M.I. & Jones, D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins. 69, 476-485. PubMed
  64. 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
  65. 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
  66. Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544. Reprint
  67. 2006


  68. 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
  69. 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
  70. Lise, S., Walker-Taylor, A. & Jones, D.T. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310. Reprint BioMed Highly accessed
  71. 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
  72. 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


  73. 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
  74. 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
  75. 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
  76. 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
  77. Lise, S., & Jones, D.T. (2005) Sequence patterns associated with disordered regions in proteins. Proteins. 58, 144-150. PubMed

    2004


  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. McGuffin, L.J., Street, S., Sorensen, S.A., Jones, D.T. (2004) The genomic threading database. Bioinformatics. 20, 131-132. PubMed

    2003


  84. Jones, D.T. (2003) Learning to speak the language of proteins. Science. 302, 1347-1348. PubMed
  85. Jones, D.T., & Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins. S6, 573-578. PubMed
  86. Jones, D.T., & McGuffin, L.J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins. S6, 480-485. PubMed
  87. 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
  88. 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
  89. 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
  90. McGuffin, L.J. & Jones, D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881. PubMed
  91. 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
  92. 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


  93. 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
  94. McGuffin, L. J. & Jones, D.T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function and Genetics 48, 44-52. PubMed
  95. Jones, D.T. & Swindells M.B. (2002) Getting the most from PSI-BLAST. TRENDS BIOCHEM SCI. 27, 161-164. PubMed

    2001


  96. Bryson, K, Luck, M., Joy, M. & Jones, D.T. (2001) Agent interaction for bioinformatics data management. Appl. Artif. Intell. 15, 917-947.
  97. Jones, D.T. (2001) Protein structure prediction in genomics. Brief. Bioinformatics. 2, 111-125. PubMed
  98. 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.
  99. Jones, D.T. (2001) Predicting novel protein folds by using FRAGFOLD. PROTEINS. Suppl 5, 127-132. PubMed
  100. Jones, D.T. (2001) Evaluating the potential of using fold-recognition models for molecular replacement. ACTA CRYSTALLOGR D. 57, 1428-1434. PubMed
  101. Jones, D.T. (2001) Critically assessing the state-of-the-art in protein structure prediction. Pharmacogenomics J. 1, 126-134. PubMed
  102. McGuffin L.J., Bryson K, Jones, D.T. (2001) What are the baselines for fold recognition? Bioinformatics 17, 63-72. PubMed

    2000


  103. Bryson, K., Luck, M., Joy, M. & Jones, D.T. (2000) Applying agents to bioinformatics in GeneWeaver. Lect. Notes Artif. Intell. 1860, 60-71. SpringerLink
  104. 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.
  105. Jones, D.T. (2000) Protein structure prediction in the postgenomic era. Curr. Opin. Struct. Biol. 10, 371-379. PubMed
  106. Jones, D.T. (2000) A practical guide to protein structure prediction. Methods Mol. Biol. 143, 131-154. PubMed
  107. McGuffin L.J., Bryson K., Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405. PubMed

    1999


  108. Fulop, V. & Jones, D.T. (1999) Beta propellers: structural rigidity and functional diversity. Curr. Opin. Struct. Biol. 9, 715-721. PubMed
  109. Jones, D.T. (1999) Bioinformatics and the Y2K problem. Bioinformatics. 15, 955-956. Reprint
  110. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. PubMed
  111. Hadley, C. & Jones, D.T. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure. 7, 1099-1112. PubMed
  112. 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
  113. 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
  114. Jones, D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815. PubMed

    1998


  115. 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.
  116. 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
  117. Jones, D.T. & Taylor, W.R. (1998) Towards structural genomics for transmembrane proteins. Biochem. Soc. Trans. 26, 429-438. PubMed
  118. 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
  119. 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
  120. 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
  121. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285. PubMed

    1997


  122. Jones, D.T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7, 377-387.
  123. 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.
  124. 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


  125. Jones, D.T. & Thornton, J.M. (1996) Potential-energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
  126. 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.
  127. 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.
  128. 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.
  129. Thorne, J.L., Goldman, N. & Jones, D.T. (1996) Combining protein evolution and secondary structure. Molecular biology and evolution. 13, 666-673.
  130. 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.
  131. 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


  132. Jones, D.T. (1995) Theoretical approaches to designing novel sequences to fit a given fold. Curr. Opin. Biotech. 6, 452-459.
  133. 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.
  134. 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.
  135. 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


  136. Thornton, J.M., Orengo, C.M., Jones, D.T. & Taylor, W.R. (1994) Protein motifs and folding recognition. Biophysical Journal. 66, 241.
  137. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994) Protein domain superfolds and superfamilies. Nature. 372, 631-634.
  138. Jones, D.T. (1994) De novo protein design using pairwise potentials and a genetic algorithm. Protein Science. 3, 567-574.
  139. Taylor, W.R., Jones, D.T. & Green, N.M. (1994) A method for alpha-helical integral membrane protein fold prediction. Proteins. 18, 281-294.
  140. 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


  141. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A mutation data matrix for transmembrane proteins. FEBS Letts. 339, 269-275. Supplementary Material
  142. Swindells, M.B., Orengo, C.A., Jones, D.T., Pearl, L.H. & Thornton, J.M. (1993) Recurrence of a binding motif. Nature. 362, 299.
  143. 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.
  144. Wilson, S.A., Wachira, S.J., Drew, R.E., Jones, D.T. & Pearl, L.H. (1993) EMBO J. 12, 3637-3642.
  145. Taylor, W.R. & Jones, D.T. (1993) Deriving an amino acid distance matrix. J. Theor. Biol. 164, 6583.
  146. 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.
  147. Jones, D.T. & Thornton, J.M. (1993) Protein fold recognition. J. Comput. Aided Mol. Des. 7:439-456.
  148. 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.
  149. Jones, D.T. (1993) More protein talk. Nature. 361, 694.

    1992


  150. 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.
  151. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature 358, 86-89. Reprint
  152. 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.
  153. 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


  154. 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.
  155. Jones, D.T. (1991) Identification of Protein Consensus Sequences - book review. Biotechnology and Applied Biochemistry. 14, 247.
  156. Taylor, W.R. & Jones, D.T. (1991) Templates, consensus patterns and motifs. Curr. Opin. Struct. Biol. 1, 327-333.
  157. 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