1. 2011
  2. Published

    A novel high-throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutation

    Wang, X., Roig-Villanova, I., Khan, S., Shanahan, H., Quail, P. H., Martinez-Garcia, J. F. & Devlin, P. F., 2011, In: Journal of Experimental Botany. 62, 8, p. 2973-2987 15 p.

    Research output: Contribution to journalArticlepeer-review

  3. Published

    An intuitive graphical visualization technique for the interrogation of transcriptome data

    Bushati, N., Smith, J., Briscoe, J. & Watkins, C., 2011, In: Nucleic Acids Research. 39, 17, p. 7380-7389

    Research output: Contribution to journalArticlepeer-review

  4. Published

    Applying Conformal Prediction to the Bovine TB Diagnosing

    Adamskiy, M., Nouretdinov, I., Mitchell, A., Coldham, N. & Gammerman, A., 2011, 12th INNS EANN-SIG International Conference, EANN 2011 and 7th IFIP WG 12.5 International Conference, Artificial Intelligence Applications and Innovations 2011, Corfu, Greece, September 15--18, 2011, Proceedings , Part II. . p. 449-

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  5. Forthcoming

    Conformal prediction in semi-supervised case

    Adamskiy, M., Nouretdinov, I. & Gammerman, A., 2011, (Accepted/In press) Post-Symposium book 'Statistical learning and Data Science'. Paris: Chapman and Hall

    Research output: Chapter in Book/Report/Conference proceedingChapter

  6. Published

    Feature Selection by Conformal Predictor

    Yang, M., Nouretdinov, I., Luo, Z. & Gammerman, A., 2011, 12th INNS EANN-SIG International Conference, EANN 2011 and 7th IFIP WG 12.5 International Conference, Artificial Intelligence Applications and Innovations 2011, Corfu, Greece, September 15-18, 2011, Proceedings, Part II. . p. 449-

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  7. 2010
  8. Published

    The identification of Transcription Factor Binding Sites using string kernels

    Shanahan, H., 10 Sep 2010.

    Research output: Contribution to conferenceOther

  9. Published

    Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

    Werren, J. H., Richards, S., Desjardins, C. A., Niehuis, O., Gadau, J., Colbourne, J. K., Werren, J. H., Richards, S., Desjardins, C. A., Niehuis, O., Gadau, J., Colbourne, J. K., Beukeboom, L. W., Desplan, C., Elsik, C. G., Grimmelikhuijzen, C. J. P., Kitts, P., Lynch, J. A., Murphy, T., Oliveira, D. C. S. G. & 31 others, Smith, C. D., van de Zande, L., Worley, K. C., Zdobnov, E. M., Aerts, M., Albert, S., Anaya, V. H., Anzola, J. M., Barchuk, A. R., Behura, S. K., Bera, A. N., Berenbaum, M. R., Bertossa, R. C., Bitondi, M. M. G., Bordenstein, S. R., Bork, P., Bornberg-Bauer, E., Brunain, M., Cazzamali, G., Chaboub, L., Chacko, J., Chavez, D., Childers, C. P., Choi, J-H., Clark, M. E., Claudianos, C., Clinton, R. A., Cree, A. G., Cristino, A. S., Solovyev, V. & Nasonia Genome Working Group, 15 Jan 2010, In: Science. 327, 5963, p. 343-8 6 p.

    Research output: Contribution to journalArticlepeer-review

  10. Published

    Community-wide assessment of GPCR structure modelling and ligand docking

    Michino, M. & Solovyev, V., 2010, In: Nature Reviews. Drug Discovery. 8, p. 455-463

    Research output: Contribution to journalArticlepeer-review

  11. Published

    Genome sequence of the pea aphid Acyrthosiphon pisum

    Solovyev, V. & International Aphid Genomics Consortium, 2010, In: PLoS Biology. 8, 2, p. e1000313

    Research output: Contribution to journalArticlepeer-review

  12. Published

    Predictions controlees en apprentissage automatique

    Gammerman, A. & Vovk, V., 2010, In: La Revue Modulad. 42, p. 16-33 18 p.

    Research output: Contribution to journalArticle

  13. Published

    SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

    Nepusz, T., Sasidharan, R. & Paccanaro, A., 2010, In: BMC Bioinformatics. 11, p. 120

    Research output: Contribution to journalArticlepeer-review

  14. 2009
  15. Published

    On-line predictive linear regression

    Vovk, V., Nouretdinov, I. & Gammerman, A., Jun 2009, In: The Annals of Statistics. 37, 3, p. 1566-1590 25 p.

    Research output: Contribution to journalArticlepeer-review

  16. Published

    Regulatory processes underscoring the light control of shoot meristem activity and leaf initiation

    Lopez Juez, E., Dillon, E., Magyar, Z., Khan, S., Hazeldine, S., Murray, J. A., Beemster, G. T., Bogre, L. & Shanahan, H., Jun 2009, p. S205-S205. 1 p.

    Research output: Contribution to conferenceAbstractpeer-review

  17. Published
  18. Published

    Serum Proteomic Abnormality Predating Screen Detection of Ovarian Cancer

    Gammerman, A., Vovk, V., Burford, B., Nouretdinov, I., Luo, Z., Chervonenkis, A., Waterfield, M., Cramer, R., Tempst, P., Villanueva, J., Kabir, M., Camuzeaux, S., Timms, J., Menon, U. & Jacobs, I., May 2009, In: The Computer Journal. 52, 3, p. 326-333 8 p.

    Research output: Contribution to journalArticlepeer-review

  19. Published

    The genome sequence of taurine cattle: a window to ruminant biology and evolution

    Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., Guigó, R., Hamernik, D. L., Kappes, S. M., Lewin, H. A., Lynn, D. J., Nicholas, F. W., Reymond, A., Rijnkels, M., Skow, L. C., Zdobnov, E. M., Schook, L. & 31 others, Womack, J., Alioto, T., Antonarakis, S. E., Astashyn, A., Chapple, C. E., Chen, H-C., Chrast, J., Câmara, F., Ermolaeva, O., Henrichsen, C. N., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Kokocinski, F., Landrum, M., Maglott, D., Pruitt, K., Sapojnikov, V., Searle, S. M., Solovyev, V., Souvorov, A., Ucla, C., Wyss, C., Anzola, J. M., Gerlach, D., Elhaik, E., Graur, D., Reese, J. T., Edgar, R. C. & Bovine Genome Sequencing and Analysis Consortium, 24 Apr 2009, In: Science. 324, 5926, p. 522-8 7 p.

    Research output: Contribution to journalArticlepeer-review

  20. Published

    The spread of awareness and its impact on epidemic outbreaks

    Funk, S., Gilad, E., Watkins, C. & Jansen, V. A. A., 21 Apr 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 16, p. 6872–6877 6 p.

    Research output: Contribution to journalArticlepeer-review

  21. Published
  22. Published

    Quantifying environmental adaptation of metabolic pathways in metagenomics

    Gianoulis, T. A., Raes, J., Patel, P. V., Bjornson, R., Korbel, J. O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L. J., Snyder, M., Bork, P. & Gerstein, M. B., 3 Feb 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 5, p. 1374–1379 6 p.

    Research output: Contribution to journalArticlepeer-review

  23. Published

    Application of Inductive Confidence Machine to ICMLA competition data

    Nouretdinov, I., Burford, B. & Gammerman, A., 2009, Proceedings of The Eighth International Conference on Machine Learning and Applications. p. 435-438 4 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  24. Published

    Can we improve on the identification of transcription factor binding sites?

    Shanahan, H. P., 2009, p. 39-40. 2 p.

    Research output: Contribution to conferenceOther

  25. Published

    Conditional prediction intervals for linear regression

    McCullagh, P., Vovk, V., Nouretdinov, I., Devetyarov, D. & Gammerman, A., 2009, Proceedings of the International Conference on Machine Learning and Applications. p. 131-138 8 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  26. Published

    Confidence Machine and its application to medical diagnosis

    Devetyarov, D., Nouretdinov, I. & Gammerman, A., 2009, International Conference on Bioinformatics and Computational Biology. p. 448-454 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  27. Published

    Confidence Predictions for the Diagnosis of Acute Abdominal Pain

    Papadopoulos, H., Gammerman, A. & Vovk, V., 2009, Artificial Intelligence Applications & Innovations III. Iliadis, L., Vlahavas, I. & Bramer, M. (eds.). Springer, Vol. 296. p. 175-184 10 p. (IFIP International Federation for Information Processing; vol. 296).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  28. Published

    Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

    Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., Chandran, S., Christopoulos, C., Nazarians-Armavil, A., Nasseri, N. K., Musso, G., Ali, M., Nazemof, N., Eroukova, V., Golshani, A., Paccanaro, A. & 3 others, Greenblatt, J. F., Moreno-Hagelsieb, G. & Emili, A., 2009, In: PLoS Biology. 7, 4, p. e96

    Research output: Contribution to journalArticlepeer-review

  29. Published

    Online Prediction of Ovarian Cancer

    Zhdanov, F., Vovk, V., Burford, B., Devetyarov, D., Nouretdinov, I. & Gammerman, A., 2009, Proceedings of the 12th Conference on Artificial Intelligence in Medicine. p. 375-379 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  30. Published

    Reliable diagnosis of acute abdominal pain with conformal prediction

    Papadopoulos, H., Gammerman, A. & Vovk, V., 2009, In: International Journal of Engineering Intelligent Systems for Electrical Engineering and Communications. 17, 2-3, p. 127-137 11 p.

    Research output: Contribution to journalArticlepeer-review

  31. 2008
  32. Published

    Predicting clinical outcome in patients diagnosed with synchronous ovarian and endometrial cancer

    Ramus, S. J., Elmasry, K., Luo, Z., Gammerman, A., Lu, K., Ayhan, A., Singh, N., McCluggage, G., Jacobs, I. J., Whittaker, J. C. & Gayther, S. A., 15 Sep 2008, In: Clinical Cancer Research. 14, 18, p. 5840-5848

    Research output: Contribution to journalArticlepeer-review

  33. Published

    Clinical mass spectrometry proteomic diagnosis by conformal predictors

    Gammerman, A., Nouretdinov, I., Burford, B., Chervonenkis, A., Vovk, V. & Luo, Z., Jul 2008, In: Statistical Applications in Genetics and Molecular Biology. 7, 2, 13.

    Research output: Contribution to journalArticlepeer-review

  34. Published

    Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis

    López-Juez, E., Dillon, E., Magyar, Z., Khan, S., Hazeldine, S., de Jager, S. M., Murray, J. A., Beemster, G. T., Bögre, L. & Shanahan, H., Apr 2008, In: Plant Cell. 20, 4, p. 947-968 22 p.

    Research output: Contribution to journalArticlepeer-review

  35. Published
  36. Published

    nGASP the nematode genome annotation assessment project

    Coghlan, A., Fiedler, T. J., McKay, S. J., Flicek, P., Harris, T. W., Blasiar, D., Stein, L. D. & Solovyev, V., 2008, In: BMC Bioinformatics. 9, p. 549-549 1 p.

    Research output: Contribution to journalArticlepeer-review

  37. Published

    Normalized nonconformity measures for regression conformal prediction

    Papadopoulos, H., Gammerman, A. & Vovk, V., 2008, Proceedings of the IASTED International Conference on Articial Intelligence and Applications. p. 64-69 6 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  38. Published

    Selective Breeding Analysed as a Communication Channel: Channel Capacity as a Fundamental Limit on Adaptive Complexity

    Watkins, C., 2008, Symbolic and Numeric Algorithms for Scientific Computing : Proceedings of SYNASC'08. IEEE, p. 514--518 5 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  39. Published

    Signal transduction networks during stress responses in Arabidopsis: high-throughput analysis and modelling

    Devoto, A. & Paccanaro, A., 2008, Plant Growth Signalling. Springer, p. 331-350 20 p. (Plant Cell Monogr).

    Research output: Chapter in Book/Report/Conference proceedingChapter

  40. Published

    Some Alternatives to Parikh Matrices Using String Kernels

    Clark, A. & Watkins, C., 2008, In: Fundamenta Informaticae. 84, 3-4, p. 291-303 13 p.

    Research output: Contribution to journalArticlepeer-review

  41. Published

    The genome of the model beetle and pest Tribolium castaneum

    Richards, S., Gibbs, R. A., Weinstock, G. M., Brown, S. J., Denell, R., Beeman, R. W., Gibbs, R., Beeman, R. W., Brown, S. J., Bucher, G., Friedrich, M., Grimmelikhuijzen, C. J. P., Klingler, M., Lorenzen, M., Richards, S., Roth, S., Schröder, R., Tautz, D., Zdobnov, E. M., Muzny, D. & 31 others, Gibbs, R. A., Weinstock, G. M., Attaway, T., Bell, S., Buhay, C. J., Chandrabose, M. N., Chavez, D., Clerk-Blankenburg, K. P., Cree, A., Dao, M., Davis, C., Chacko, J., Dinh, H., Dugan-Rocha, S., Fowler, G., Garner, T. T., Garnes, J., Gnirke, A., Hawes, A., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Jackson, L., Kovar, C., Kowis, A., Solovyev, V. & Tribolium Genome Sequencing Consortium, 2008, In: Nature. 452, 7190, p. 949-55 7 p.

    Research output: Contribution to journalArticlepeer-review

  42. 2007
  43. Published

    Hedging predictions in machine learning - The second Computer Journal Lecture

    Gammerman, A. & Vovk, V., Mar 2007, In: The Computer Journal. 50, 2, p. 151-163 13 p.

    Research output: Contribution to journalArticlepeer-review

  44. Published

    Rejoinder - Hedging predictions in machine learning

    Gammerman, A. & Vovk, V., Mar 2007, In: The Computer Journal. 50, 2, p. 173-177 5 p.

    Research output: Contribution to journalEditorialpeer-review

  45. Published

    A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

    Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D. A., Cestaro, A., Pruss, D., Pindo, M., Fitzgerald, L. M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J. T., Perazzolli, M., Eldredge, G. & 37 others, Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J. A., Sterck, L., Vandepoele, K., Grando, S. M., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S. K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F. & Viola, R., 2007, In: PLoS ONE. 2, 12, p. e1326

    Research output: Contribution to journalArticlepeer-review

  46. Published

    Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

    Zhang, Z. D., Paccanaro, A., Fu, Y., Weissman, S., Weng, Z., Chang, J., Snyder, M. & Gerstein, M. B., 2007, In: Genome Research. 17, 6, p. 787-97 11 p.

    Research output: Contribution to journalArticlepeer-review

  47. Published

    Statistical approaches in Eukaryotic gene prediction

    Solovyev, V., 2007, Handbook of Statistical genetics. Balding, D., Canning, C. & Bishop, M. (eds.). 3rd ed. Wiley-Interscience

    Research output: Chapter in Book/Report/Conference proceedingChapter

  48. 2006
  49. Published

    The genome of the sea urchin Strongylocentrotus purpuratus

    Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., Coffman, J. A., Dean, M., Elphick, M. R., Ettensohn, C. A., Foltz, K. R., Hamdoun, A., Hynes, R. O., Klein, W. H., Marzluff, W., McClay, D. R. & 31 others, Morris, R. L., Mushegian, A., Rast, J. P., Smith, L. C., Thorndyke, M. C., Vacquier, V. D., Wessel, G. M., Wray, G., Zhang, L., Elsik, C. G., Ermolaeva, O., Hlavina, W., Hofmann, G., Kitts, P., Landrum, M. J., Mackey, A. J., Maglott, D., Panopoulou, G., Poustka, A. J., Pruitt, K., Sapojnikov, V., Song, X., Souvorov, A., Solovyev, V., Wei, Z., Whittaker, C. A., Worley, K., Durbin, K. J., Shen, Y., Fedrigo, O. & Sea Urchin Genome Sequencing Consortium, 10 Nov 2006, In: Science. 314, 5801, p. 941-52 12 p.

    Research output: Contribution to journalArticlepeer-review

  50. Published

    Insights into social insects from the genome of the honeybee Apis mellifera

    Solovyev, V. & Honeybee Genome Sequencing Consortium, 26 Oct 2006, In: Nature. 443, 7114, p. 931-49 19 p.

    Research output: Contribution to journalArticlepeer-review

  51. Published

    Automatic annotation of eukaryotic genes, pseudogenes and promoters

    Solovyev, V., Kosarev, P., Seledsov, I. & Vorobyev, D., 2006, In: Genome Biology. 7 Suppl 1, p. S10.1-12

    Research output: Contribution to journalArticlepeer-review

  52. Published

    Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

    Waite, R. D., Paccanaro, A., Papakonstantinopoulou, A., Hurst, J. M., Saqi, M., Littler, E. & Curtis, M. A., 2006, In: BMC Genomics. 7, p. 162

    Research output: Contribution to journalArticlepeer-review

  53. Published

    Integration of curated databases to identify genotype-phenotype associations

    Goh, C-S., Gianoulis, T. A., Liu, Y., Li, J., Paccanaro, A., Lussier, Y. A. & Gerstein, M., 2006, In: BMC Genomics. 7, p. 257

    Research output: Contribution to journalArticlepeer-review

  54. Published

    Languages as Hyperplanes: grammatical inference with string kernels

    Clark, A., Costa Florêncio, C. & Watkins, C., 2006, Proceedings of ECML. p. 90-101

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  55. Published

    Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

    Bajic, V. B., Brent, M. R., Brown, R. H., Frankish, A., Harrow, J., Ohler, U., Solovyev, V. V. & Tan, S. L., 2006, In: Genome Biology. 7, Suppl. 1, p. 3.1-3.13 13 p.

    Research output: Contribution to journalLiterature reviewpeer-review

  56. Published

    Planar Languages and Learnability

    Clark, A., Costa Florêncio, C., Watkins, C. & Serayet, M., 2006, p. 148-160.

    Research output: Contribution to conferencePaper

  57. Published

    Predicting essential genes in fungal genomes

    Seringhaus, M., Paccanaro, A., Borneman, A., Snyder, M. & Gerstein, M., 2006, In: Genome Research. 16, 9, p. 1126-35 10 p.

    Research output: Contribution to journalArticlepeer-review

  58. Published

    Predicting interactions in protein networks by completing defective cliques

    Yu, H., Paccanaro, A., Trifonov, V. & Gerstein, M., 2006, In: Bioinformatics. 22, 7, p. 823-9 7 p.

    Research output: Contribution to journalArticlepeer-review

  59. Published

    Spectral clustering of protein sequences

    Paccanaro, A., Casbon, J. A. & Saqi, M. A. S., 2006, In: Nucleic Acids Research. 34, 5, p. 1571-80 10 p.

    Research output: Contribution to journalArticlepeer-review

  60. Published

    Spectral clustering of protein sequences using sequence-profile scores

    Sasidharan, R., Gerstein, M. B. & Paccanaro, A., 2006, Proceedings of ICNPSC – 3rd International Conference on Neural Parallel and Scientific Computations.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  61. 2005
  62. Published

    HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

    Ferrer-Costa, C., Shanahan, H. P., Jones, S. & Thornton, J. M., 15 Sep 2005, In: Bioinformatics. 21, 18, p. 3679-3680 2 p.

    Research output: Contribution to journalArticlepeer-review

  63. Published

    Amino acid architecture and the distribution of polar atoms on the surfaces of proteins

    Shanahan, H. P. & Thornton, J. M., 15 Aug 2005, In: BIOPOLYMERS. 78, 6, p. 318-328 11 p.

    Research output: Contribution to journalArticlepeer-review

  64. Published

    Algorithmic Learning in a Random World

    Vovk, V., Gammerman, A. & Shafer, G., 2005, Springer.

    Research output: Book/ReportBook

  65. Published

    Assessing the limits of genomic data integration for predicting protein networks

    Lu, L. J., Xia, Y., Paccanaro, A., Yu, H. & Gerstein, M., 2005, In: Genome Research. 15, 7, p. 945-53 9 p.

    Research output: Contribution to journalArticlepeer-review

  66. Published

    Inferring protein-protein interactions using interaction network topologies

    Paccanaro, A., Trifonov, V., Yu, H. & Gerstein, M. B., 2005, Proceedings of the International Joint Conference on Neural Networks. p. 161 166 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  67. Published

    Plant promoter prediction with confidence estimation

    Shahmuradov, I. A., Solovyev, V. V. & Gammerman, A. J., 2005, In: Nucleic Acids Research. 33, 3, p. 1069-1076 8 p.

    Research output: Contribution to journalArticlepeer-review

  68. Published

    Spectral clustering of protein sequences

    Paccanaro, A., Trifonov, V., Yu, H. & Gerstein, M. B., 2005, International Joint Conference on Neural Networks. p. 161-166

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  69. 2004
  70. Published

    An examination of the conservation of surface patch polarity for proteins

    Shanahan, H. P. & Thornton, J. M., 22 Sep 2004, In: Bioinformatics. 20, 14, p. 2197-2204 8 p.

    Research output: Contribution to journalArticlepeer-review

  71. Published

    Data classication apparatus and method thereof

    Gammerman, A. & Vovk, V., Jul 2004, Patent No. 1129428

    Research output: Patent

  72. Published

    Automated whole-genome multiple alignment of rat, mouse, and human

    Brudno, M., Poliakov, A., Salamov, A., Cooper, G. M., Sidow, A., Rubin, E. M., Solovyev, V., Batzoglou, S. & Dubchak, I., 1 Apr 2004, In: Genome Research. 14, 4, p. 685-92 8 p.

    Research output: Contribution to journalArticlepeer-review

  73. Published

    The DNA sequence and biology of human chromosome 19

    Grimwood, J., Gordon, L. A., Olsen, A., Terry, A., Schmutz, J., Lamerdin, J., Hellsten, U., Goodstein, D., Couronne, O., Tran-Gyamfi, M., Aerts, A., Altherr, M., Ashworth, L., Bajorek, E., Black, S., Branscomb, E., Caenepeel, S., Carrano, A., Caoile, C., Chan, Y. M. & 78 others, Christensen, M., Cleland, C. A., Copeland, A., Dalin, E., Dehal, P., Denys, M., Detter, J. C., Escobar, J., Flowers, D., Fotopulos, D., Garcia, C., Georgescu, A. M., Glavina, T., Gomez, M., Gonzales, E., Groza, M., Hammon, N., Hawkins, T., Haydu, L., Ho, I., Huang, W., Israni, S., Jett, J., Kadner, K., Kimball, H., Kobayashi, A., Larionov, V., Leem, S-H., Lopez, F., Lou, Y., Lowry, S., Malfatti, S., Martinez, D., McCready, P., Medina, C., Morgan, J., Nelson, K., Nolan, M., Ovcharenko, I., Pitluck, S., Pollard, M., Popkie, A. P., Predki, P., Quan, G., Ramirez, L., Rash, S., Retterer, J., Rodriguez, A., Rogers, S., Salamov, A., Salazar, A., She, X., Smith, D., Slezak, T., Solovyev, V., Thayer, N., Tice, H., Tsai, M., Ustaszewska, A., Vo, N., Wagner, M., Wheeler, J., Wu, K., Xie, G., Yang, J., Dubchak, I., Furey, T. S., DeJong, P., Dickson, M., Gordon, D., Eichler, E. E., Pennacchio, L. A., Richardson, P., Stubbs, L., Rokhsar, D. S., Myers, R. M., Rubin, E. M. & Lucas, S. M., 1 Apr 2004, In: Nature. 428, 6982, p. 529-35 7 p.

    Research output: Contribution to journalArticlepeer-review

  74. Published

    Community structure and metabolism through reconstruction of microbial genomes from the environment

    Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S. & Banfield, J. F., 4 Mar 2004, In: Nature. 428, 6978, p. 37-43 7 p.

    Research output: Contribution to journalArticlepeer-review

  75. Published

    Identifying DNA-binding proteins using structural motifs and the electrostatic potential

    Shanahan, H. P., Garcia, M. A., Jones, S. & Thornton, J. M., 2004, In: Nucleic Acids Research. 32, 16, p. 4732-4741 10 p.

    Research output: Contribution to journalArticlepeer-review

  76. 2003
  77. Published

    Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

    Jones, S., Shanahan, H. P., Berman, H. M. & Thornton, J. M., 15 Dec 2003, In: Nucleic Acids Research. 31, 24, p. 7189-7198 10 p.

    Research output: Contribution to journalArticlepeer-review

  78. Published

    Sequence alignment kernel for recognition of promoter regions

    Gordon, L., Chervonenkis, A. Y., Gammerman, A. J., Shahmuradov, I. A. & Solovyev, V. V., 12 Oct 2003, In: Bioinformatics. 19, 15, p. 1964-1971 8 p.

    Research output: Contribution to journalArticlepeer-review

  79. Published

    PromH: promoters identification using orthologous genomic sequences

    Solovyev, V. V. & Shahmuradov, I. A., 1 Jul 2003, In: Nucleic Acids Research. 31, 13, p. 3540-3545 6 p.

    Research output: Contribution to journalArticlepeer-review

  80. Published

    Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis

    Shahmuradov, I. A., Akbarova, Y. Y., Solovyev, V. V. & Aliyev, J. A., Jul 2003, In: Plant Molecular Biology. 52, 5, p. 923-934 12 p.

    Research output: Contribution to journalArticlepeer-review

  81. Published

    Mondrian Condence Machine

    Vovk, V., Lindsay, D., Nouretdinov, I. & Gammerman, A., Mar 2003, (On-line Compression Modelling project).

    Research output: Working paper

  82. Published

    Mondrian Confidence Machine

    Vovk, V., Lindsay, D., Nouretdinov, I. & Gammerman, A., Mar 2003, (On-line Compression Modelling project).

    Research output: Working paper

  83. Published

    Online region prediction with real teachers

    Ryabko, D., Vovk, V. & Gammerman, A., Mar 2003, (On-line Compression Modelling project).

    Research output: Working paper

  84. Published

    Testing Exchangeability On-line

    Vovk, V., Nouretdinov, I. & Gammerman, A., Feb 2003, (On-line Compression Modelling project).

    Research output: Working paper

  85. Published

    PlantProm: a database of plant promoter sequences

    Shahmuradov, I. A., Gammerman, A. J., Hancock, J. M., Bramley, P. M. & Solovyev, V. V., 1 Jan 2003, In: Nucleic Acids Research. 31, 1, p. 114-117 4 p.

    Research output: Contribution to journalArticlepeer-review

  86. Published

    An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome

    Hild, M., Beckmann, B., Haas, S. A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., Hoheisel, J. D. & Paro, R., 2003, In: Genome Biology. 5, 1, p. R3

    Research output: Contribution to journalArticlepeer-review

  87. Published

    Markov analysis of protein sequence similarities

    Chennubhotla, C. & Paccanaro, A., 2003, Lecture Notes in Computer Science. Springer, Vol. 2859. p. 278-286

    Research output: Chapter in Book/Report/Conference proceedingChapter

  88. Published

    Testing exchangeability on-line

    Vovk, V., Nouretdinov, I. & Gammerman, A., 2003, Proceedings of the Twentieth International Conference on Machine Learning. Fawcett, T. & Mishra, N. (eds.). Menlo Park, CA: AAAI Press, p. 768-775

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  89. Published

    Transductive Confidence Machine is universal

    Nouretdinov, I., Vyugin, V. & Gammerman, A., 2003, Lecture Notes in Artificial Intelligence. Springer, Vol. 2842. p. 283-297 16 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  90. 2002
  91. Published

    Reinforcement Learning

    Watkins, C. & Dayan, P., 1 Dec 2002, Encyclopaedia of Cognitive Science. Nadel, L. (ed.). Wiley-Blackwell

    Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionary

  92. Published

    Light hadron spectroscopy with two flavors of dynamical quarks on the lattice

    Khan, A. A., Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Mar 2002, In: Physical Review D . 65, 5, p. - 50 p.

    Research output: Contribution to journalArticlepeer-review

  93. Published

    THE PEDANT HUMAN GENOME DATABASE — FUNCTIONAL ANNOTATION OF THE HUMAN GENOME

    Schüller, C. M. E., Geier, B., Fritz, A., Salamov, A., Seledsov, I., Solovyev, V. & Frishman, D., 2 Jan 2002, In: TheScientificWorldJOURNAL. 2, p. 82-83 2 p.

    Research output: Contribution to journalArticlepeer-review

  94. Published

    Finding genes by computer: probabilistic and discriminative approaches

    Solovyev, V., 2002, Current Topics in Computational Biology. Jiang, T., Smith, T., Xu, Y. & Zhang, M. (eds.). MIT Press, p. 365-401

    Research output: Chapter in Book/Report/Conference proceedingChapter

  95. Published

    Inductive Confidence Machine for pattern recognition

    Surkov, D., Gammerman, A. & Vovk, V., 2002, Proceedings of the ICDM 2002 Workshop on the Foundation of Data Mining and Knowledge Discovery. Lin, T. & Ohsuga, S. (eds.). Shimane Medical University, p. 249-255 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  96. Published

    Properties and Prediction of Protein Secondary Structure

    Solovyev, V. & Shindyalov, I. N., 2002, Current Topics in Computational Biology. Jiang, T., Smith, T., Xu, Y. & Zhang, M. (eds.). MIT Press, p. 201–248

    Research output: Chapter in Book/Report/Conference proceedingChapter

  97. Published

    Qualified predictions for large data sets in the case of pattern recognition

    Papadopoulos, H., Vovk, V. & Gammerman, A., 2002, Proceedings of the International Conference on Machine Learning and Applications. Wani, M., Arabnia, H., Cios, K., Hafeez, K. & Kendall, G. (eds.). CSREA Press, p. 159-163 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  98. Published

    Structure, Properties and Computer Identification of Eukaryotic genes

    Solovyev, V., 2002, Bioinformatics from Genomes to Drugs. V.1. Basic Technologies. Lengauer, T. (ed.). p. 59-111

    Research output: Chapter in Book/Report/Conference proceedingChapter

  99. Published

    Text classification using string kernels

    Lodhi, H., Saunders, C., Shawe-Taylor, J., Cristianini, N. & Watkins, C., 2002, In: Journal of Machine Learning Research. 2, p. 444 1 p.

    Research output: Contribution to journalArticlepeer-review

  100. Published

    The Channel Capacity of Evolution: Ultimate Limits on the Amount of Information Maintainable in the Genome

    Watkins, C., 2002, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure. Novisibirsk, Russia, Vol. 2. p. 58--60 3 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  101. 2001
  102. Published

    Kaon B parameter from quenched domain-wall QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K. I., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Dec 2001, In: Physical Review D . 6411, 11, p. - 21 p.

    Research output: Contribution to journalArticlepeer-review

  103. Published

    Topological susceptibility in lattice QCD with two flavors of dynamical quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Dec 2001, In: Physical Review D . 6411, 11, p. - 10 p.

    Research output: Contribution to journalArticlepeer-review

  104. Published

    Hybrid quarkonia with dynamical sea quarks

    Manke, T., Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Nov 2001, In: Physical Review D . 6409, 9, p. - 4 p.

    Research output: Contribution to journalArticlepeer-review

  105. Published

    Equation of state in finite-temperature QCD with two flavors of improved Wilson quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K. I., Okamoto, M., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A. & Yoshie, T., 1 Oct 2001, In: Physical Review D . 6407, 7, p. art. no.-074510 17 p.

    Research output: Contribution to journalArticlepeer-review

  106. Published

    B meson decay constants from two-flavor lattice QCD with nonrelativistic heavy quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A. & Yoshie, T., 1 Sep 2001, In: Physical Review D . 6405, 5, p. - 24 p.

    Research output: Contribution to journalArticlepeer-review

  107. Published

    Decay constants of B and D mesons from improved relativistic lattice QCD with two flavors of sea quarks

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 1 Aug 2001, In: Physical Review D . 6403, 3, p. - 17 p.

    Research output: Contribution to journalArticlepeer-review

  108. Published

    Chiral properties of domain-wall quarks in quenched QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K. I., Noaki, J., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A. & 2 others, Yoshie, T. & CP-PACS Collaboration, 1 Jun 2001, In: Physical Review D . 6311, 11, p. - 19 p.

    Research output: Contribution to journalArticlepeer-review

  109. Published

    Calculation of K -> pi matrix elements in quenched domain-wall QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K. I., Noaki, J., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & 1 others, CP-PACS collaboration, Mar 2001, In: Nuclear Physics B - Proceedings Supplements. 94, p. 283-286 4 p.

    Research output: Contribution to journalArticlepeer-review

  110. Published

    Eigenvalues of the hermitian Wilson-Dirac operator and chiral properties of the domain-wall fermion

    Khan, A. A., Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Izubuchi, T., Kanaya, K., Kanebo, T., Kuramashi, Y., Manke, T., Nagai, K. I., Noaki, J., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A. & Yoshie, T., Mar 2001, In: Nuclear Physics B - Proceedings Supplements. 94, p. 725-728 4 p.

    Research output: Contribution to journalArticlepeer-review

  111. Published

    Full QCD light hadron spectrum and quark masses: Final results from CP-PACS

    Khan, A. A., Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Ishizuka, N., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Manke, T., Nagai, K. I., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP PACS Collaboration, Mar 2001, In: Nuclear Physics B - Proceedings Supplements. 94, p. 229-232 4 p.

    Research output: Contribution to journalArticlepeer-review