Publications by David T. Jones (as of July 2009)

Click here for my most up-to-date publication list with PubMed links and some reprints.

Click here for a list of my top 20 papers according to Google Scholar.

Bibliometric data
Published papers 108
Total citations 13203
Average citations per paper 120
Average citations per year 660
Max citations per paper 1834
H-index 42

    Books

  1. Bioinformatics: Genes, Proteins and Computers

    2. Unpublished Papers and Technical Reports

  2. Improved CRC-64 algorithm for biological sequences
  3. On possible use of fold recognition models for molecular replacement
  4. Advice on random number generators in bioinformatics applications

    5. Published Papers

  5. Nugent, T. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10, 159. Epub.
  6. 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.
  7. 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.
  8. Koussounadis, A., Redfern, O.C. & Jones, D.T. (2009) Improving classification in protein structure databases using text mining. BMC Bioinformatics. 10, 12.
  9. Sadowski, M.I. & Jones, D.T. (2009) The sequence-structure relationship and protein function prediction. Curr. Opin. Struct. Biol. Apr 28.
  10. 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.
  11. Sadowski, M.I. & Jones, D.T. (2009) An automatic method for assessing structural importance of amino acid positions. BMC Struct Biol. 9:10.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Tan, C. & Jones, D.T. (2008) Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics. 9, 94.
  17. 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.
  18. Sadowski, M.I. & Jones, D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins. 69, 476-485.
  19. 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.
  20. 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.
  21. Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544.
  22. 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.
  23. 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.
  24. Lise, S., Walker-Taylor, A. & Jones, D. T. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310.
  25. 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.
  26. 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.
  27. 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 Suppl 7:143-51.
  28. 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).
  29. 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.
  30. 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.
  31. Lise, S. & Jones, D. T. (2005) Sequence patterns associated with disordered regions in proteins. Proteins. 58, 144-150.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. McGuffin, L.J., Street, S., Sorensen, S.A., Jones, D.T. (2004) The genomic threading database. Bioinformatics. 20, 131-132.
  38. Jones, D.T. (2003) Learning to speak the language of proteins. Science. 302, 1347-1348.
  39. Jones, D.T. & Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins. S6, 573-578.
  40. Jones, D.T. & McGuffin, L.J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins. S6, 480-485.
  41. 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.
  42. Ward, J.J., McGuffin, L.J., Buxton, B.F. & Jones, D.T. (2003) Secondary structure prediction using support vector machines. Bioinformatics, 19, 1650-1655.
  43. Tress, M.L., Jones, D.T. & Valencia, A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 18, 705-718.
  44. McGuffin, L.J. & Jones, D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
  45. McGuffin, L.J. & Jones, D.T. (2003) Benchmarking protein secondary structure prediction for protein fold recognition. Proteins: Structure, Function and Genetics, 52, 166-175.
  46. 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.
  47. 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.
  48. McGuffin, L. J. & Jones, D.T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function and Genetics 48, 44-52.
  49. Jones, D.T. & Swindells M.B. (2002) Getting the most from PSI-BLAST. TRENDS BIOCHEM SCI. 27, 161-164.
  50. Bryson, K, Luck, M., Joy, M. & Jones, D.T. (2001) Agent interaction for bioinformatics data management. Appl. Artif. Intell. 15, 917-947.
  51. Jones, D.T. (2001) Protein structure prediction in genomics. Brief. Bioinformatics. 2, 111-125.
  52. 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.
  53. Jones, D.T. (2001) Predicting novel protein folds by using FRAGFOLD. PROTEINS. Suppl 5, 127-132.
  54. Jones, D.T. (2001) Evaluating the potential of using fold-recognition models for molecular replacement. ACTA CRYSTALLOGR D. 57, 1428-1434.
  55. Jones, D.T. (2001) Critically assessing the state-of-the-art in protein structure prediction. Pharmacogenomics J. 1, 126-134.
  56. McGuffin L.J., Bryson K, Jones, D.T. (2001) What are the baselines for fold recognition? Bioinformatics 17, 63-72.
  57. Bryson, K., Luck, M., Joy, M. & Jones, D.T. (2000) Applying agents to bioinformatics in GeneWeaver. Lect. Notes Artif. Intell. 1860, 60-71.
  58. 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.
  59. Jones, D.T. (2000) Protein structure prediction in the postgenomic era. Curr. Opin. Struct. Biol. 10, 371-379.
  60. Jones, D.T. (2000) A practical guide to protein structure prediction. Methods Mol. Biol. 143, 131-154.
  61. McGuffin L.J., Bryson K., Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.
  62. Fulop, V. & Jones, D.T. (1999) Beta propellers: structural rigidity and functional diversity. Curr. Opin. Struct. Biol. 9, 715-721.
  63. Jones, D.T. (1999) Bioinformatics and the Y2K problem. Bioinformatics. 15, 955-956.
  64. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202.
  65. Hadley, C. & Jones, D.T. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure. 7, 1099-1112.
  66. 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.
  67. 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.
  68. Jones, D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
  69. 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.
  70. 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.
  71. Jones, D.T. & Taylor, W.R. (1998) Towards structural genomics for transmembrane proteins. Biochem. Soc. Trans. 26, 429-438.
  72. 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.
  73. Lio, P., Goldman, N., Thorne, J.L. & Jones, D.T. (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics. 14, 726-733.
  74. 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.
  75. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285.
  76. Jones, D.T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7, 377-387.
  77. 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.
  78. 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.
  79. Jones, D.T. & Thornton, J.M. (1996) Potential-energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
  80. 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.
  81. 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.
  82. 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.
  83. Thorne, J.L., Goldman, N. & Jones, D.T. (1996) Combining protein evolution and secondary structure. Molecular biology and evolution. 13, 666-673.
  84. 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.
  85. 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.
  86. Jones, D.T. (1995) Theoretical approaches to designing novel sequences to fit a given fold. Curr. Opin. Biotech. 6, 452-459.
  87. 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.
  88. 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.
  89. 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.
  90. Thornton, J.M., Orengo, C.M., Jones, D.T. & Taylor, W.R. (1994) Protein motifs and folding recognition. Biophysical Journal. 66, 241.
  91. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994) Protein domain superfolds and superfamilies. Nature. 372, 631-634.
  92. Jones, D.T. (1994) De novo protein design using pairwise potentials and a genetic algorithm. Protein Science. 3, 567-574.
  93. Taylor, W.R., Jones, D.T. & Green, N.M. (1994) A method for alpha-helical integral membrane protein fold prediction. Proteins. 18, 281-294.
  94. 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.
  95. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A mutation data matrix for transmembrane proteins. FEBS Letts. 339, 269-275. Supplementary Material
  96. Swindells, M.B., Orengo, C.A., Jones, D.T., Pearl, L.H. & Thornton, J.M. (1993) Recurrence of a binding motif. Nature. 362, 299.
  97. 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.
  98. Wilson, S.A., Wachira, S.J., Drew, R.E., Jones, D.T. & Pearl, L.H. (1993) EMBO J. 12, 3637-3642.
  99. Taylor, W.R. & Jones, D.T. (1993) Deriving an amino acid distance matrix. J. Theor. Biol. 164, 6583.
  100. 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.
  101. Jones, D.T. & Thornton, J.M. (1993) Protein fold recognition. J. Comput. Aided Mol. Des. 7:439-456.
  102. 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.
  103. Jones, D.T. (1993) More protein talk. Nature. 361, 694.
  104. 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.
  105. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature 358, 86-89.
  106. 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.
  107. 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.
  108. 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.
  109. Jones, D.T. (1991) Identification of Protein Consensus Sequences - book review. Biotechnology and Applied Biochemistry. 14, 247.
  110. Taylor, W.R. & Jones, D.T. (1991) Templates, consensus patterns and motifs. Curr. Opin. Struct. Biol. 1, 327-333.
  111. Jones, D.T. (1991) The application of fractal clustering to efficient molecular ray-tracing on low-cost computers. J. Mol. Graphics. 9, 249-253.
dtj@cs.ucl.ac.uk