1. Submitted

    “Ethics When You Least Expect It”: A Modular Approach to Data Ethics Instruction

    Shanahan, H., Bezuidenhout, L. & Quick, R., 2018, (Submitted).

    Research output: Contribution to conferencePaperpeer-review

  2. Published

    12 paragraphs

    Solovyev, V., 1994, Computer analysis of Genetic Macromolecules. Structure, Function and Evolution. Kolchanov, N. A. & Lim, H. A. (eds.). World Scientific

    Research output: Chapter in Book/Report/Conference proceedingChapter

  3. Published

    3D-structure calculations of a-helical domains of protein molecules using the quasispherical primary approximations

    Solovyev, V., Salikhova, A. K., Lim, H. A. & Witten, M., 1992, Biomedical Modeling and Simulation. Eisenfeld, J. & Levin, D. (eds.). Elsevier Science Publishers B.V. (North-Holland), p. 201-211

    Research output: Chapter in Book/Report/Conference proceedingChapter

  4. Submitted

    9 Simple recommendations for teaching data skills

    Shanahan, H., 16 Apr 2019, (Submitted) In: Data Science Journal.

    Research output: Contribution to journalArticlepeer-review

  5. Published

    A Census of Human Soluble Protein Complexes

    Havugimana, P. C., Hart, G. T., Nepusz, T., Yang, H., Turinsky, A. L., Li, Z., Wang, P. I., Boutz, D. R., Fong, V., Phanse, S., Babu, M., Craig, S. A., Hu, P., Wan, C., Vlasblom, J., Dar, V-N., Bezginov, A., Clark, G. W., Wu, G. C., Wodak, S. J. & 4 others, Tillier, E. R. M., Paccanaro, A., Marcotte, E. M. & Emili, A., 31 Aug 2012, In: Cell. 150, 5, p. 1068–1081

    Research output: Contribution to journalArticlepeer-review

  6. Published

    A Comparison of Venn Machine with Platt's Method in Probabilistic Outputs

    Zhou, C., Nouretdinov, I., Luo, Z., Adamskiy, M., 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. 483-

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

  7. 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

  8. Published

    A large-scale evaluation of computational protein function prediction

    Radivojac, P., Clark, W. T., Oron, T. R., 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. & 82 others, Gough, J., Koskinen, P., Törönen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D. W. A., Bryson, K., Jones, D. T., Limaye, B., Inamdar, H., Datta, A., Manjari, S. K., Joshi, R., Chitale, M., Kihara, D., Lisewski, A. M., Erdin, S., Venner, E., Lichtarge, O., Rentzsch, R., Yang, H., Romero, A. E., Bhat, P., Paccanaro, A., Hamp, T., Kaßner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., Auer, F., Boehm, A., Braun, T., Hecht, M., Heron, M., Hönigschmid, P., Hopf, T. A., Kaufmann, S., Kiening, M., Krompass, D., Landerer, C., Mahlich, Y., Roos, M., Björne, J., Salakoski, T., Wong, A., Shatkay, H., Gatzmann, F., Sommer, I., Wass, M. N., Sternberg, M. J. E., Škunca, N., Supek, F., Bošnjak, M., Panov, P., Džeroski, S., Šmuc, T., Kourmpetis, Y. A. I., van Dijk, A. D. J., ter Braak, C. J. F., Zhou, Y., Gong, Q., Dong, X., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Di Camillo, B., Toppo, S., Lan, L., Djuric, N., Guo, Y., Vucetic, S., Bairoch, A., Linial, M., Babbitt, P. C., Brenner, S. E., Orengo, C., Rost, B., Mooney, S. D. & Friedberg, I., Mar 2013, In: Nature Methods. 10, 3, p. 221-7 7 p.

    Research output: Contribution to journalArticlepeer-review

  9. Published
  10. E-pub ahead of print

    A network medicine approach to quantify distance between hereditary disease modules on the interactome

    Caniza, H., Romero, A. E. & Paccanaro, A., 3 Dec 2015, In: Scientific Reports. 5, p. 1-10 10 p., 17658.

    Research output: Contribution to journalArticlepeer-review

  11. Published

    A new approach for the classification of functional regions of DNA sequences based on fractal representation

    Solovyev, V., Korolev, S. V. & Lim, H. A., 1993, In: Int.J. Genomic. Res.. 1, 2, p. 108-127

    Research output: Contribution to journalArticlepeer-review

  12. Published

    A non-perturbative calculation of the mass of the B-c

    Shanahan, H. P., Boyle, P., Davies, C. T. H., Newton, H. & UKQCD Collaboration, 6 May 1999, In: Physics Letters B. 453, 3-4, p. 289-294 6 p.

    Research output: Contribution to journalArticlepeer-review

  13. 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

  14. Published

    A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization

    Solovyev, V. V. & Makarova, K. S., 1 Feb 1993, In: Bioinformatics. 9, 1, p. 17-24 8 p.

    Research output: Contribution to journalArticlepeer-review

  15. Published

    A Novel Method to Detect Bias in Short Read NGS Data

    Alnasir, J. & Shanahan, H., 2017, In: Journal of Integrative Bioinformatics. 14, 3, p. 1-9 9 p.

    Research output: Contribution to journalArticlepeer-review

  16. Published

    A novel type of RNase III family proteins in eukaryotes

    Filippov, V., Solovyev, V., Filippova, M. & Gill, S. S., 7 Mar 2000, In: Gene. 245, 1, p. 213-21 9 p.

    Research output: Contribution to journalArticlepeer-review

  17. Published

    A Recommender System Approach for Predicting Drug Side Effects

    Galeano Galeano, D. & Paccanaro, A., 2018, IJCNN 2018: International Joint Conference on Neural Networks. IEEE Xplore, p. 1-7 7 p.

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

  18. Published
  19. Published

    A stochastic simulation system and its application to causal models

    Luo, Z. & Gammerman, A., 1990, Proceeding of 3rd International Conference on IPMU in Knowledge-Based Systems. p. 186-189

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

  20. Published

    A study of the quenched (b)over-bar-c mass spectrum at beta=6.2

    Davies, C. T. H., Lidsey, A. J. & Shanahan, H. P., Apr 1998, In: Nuclear Physics B - Proceedings Supplements. 63, p. 323-325 3 p.

    Research output: Contribution to journalArticlepeer-review

  21. Published

    Ab initio gene finding in Drosophila genomic DNA

    Salamov, A. A. & Solovyev, V. V., Apr 2000, In: Genome Research. 10, 4, p. 516-522 7 p.

    Research output: Contribution to journalArticlepeer-review

  22. 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

  23. Published

    Alexey Chervonenkis's Bibliography: Introductory Comments

    Gammerman, A. & Vovk, V., Sep 2015, In: Journal of Machine Learning Research. 16, p. 2051-2066 16 p.

    Research output: Contribution to journalEditorial

  24. Published

    Alexey Chervonenkis's Bibliography

    Gammerman, A. & Vovk, V., Sep 2015, In: Journal of Machine Learning Research. 16, p. 2067-2080 14 p.

    Research output: Contribution to journalEditorial

  25. Published

    Algorithmic Learning in a Random World

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

    Research output: Book/ReportBook

  26. 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

  27. Published

    An evolutionary model that satisfies detailed balance

    Lember, J. & Watkins, C., 9 Nov 2020, In: Methodology and Computing in Applied Probability. 37 p.

    Research output: Contribution to journalArticlepeer-review

  28. 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

  29. Published

    An Exploratory Analysis on Drug Target Locality

    Caceres Silva, J. & Paccanaro, A., Sep 2017, AGRANDA - Simposio Argentino de GRANdes DAtos 2017.

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

  30. 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

  31. 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

  32. Forthcoming

    An Overview of Gene Regulation

    Shanahan, H. & Harrison, A., 2013, (Accepted/In press) Approaches to Integrative Bioinformatics. Chen, MI. & Hofstaedt, R. (eds.). Springer, p. 21-69

    Research output: Chapter in Book/Report/Conference proceedingChapter

  33. Published

    Analysis of canonical and non-canonical splice sites in mammalian genomes

    Burset, M., Seledtsov, I. A. & Solovyev, V. V., 1 Nov 2000, In: Nucleic Acids Research. 28, 21, p. 4364-4375 12 p.

    Research output: Contribution to journalArticlepeer-review

  34. Published

    Analysis of functional sites in pro- and eukaryotic genes

    Solovyev, V., 1990, Methods of molecular genetics and gene engineering. Salganik, R. I. (ed.). Novosibirsk, p. 154-190

    Research output: Chapter in Book/Report/Conference proceedingChapter

  35. Published

    Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven.

    Agulnik, A. I., Bishop, C. E., Lerner, J. L., Agulnik, S. I. & Solovyev, V. V., 1997, p. 134-138. 5 p.

    Research output: Contribution to conferenceAbstract

  36. Published

    Annotation of next-generation sequencing protocol steps in the SRA (sequence read archive) and Big data for Science

    AlNasir, J. & Shanahan, H., 17 Feb 2015, p. 27. 1 p.

    Research output: Contribution to conferenceAbstractpeer-review

  37. Published

    Anomaly Detection in Video Games

    Wilkins, B., Watkins, C. & Stathis, K., 20 May 2020, In: ArXiv.org. p. 1-4 4 p., 2005.10211.

    Research output: Contribution to journalArticle

  38. Published

    Anomaly Detection of Trajectories with Kernel Density Estimation by Conformal Prediction

    Smith, J., Nouretdinov, I., Craddock, R., Offer, C. & Gammerman, A., 19 Sep 2014, Artificial Intelligence Applications and Innovations: AIAI2014 Workshops. Rhodes, Greece: Springer, p. 271-280 10 p.

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

  39. 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

  40. 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

  41. 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

  42. Published

    Assignment of position-specific error probability to primary DNA sequence data.

    Lawrence, C. B. & Solovyev, V. V., 1994, p. 1272-1280. 9 p.

    Research output: Contribution to conferenceAbstract

  43. 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

  44. 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

  45. 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

  46. Published

    Bioinformatics on the cloud computing platform Azure

    Shanahan, H., Harrison, A. & Owen, A. M., 22 Jul 2014, In: PLoS ONE. 9, 7, p. e102642

    Research output: Contribution to journalArticlepeer-review

  47. Published

    Biological Big Bytes: Integrative Analysis of Large Biological Datasets

    Shanahan, H., Chen, M., Harrison, A. & Orlov, Y., 13 Sep 2017, In: Journal of Integrative Bioinformatics. 14, 3, 2 p.

    Research output: Contribution to journalEditorial

  48. Published

    Biomedical Applications: Diagnostic and Prognostic

    Nouretdinov, I., Bellotti, T. & Gammerman, A., 2014, Conformal Prediction for Reliable Machine Learning: Theory, Adaptations and Applications. Balasubramanian, V., Ho, S-S. & Vovk, V. (eds.). Elsevier, p. 217-230 14 p. 11

    Research output: Chapter in Book/Report/Conference proceedingChapter

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. Published

    Co-location epidemic tracking on London public transports using low power mobile magnetometer

    Nguyen, D. K. A., Watkins, C. & Luo, Z., 23 Nov 2017, The 8th International Conference on Indoor Positioning and Indoor Navigation, Sept 18-21, 2017, Japan. IEEE, p. 1-8 8 p.

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

  55. Published

    Combination of Conformal Predictors for Classification

    Toccaceli, P. & Gammerman, A., 13 Jun 2017, Proceedings of Machine Learning Research. Lawrence, N. & Reid, M. (eds.). Vol. 60. p. 39-61 23 p. (The Proceedings of Machine Learning Research; vol. 60).

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

  56. Published

    Combining Cross-Validation and Search

    Watkins, C., 1987, Progress in Machine Learning. Sigma Press, p. 79--87 9 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

  57. 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

  58. 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

  59. Published

    Complexity approximation principle

    Vovk, V. & Gammerman, A., 1999, In: The Computer Journal. 42, 4, p. 318-322 5 p.

    Research output: Contribution to journalArticlepeer-review

  60. Published

    Computational selection of transcriptomics experiments improves Guilt-by-Association analyses

    Bhat, P., Yang, H., Bogre, L., Devoto, A. & Paccanaro, A., 7 Aug 2012, In: PLoS ONE. 7, 8, e39681.

    Research output: Contribution to journalArticlepeer-review

  61. 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

  62. 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

  63. 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

  64. Published

    Conformal Anomaly Detection of Trajectories with a Multi-class Hierarchy

    Smith, J., Nouretdinov, I., Craddock, R., Offer, C. & Gammerman, A., 3 Apr 2015, Statistical Learning and Data Sciences: Third International Symposium, SLDS 2015, Egham, UK, April 20-23, 2015, Proceedings. Gammerman, A., Vovk, V. & Papadopoulos, H. (eds.). Springer, p. 281-290 10 p. (Lecture Notes in Computer Science; vol. 9047).

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

  65. Published

    Conformal Clustering and Its Application to Botnet Traffic

    Cherubin, G., Nouretdinov, I., Gammerman, A., Jordaney, R., Wang, Z., Papini, D. & Cavallaro, L., 3 Apr 2015, Statistical Learning and Data Sciences: Third International Symposium, SLDS 2015, Egham, UK, April 20-23, 2015, Proceedings. Gammerman, A., Vovk, V. & Papadopoulos, H. (eds.). Springer, p. 313-322 10 p. (Lecture Notes in Computer Science; vol. 9047).

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

  66. Published

    Conformal prediction and testing exchangeability assumption

    Fedorova, V., Nouretdinov, I. & Gammerman, A., Jul 2011, p. 35. 1 p.

    Research output: Contribution to conferenceAbstract

  67. 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

  68. Published

    Conformal prediction of biological activity of chemical compounds

    Toccaceli, P., Nouretdinov, I. & Gammerman, A., Oct 2017, In: Annals of Mathematics and Artificial Intelligence. 81, p. 105–123 19 p.

    Research output: Contribution to journalArticlepeer-review

  69. Published

    Conformal prediction under hypergraphical models

    Fedorova, V., Gammerman, A., Nouretdinov, I. & Vovk, V., Oct 2013, The 9th Artificial Intelligence Applications and Innovations Conference (AIAI): 2nd Workshop on Conformal Prediction and its Applications. p. 371-383 13 p.

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

  70. Published

    Conformal Predictors for Compound Activity Prediction

    Toccaceli, P., Nouretdinov, I. & Gammerman, A., 17 Apr 2016, Conformal and Probabilistic Prediction with Applications: 5th International Symposium, COPA 2016 Madrid, Spain, April 20–22, 2016 Proceedings. Springer, Vol. 9653. p. 51-66 16 p. (Lecture Notes in Computer Science; vol. 9653).

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

  71. Published

    Conformal predictors in early diagnostics of ovarian and breast cancers

    Devetyarov, D., Nouretdinov, I., Burford, B., Camuzeaux, S., Gentry-Maharaj, A., Tiss, A., Smith, C., Luo, Z., Chervonenkis, A., Hallett, R., Vovk, V., Waterfield, M., Cramer, R., Timms, J. F., Sinclair, J., Menon, U., Jacobs, I. & Gammerman, A., 2012, In: Progress in Artificial Intelligence. 1, p. 245 - 257 13 p.

    Research output: Contribution to journalArticlepeer-review

  72. Published

    Conformational changings in the Globins Family during Evolution 1. Analysis of the Evolutionary Role of Insertions and Deletions

    Zharkikh, A. A., Solovyev, V. & Kolchanov, N. A., 1984, In: J.Mol.Evol.. 21, p. 42-53

    Research output: Contribution to journalArticlepeer-review

  73. Published

    Criteria of Efficiency for Conformal Prediction

    Vovk, V., Fedorova, V., Nouretdinov, I. & Gammerman, A., 17 Apr 2016, Conformal and Probabilistic Prediction with Applications: 5th International Symposium, COPA 2016 Madrid, Spain, April 20–22, 2016 Proceedings. Springer, Vol. 9653. p. 23-39 17 p. (Lecture Notes in Computer Science; vol. 9653).

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

  74. Published

    Criteria of efficiency for set-valued classification

    Vovk, V., Nouretdinov, I., Fedorova, V., Petej, I. & Gammerman, A., Oct 2017, In: Annals of Mathematics and Artificial Intelligence. 81, p. 21-46 26 p.

    Research output: Contribution to journalArticlepeer-review

  75. Published

    Data classication apparatus and method thereof

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

    Research output: Patent

  76. 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

  77. Published

    Detecting overlapping protein complexes in protein-protein interaction networks

    Nepusz, T., Yu, H. & Paccanaro, A., 2012, In: Nature Methods. 9, 5, p. 471–472 2 p.

    Research output: Contribution to journalArticlepeer-review

  78. Forthcoming

    Determining Confidence of Predicted Interactions Between HIV-1 and Human Proteins Using Conformal Method

    Nouretdinov, I., Gammerman, A., Qi, Y. & Klein-Seetharaman, J., 2012, (Accepted/In press) Pacific Symposium on Biocomputing. Vol. 17. p. 311-322 12 p.

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

  79. Published

    DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering

    Makarova, K. S., Mazin, A. V., Wolf, Y. I. & Solovyev, V., 1 Oct 1992, In: Bioinformatics. 8, 5, p. 425-431 7 p.

    Research output: Contribution to journalArticlepeer-review

  80. Published

    Disease gene prediction for molecularly uncharacterized diseases

    Caceres, J. & Paccanaro, A., 5 Jul 2019, In: PLoS Computational Biology. 15, 7, p. 1-14 14 p., e1007078.

    Research output: Contribution to journalArticlepeer-review

  81. E-pub ahead of print

    Dissecting the chromatin interactome of microRNA genes

    Chen, D., Fu, L-Y., Zhang, Z., Yu, G., Zhang, H., Jiang, L., Harrison, A., Shanahan, H., Klukas, C., Zhang, H-Y., Ruan, Y., Chen, LI-LI. & Chen, M., 20 Dec 2013, In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  82. 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

  83. Published

    Drug cocktail selection for the treatment of chagas disease: A multi-objective approach

    Torres Bobadilla, M., Caceres Silva, J., Jimenez, R., Yubero, V., Vega, C., Rolón, M., Cernuzzi, L., Barán, B. & Paccanaro, A., 21 Dec 2017, SLIOIA - Simposio Latinoamericano de Investigación de Operaciones e Inteligencia Artificial 2017. p. 1-5 5 p.

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

  84. Published

    Drug targets prediction using chemical similarity

    Galeano Galeano, D. & Paccanaro, A., 26 Jan 2017, XLII Conferencia Latinoamericana de Informatica (CLEI). IEEE Xplore, p. 1-7 7 p. (2016 XLII Latin American Computing Conference (CLEI)).

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

  85. Published

    Dynamic alignment kernels

    Watkins, C., 1999, In: ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS. p. 39-50 12 p.

    Research output: Contribution to journalArticlepeer-review

  86. Published

    Dynamical quark effects on light quark masses

    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, 27 Nov 2000, In: Physical Review Letters. 85, 22, p. 4674-4677 4 p.

    Research output: Contribution to journalArticlepeer-review

  87. Published

    Early detection of ovarian cancer in samples pre-diagnosis using CA125 and MALDI-MS peaks

    Timms, J. F., Menon, U., Devetyarov, D., Tiss, A., Camuzeaux, S., McCurrie, K., Nouretdinov, I., Burford, B., Smith, C., Gentry-Maharaj, A., Hallett, R., Ford, J., Luo, Z., Vovk, V., Gammerman, A., Cramer, R. & Jacobs, I., Nov 2011, In: Cancer Genomics and Proteomics. 8, 6, p. 289-305

    Research output: Contribution to journalArticlepeer-review

  88. Published

    Editorial: Kolmogorov complexity

    Gammerman, A. & Vovk, V., 1999, In: The Computer Journal. 42, p. 251 1 p.

    Research output: Contribution to journalEditorial

  89. Published

    Effect of secondary structure prediction on protein fold recognition and database search

    Alexandrov, N. N. & Solovyev, V., 1996, In: Genome Informatics. 7, p. 119-127

    Research output: Contribution to journalArticlepeer-review

  90. Published

    Effect of tree-level and mean-field improvement on the light-hadron spectrum in quenched QCD

    Shanahan, H. P., Davies, C. T. H., Bowler, K. C., Kenway, R. D., Richards, D. G., Rowland, P. A., Ryan, S. M., Lacock, P., Michael, C., Burford, D. R., Stella, N. & Wittig, H., 1 Feb 1997, In: Physical Review D . 55, 3, p. 1548-1558 11 p.

    Research output: Contribution to journalArticlepeer-review

  91. Published

    Efficient Sampling with Small Populations: a Genetic Algorithm Satisfying Detailed Balance

    Watkins, C. & Buttkewitz, Y., 11 Jul 2015, Gecco Companion '15: Proceedings of the Companion Publication of the 2015 Genetic and Evolutionary Computation Conference. p. 1517-1518 2 p.

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

  92. 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

  93. Submitted

    Embedding Open Science practice into Data Science Training

    Shanahan, H., 1 Jan 2019, (Submitted).

    Research output: Contribution to conferencePosterpeer-review

  94. E-pub ahead of print

    Epidemic contact tracing with smartphone sensors

    Nguyen, D. K. A., Luo, Z. & Watkins, C., 1 Sep 2020, In: Journal of Location Based Services. 37 p.

    Research output: Contribution to journalArticlepeer-review

  95. Published

    Equation of state in finite-temperature QCD with 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., Okamoto, M., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP PACS Collaboration, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 360-362 3 p.

    Research output: Contribution to journalArticlepeer-review

  96. 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

  97. Published

    Eta meson mass and topology in QCD with two light flavors

    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, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 162-164 3 p.

    Research output: Contribution to journalArticlepeer-review

  98. E-pub ahead of print

    Explaining Deep Learning Models with Constrained Adversarial Examples

    Moore, J., Hammerla, N. & Watkins, C., 23 Aug 2019, Pacific Rim International Conference on Artificial Intelligence. Springer, p. 43-56 14 p. (Lecture Notes in Computer Science; vol. 11670).

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

  99. Published

    Exploring the evolutionary path of plant MAPK networks

    Dóczi, R., Okrész, L., Romero, A. E., Paccanaro, A. & Bogre, L., 2012, In: Trends in Plant Science.

    Research output: Contribution to journalArticlepeer-review

  100. Published

    Expression of msl-2 causes assembly of dosage compensation regulators on the X chromosomes and female lethality in Drosophila

    Kelley, R. L., Solovyeva, I., Lyman, L. M., Richman, R., Solovyev, V. & Kuroda, M. I., 16 Jun 1995, In: Cell. 81, 6, p. 867-77 11 p.

    Research output: Contribution to journalArticlepeer-review

  101. Published

    Feature Selection

    Bellotti, T., Nouretdinov, I., Yang, M. & Gammerman, A., 2014, Conformal Prediction for Reliable Machine Learning: Theory, Adaptations and Applications. Balasubramanian, V., Ho, S-S. & Vovk, V. (eds.). Elsevier, p. 115-130 16 p. 6

    Research output: Chapter in Book/Report/Conference proceedingChapter

  102. 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

  103. Published

    Feeder-Level Deep Learning-based Photovoltaic Penetration Estimation Scheme

    Zhang, X., Kuenzel, S. & Watkins, C., 13 Oct 2020.

    Research output: Contribution to conferencePaperpeer-review

  104. 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

  105. Published

    First International Conference on Bioinformatics of Genome Regulation and Structure 1998

    Kolchanov, N. A. & Solovyev, V. V., 1999, In: Bioinformatics. 15, 7-8, p. 527-527 1 p.

    Research output: Contribution to journalEditorialpeer-review

  106. Published

    FORM-FACTORS FOR B-]PI-L(V)OVER-BAR(L) AND B-]K-ASTERISK-GAMMA DECAYS ON THE LATTICE

    BURFORD, D. R., DUONG, H. D., FLYNN, J. M., GOUGH, B. J., HAZEL, N. M., NIEVES, J. & SHANAHAN, H. P., 7 Aug 1995, In: Nuclear Physics B. 447, 2-3, p. 425-437 13 p.

    Research output: Contribution to journalArticlepeer-review

  107. E-pub ahead of print

    Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

    Research Data Alliance & Shanahan, H., 9 Nov 2020, In: Wellcome Open Research. 267.

    Research output: Contribution to journalArticlepeer-review

  108. Published

    Fractal graphical representation and analysis of DNA and protein sequences: Computational Molecular Biology

    Solovyev, V. V., 1993, In: BioSystems. 30, 1-3, p. 137-160 24 p.

    Research output: Contribution to journalArticlepeer-review

  109. 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

  110. Published

    Full QCD light hadron spectrum from the CP-PACS

    Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, Mar 1999, In: Nuclear Physics B - Proceedings Supplements. 73, p. 192-194 3 p.

    Research output: Contribution to journalArticlepeer-review

  111. 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

  112. 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

  113. Published

    Genomic organization, evolution, and structural peculiarities of highly repetitive DNA of Hordeum vulgare

    Vershinin, A. V., Salina, E. A., Solovyev, V. & Timofeyeva, L. L., 1990, In: Genome. 33, p. 441-449

    Research output: Contribution to journalArticlepeer-review

  114. Published

    GFam: a platform for automatic annotation of gene families

    Sasidharan, R., Nepusz, T., Swarbreck, D., Huala, E. & Paccanaro, A., 2012, In: Nucleic Acids Research. 40, 19, 15 p., e152.

    Research output: Contribution to journalArticlepeer-review

  115. 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

  116. Published

    Health Advice from Internet Discussion Forums: How Bad is Dangerous?

    Cole, J., Watkins, C. & Kleine, D., 6 Jan 2016, In: Journal of Medical Internet Research. 18, 1, p. 1-15 15 p., e4.

    Research output: Contribution to journalArticlepeer-review

  117. Published

    Heavy hybrid states from NRQCD

    Manke, T., Drummond, I. T., Horgan, R. R. & Shanahan, H. P., 1 Apr 1998, In: Physical Review D . 57, 7, p. R3829-R3832 4 p.

    Research output: Contribution to journalArticlepeer-review

  118. Published

    Heavy quark physics in N-f=2 QCD

    Aoki, S., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, Mar 1999, In: Nuclear Physics B - Proceedings Supplements. 73, p. 375-377 3 p.

    Research output: Contribution to journalArticlepeer-review

  119. Published

    Heavy quarkonia from anisotropic and isotropic lattices

    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, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 319-321 3 p.

    Research output: Contribution to journalArticlepeer-review

  120. Published

    Heavy-light decay constants from clover heavy quark action in 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, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 331-333 3 p.

    Research output: Contribution to journalArticlepeer-review

  121. Published

    Heavy-light decay constants from relativistic N-f=2, 0 QCD

    Shanahan, H. P. & CP-PACS Collaboration, 2000, HIGH ENERGY PHYSICS 99, PROCEEDINGS. BRISTOL: IOP PUBLISHING LTD, p. 943-944 2 p.

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

  122. Published

    Heavy-light spectrum and decay constant from NRQCD 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, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 265-267 3 p.

    Research output: Contribution to journalArticlepeer-review

  123. 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

  124. E-pub ahead of print

    Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data

    McQuilton, P., Batista, D., Beyan, O., Granell, R., Coles, S., Izzo, M., Lister, A. L., Pergl, R., Rocca-Serra, P., Schaap, B., Shanahan, H., Thurston, M. & Sansone, S-A., 31 Jan 2020, In: Data Intelligence. 2, 1-2, p. 151-157 7 p.

    Research output: Contribution to journalArticlepeer-review

  125. 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

  126. Published

    Hybrid quarkonia on asymmetric lattices

    Manke, T., Shanahan, H. P., 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., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 31 May 1999, In: Physical Review Letters. 82, 22, p. 4396-4399 4 p.

    Research output: Contribution to journalArticlepeer-review

  127. 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

  128. Published

    Hybrid quarkonia with high statistics from NRQCD

    Manke, T., Drummond, I. T., Horgan, R. R., Shanahan, H. P. & UKQCD Collaboration, Apr 1998, In: Nuclear Physics B - Proceedings Supplements. 63, p. 332-334 3 p.

    Research output: Contribution to journalArticlepeer-review

  129. Published

    Hypergraphical Conformal Predictors

    Fedorova, V., Gammerman, A., Nouretdinov, I. & Vovk, V., 21 Dec 2015, In: International Journal on Artificial Intelligence Tools. 24, 6, 1560003.

    Research output: Contribution to journalArticlepeer-review

  130. Published

    Identification of human gene functional regions based on oligonucleotide composition

    Solovyev, V. V. & Lawrence, C. B., 1 Jan 1993, In: Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 1, p. 371-9 9 p.

    Research output: Contribution to journalArticlepeer-review

  131. Published

    Identification of human gene structure using linear discriminant functions and dynamic programming

    Solovyev, V. V., Salamov, A. A. & Lawrence, C. B., 1 Jan 1995, In: Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 3, p. 367-75 9 p.

    Research output: Contribution to journalArticlepeer-review

  132. 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

  133. E-pub ahead of print

    Immune tolerance maintained by cooperative interactions between T cells and antigen presenting cells shapes a diverse TCR repertoire

    Best, K., Chain, B. & Watkins, C., 7 Aug 2015, In: Frontiers in Immunology. 6, p. 1-14 14 p., 360.

    Research output: Contribution to journalArticlepeer-review

  134. Published

    Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty

    Yang, H., Nepusz, T. & Paccanaro, A., 2012, In: Bioinformatics. 28, 10, p. 1383-1389 7 p.

    Research output: Contribution to journalArticlepeer-review

  135. 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

  136. Published

    Inductive Conformal Martingales for Change-Point Detection

    Volkhonskiy, D., Burnaev, E., Nouretdinov, I., Gammerman, A. & Vovk, V., 2017, 6th Symposium on Conformal and Probabilistic Prediction with Applications (COPA 2017). p. 1-22 22 p.

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

  137. 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

  138. Published

    INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects

    Solovyev, V. V. & Salamov, A. A., 1 Jan 1999, In: Nucleic Acids Research. 27, 1, p. 248-250 3 p.

    Research output: Contribution to journalArticlepeer-review

  139. 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

  140. Published

    Integrated databases and computer systems for studying eukaryotic gene expression

    Kolchanov, N. A., Ponomarenko, M. P., Frolov, A. S., Ananko, E. A., Kolpakov, F. A., Ignatieva, E. V., Podkolodnaya, O. A., Goryachkovskaya, T. N., Stepanenko, I. L., Merkulova, T. I., Babenko, V. V., Ponomarenko, Y. V., Kochetov, A. V., Podkolodny, N. L., Vorobiev, D. V., Lavryushev, S. V., Grigorovich, D. A., Kondrakhin, Y. V., Milanesi, L., Wingender, E. & 2 others, Solovyev, V. & Overton, G. C., 1999, In: Bioinformatics. 15, 7-8, p. 669-86 18 p.

    Research output: Contribution to journalArticlepeer-review

  141. 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

  142. Published

    International employees’ concerns during serious disease outbreaks and the potential impact on business continuity: Lessons identified from the 2014–15 West African Ebola outbreak

    Cole, J. & Watkins, C., 1 Dec 2015, In: Journal of Business Continuity and Emergency Planning. 9, 2, p. 149-162 14 p.

    Research output: Contribution to journalArticlepeer-review

  143. Published

    Internet discussion forums: Maximizing choice in health-seeking behaviour during public health emergencies

    Cole, J., Kleine, D. & Watkins, C., 13 Jun 2016, 2016 International Conference On Cyber Situational Awareness, Data Analytics And Assessment (CyberSA). Onwubiko, C. (ed.). London: IEEE, p. 99 104 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  144. Published

    Investigation into the annotation of protocol sequencing steps in the sequence read archive

    Alnasir, J. & Shanahan, H., Dec 2015, In: GigaScience. 4, 1, p. 1-11 11 p.

    Research output: Contribution to journalArticlepeer-review

  145. Published

    Jasmonate controls leaf growth by repressing cell proliferation and the onset of endoreduplication while maintaining a potential stand-by mode

    Noir, S., Bömer, M., Takahashi, N., Ishida, T., Tsui, T-L., Balbi, V., Shanahan, H., Sugimoto, K. & Devoto, A., Apr 2013, In: Plant physiology. 161, 4, p. 1930-1951

    Research output: Contribution to journalArticlepeer-review

  146. 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

  147. Published

    Kaon B-parameter from quenched domain-wall QCD

    Khan, A. A., Aoki, S., Aoki, Y., Burkhalter, R., Ejiri, S., Fikugita, 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. 287-290 4 p.

    Research output: Contribution to journalArticlepeer-review

  148. Published

    Kernels from matching operations

    Watkins, C., 1999.

    Research output: Working paper

  149. Published

    Kolmogorov complexity: Sources, theory and applications

    Gammerman, A. & Vovk, V., 1999, In: The Computer Journal. 42, 4, p. 252-255 4 p.

    Research output: Contribution to journalArticlepeer-review

  150. 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

  151. Published

    Languages as hyperplanes: grammatical inference with string kernels

    Clark, A., Costa Florêncio, C. & Watkins, C., 1 Mar 2011, In: Machine Learning. 82, 3, p. 351-373

    Research output: Contribution to journalArticlepeer-review

  152. Published

    Lattice calculation of the branching ratio for some of the exclusive modes of B-]S-gamma

    BOWLER, K. C., HAZEL, N. M., HENTY, D. S., HOEBER, H., KENWAY, R. D., RICHARDS, D. G., SHANAHAN, H. P., SIMONE, J. N., FLYNN, J. M., GOUGH, B. J., ALLTON, C., LELLOUCH, L., NIEVES, J. & WITTIG, H., 1 May 1995, In: Physical Review D . 51, 9, p. 4955-4970 16 p.

    Research output: Contribution to journalArticlepeer-review

  153. Published

    Lattice calculation of the penguin diagram decay B→K*γ

    BOWLER, K. C., HAZEL, N. M., HENTY, D. S., HOEBER, H., KENWAY, R. D., RICHARDS, D. G., SHANAHAN, H. P., SIMONE, J. N., FLYNN, J. M. & GOUGH, B. J., 7 Mar 1994, In: Physical Review Letters. 72, 10, p. 1398-1401 4 p.

    Research output: Contribution to journalArticlepeer-review

  154. Published

    Lattice study of the decay (B)over-bar(0)->p(+)l(-)(v)over-bar(l): Model-independent determination of vertical bar V-ub vertical bar

    Flynn, J. M., Nieves, J., Bowler, K. C., Hazel, N. M., Henty, D. S., Hoeber, H., Kenway, R. D., Richards, D. G., Gough, B. J., Lellouch, L. P. & Shanahan, H. P., 19 Feb 1996, In: Nuclear Physics B. 461, 1-2, p. 327-349 23 p.

    Research output: Contribution to journalArticlepeer-review

  155. Published

    Learning by Support Vector Machine

    Gammerman, A. & Vovk, V., 1998.

    Research output: Contribution to conferenceOther

  156. Published

    Learning by transduction

    Gammerman, A., Vapnik, V. & Vovk, V., 1998, Proceedings of the Fourteenth Conference on Uncertainty in Articial Intelligence. San Francisco, CA: Morgan Kaufmann, p. 148-156 9 p.

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

  157. Forthcoming

    Learning interpretable disease self-representations for drug repositioning

    Galeano Galeano, D., Frasca, F., Gonzalez, G., Lapanogov, I., Veselkov, K., Paccanaro, A. & Bronstein, M. M., 2019, (Accepted/In press) Conference on Neural Information Processing Systems (NeurIPS) 2019: Graph representation Learning Workshop .

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

  158. 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

  159. Published

    Light hadron spectrum and quark masses in QCD with two flavors of dynamical quarks

    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, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 176-178 3 p.

    Research output: Contribution to journalArticlepeer-review

  160. Published

    Location Tracking Using Smartphone Accelerometer and Magnetometer Traces

    Nguyen, D. K. A., Akram, R. N., Markantonakis, K., Luo, Z. & Watkins, C., 26 Aug 2019, The First Location Privacy Workshop (LPW 2019), the 14th International Conference on Availability, Reliability and Security (ARES 2019). Association for Computing Machinery (ACM), p. 1-9 9 p. 96

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

  161. Published

    Machine learning classification with confidence: Application of transductive conformal predictors to MRI-based diagnostic and prognostic markers in depression

    Nouretdinov, I., Costafreda, S. G., Gammerman, A., Chervonenkis, A., Vovk, V., Vapnik, V. & Fu, C. H. Y., 15 May 2011, In: NeuroImage. 56, 2, p. 809-813 5 p.

    Research output: Contribution to journalArticlepeer-review

  162. 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

  163. Published

    Method for Separately Permissioned Communication

    Watkins, C. & Denker, J., 2000, IPC No. US Patent, Patent No. 6064878

    Research output: Patent

  164. Published

    Method of Automatic Verification of Personal Identity

    Watkins, C., 1998, IPC No. US Patent, Patent No. 5719560

    Research output: Patent

  165. Published

    Mining the biomedical literature to predict shared drug targets in DrugBank

    Caniza Vierci, H., Galeano Galeano, D. & Paccanaro, A., 2017, XLIII Conferencia Latinoamericana en Informática CLEI 2017. IEEE Xplore, p. 1-5 5 p.

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

  166. In preparation

    modCDF - modifying CDF's for microarrays using sequence similarity

    Shanahan, H., Harrison, A., Upton, G. & Memon, F., 2012, (In preparation) In: Bioinformatics. 2 p.

    Research output: Contribution to journalArticlepeer-review

  167. Published

    Molecular evolution

    Ratner, V. A., Zharkikh, A. A., Kolchanov, N. A., Rodin, S. N., Solovyev, V. & Antonoc, A. S., 1996, In: Biomathematics. 24

    Research output: Contribution to journalArticlepeer-review

  168. Published

    Molecular mechanism of the somatic hypermutagenesis in immunoglobulin genes

    Kolchanov, N. A., Solovyev, V. & Rogozin, I. B., 1985, In: Proceedings of the USSR Academy of Science (Russ). 281, p. 994-999

    Research output: Contribution to journalArticlepeer-review

  169. Published

    Mondrian Condence Machine

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

    Research output: Working paper

  170. Published

    Mondrian Confidence Machine

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

    Research output: Working paper

  171. Published

    Multiple sequence alignment based on new approaches of tree construction and sequences comparison

    Solovyev, V., Streletc, V. B., Milanesi, L., Lim, H. (ed.), Fickett, J. (ed.), Cantor, C. (ed.) & Robbins, R. (ed.), 1993, Proceedings of the 2nd International conference on Bioinformatics, Supercomputing, and Complex genome analysis.. World Scientific, p. 419-428

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

  172. Published

    Multiprobabilistic prediction in early medical diagnoses

    Nouretdinov, I., Devetyarov, D., Vovk, V., Burford, B., Camuzeaux, S., Gentry-Maharaj, A., Tiss, A., Smith, C., Luo, Z., Chervonenkis, A., Hallett, R., Waterfield, M., Cramer, R., Timms, J. F., Jacobs, I. & Gammerman, A., Jun 2015, In: Annals of Mathematics and Artificial Intelligence. 74, 1-2, p. 203-222 20 p.

    Research output: Contribution to journalArticlepeer-review

  173. Published

    Multiprobabilistic Venn Predictors with Logistic Regression

    Nouretdinov, I., Devetyarov, D., Burford, B., Camuzeaux, S., Gentry-Maharaj, A., Tiss, A., Smith, C., Luo, Z., Chervonenkis, A., Hallett, R., Vovk, V., Waterfield, M., Cramer, R., Timms, J. F., Jacobs, I., Menon, U. & Gammerman, A., 2012, Artificial Intelligence Applications and Innovations - AIAI 2012 International Workshops: AIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB, Halkidiki, Greece, September 27-30, 2012, Proceedings, Part II. Iliadis, L., Maglogiannis, I., Papadopoulos, H., Karatzas, K. & Sioutas, S. (eds.). Springer, Vol. 382. (IFIP Advances in Information and Communication Technology).

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

  174. Published

    mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

    Meyer, M. J., Lapcevic, R., Romero, A. E., Yoon, M., Das, J., Beltrán, J. F., Mort, M., Stenson, P. D., Cooper, D. N., Paccanaro, A. & Yu, H., May 2016, In: Human Mutation. 37, 5, p. 447-456 10 p.

    Research output: Contribution to journalArticlepeer-review

  175. Published

    Network modeling of patients’ biomolecular profiles for clinical phenotype/outcome prediction

    Gliozzo, J., Perlasca, P., Mesiti, M., Casiraghi, E., Vallacchi, V., Vergani, E., Frasca, M., Grossi, G., Petrini, A., Re, M., Paccanaro, A. & Valentini, G., 27 Feb 2020, In: Scientific Reports. 10, p. 1-15 15 p., 3612.

    Research output: Contribution to journalArticlepeer-review

  176. Published

    Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator

    Manfredini, F., Romero Lopez, A., Pedroso Rovira, I., Paccanaro, A., Sumner, S. & Brown, M., 1 Nov 2017, In: Genome Biology and Evolution. 9, 11, p. 3059-3072 14 p.

    Research output: Contribution to journalArticlepeer-review

  177. Published

    New elements of glucocorticoid-receptor binding sites of hormone-regulated genes

    Seledtsov, I. A., Solovyev, V. V. & Merkulova, T. I., 23 Jul 1991, In: BBA - Gene Structure and Expression . 1089, 3, p. 367-376 10 p.

    Research output: Contribution to journalArticlepeer-review

  178. 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

  179. Published

    Non-conformity measures in multi-class prediction

    Nouretdinov, I., Santos, M. & Gammerman, A., Jul 2011, p. 57. 1 p.

    Research output: Contribution to conferenceAbstract

  180. Published

    Normalized Affymetrix expression data are biased by G-quadruplex formation

    Shanahan, H. P., Memon, F. N., Upton, G. J. G. & Harrison, A. P., 1 Apr 2012, In: Nucleic Acids Research. 40, 8, p. 3307-3315 9 p.

    Research output: Contribution to journalArticlepeer-review

  181. 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

  182. Published

    NRQCD on an anisotropic lattice

    Drummond, I. T., Horgan, R. R., Manke, T. & Shanahan, H. P., Mar 1999, In: Nuclear Physics B - Proceedings Supplements. 73, p. 336-338 3 p.

    Research output: Contribution to journalArticlepeer-review

  183. Published
  184. 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

  185. 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

  186. Published

    Online region prediction with real teachers

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

    Research output: Working paper

  187. Published

    OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast

    Abbruscato, P., Nepusz, T., Mizzi, L., Del Corvo, M., Morandini, P., Fumasoni, I., Michel, C., Paccanaro, A., Guiderdoni, E., Schaffrath, U., Morel, J-B., Piffanelli, P. & Faivre-Rampant, O., 2012, In: Molecular Plant Pathology.

    Research output: Contribution to journalArticlepeer-review

  188. Published

    PDB-Hadoop: Parallelising user applications on the protein databank using Apache Hadoop

    AlNasir, J. & Shanahan, H., Jul 2015.

    Research output: Contribution to conferencePosterpeer-review

  189. In preparation

    PDB-Hadoop: Parallelising Legacy applications on the Protein Databank using Apache Hadoop

    AlNasir, J. & Shanahan, H., 2015, (In preparation) In: Bioinformatics.

    Research output: Contribution to journalArticlepeer-review

  190. 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

  191. Published

    Planar Languages and Learnability

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

    Research output: Contribution to conferencePaper

  192. 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

  193. 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

  194. Published

    Plug-in martingales for testing exchangeability on-line

    Fedorova, V., Gammerman, A., Nouretdinov, I. & Vovk, V., 2012, Proceedings of the 29th International Conference on Machine Learning (ICML-12). Langford, J. & Pineau, J. (eds.). Omnipress, p. 1639-1646 8 p.

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

  195. Published

    Predicting {alpha}-helix and {beta}-strand segments of globular proteins

    Solovyev, V. V. & Salamov, A. A., 1 Dec 1994, In: Bioinformatics. 10, 6, p. 661-669 9 p.

    Research output: Contribution to journalArticlepeer-review

  196. 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

  197. 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

  198. 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

  199. Published

    Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

    Solovyev, V. V., Salamov, A. A. & Lawrence, C. B., 11 Dec 1994, In: Nucleic Acids Research. 22, 24, p. 5156-63 8 p.

    Research output: Contribution to journalArticlepeer-review

  200. Published

    Predicting the Frequencies of Drug Side effects

    Galeano, D., Li, S., Gerstein, M. & Paccanaro, A., 11 Sep 2020, In: Nature Communications. 11, p. 1-14 14 p., 4575.

    Research output: Contribution to journalArticlepeer-review

  201. Published

    Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments.

    Salamov, A. A. & Solovyev, V. V., 1995, p. 11-15. 5 p.

    Research output: Contribution to conferenceAbstract

  202. 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

  203. Published

    Preface to this Special Issue

    Gammerman, A. & Vovk, V., Sep 2015, In: Journal of Machine Learning Research. 16, p. 1677-1681 5 p.

    Research output: Contribution to journalEditorial

  204. Published

    Privacy-Functionality Trade-off: A Privacy-Preserving Multi-Channel Smart Metering System

    Zhang, X., Kuenzel, S., Córdoba-Pachón, J-R. & Watkins, C., 21 Jun 2020, In: Energies. 13, 12, p. 1-30 30 p., 3221.

    Research output: Contribution to journalArticlepeer-review

  205. 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

  206. 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

  207. Published

    Protein secondary structure prediction using local alignments.

    Salamov, A. A. & Solovyev, V. V., 1997, p. 31-36. 6 p.

    Research output: Contribution to conferenceAbstract

  208. Published

    Q-learning

    Watkins, C. J. C. H. & Dayan, P., 1992, In: Machine Learning. 8, 3, p. 279-292 14 p.

    Research output: Contribution to journalArticlepeer-review

  209. 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

  210. 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

  211. Published

    Quenched charmonium spectrum on anisotropic lattices

    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. I., Okamoto, M., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & CP-PACS collaboration, Mar 2001, In: Nuclear Physics B - Proceedings Supplements. 94, p. 325-328 4 p.

    Research output: Contribution to journalArticlepeer-review

  212. Published

    Quenched heavy-light decay constants

    BAXTER, R. M., BOOTH, S. P., BOWLER, K. C., COLLINS, S., HENTY, D. S., KENWAY, R. D., RICHARDS, D. G., SHANAHAN, H. P., SIMONE, J. N., SIMPSON, A. D., WILKES, B. E., EWING, A. K., LELLOUCH, L., SACHRAJDA, C. T. & WITTIG, H., 1 Feb 1994, In: Physical Review D . 49, 3, p. 1594-1605 12 p.

    Research output: Contribution to journalArticlepeer-review

  213. Published

    Quenched light hadron spectrum

    Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, 10 Jan 2000, In: Physical Review Letters. 84, 2, p. 238-241 4 p.

    Research output: Contribution to journalArticlepeer-review

  214. Published

    Quenched light hadron spectrum with the Wilson quark action: Final results from CP-PACS

    Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, Mar 1999, In: Nuclear Physics B - Proceedings Supplements. 73, p. 189-191 3 p.

    Research output: Contribution to journalArticlepeer-review

  215. Published

    Quenched QCD with domain-wall fermions on coarse lattices

    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., Okawa, M., Shanahan, H. P., Taniguchi, Y., Ukawa, A., Yoshie, T. & 1 others, CP-PACS Collaboration, Apr 2000, In: Nuclear Physics B - Proceedings Supplements. 83-4, p. 591-593 3 p.

    Research output: Contribution to journalArticlepeer-review

  216. Published

    Quenched QCD with O(a) improvement: The spectrum of light hadrons

    Bowler, K. C., Boyle, P., Garden, J., Kenway, R. D., Richards, D. G., Rowland, P. A., Ryan, S. M., Simma, H., Michael, C., Shanahan, H. P. & Wittig, H., 1 Sep 2000, In: Physical Review D . 6205, 5, p. - 19 p.

    Research output: Contribution to journalArticlepeer-review

  217. Published

    RDA COVID-19 Recommendations and Guidelines on Data Sharing

    Research Data Alliance COVID-19 Working Group, 30 Jun 2020, 144 p.

    Research output: Book/ReportBook

  218. Published

    Recognition of 3' -processing sites of human mRNA precursors

    Salamov, A. A. & Solovyev, V. V., 1 Feb 1997, In: Bioinformatics. 13, 1, p. 23-28 6 p.

    Research output: Contribution to journalArticlepeer-review

  219. 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

  220. Published
  221. 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

  222. 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

  223. 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

  224. Published

    Reliable Probability Estimates Based on Support Vector Machines for Large Multiclass Datasets

    Lambrou, A., Papadopoulos, H., Nouretdinov, I. & Gammerman, A., Sep 2012, Artificial Intelligence Applications and Innovations - AIAI 2012 International Workshops: AIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB, Proceedings.. Halkidiki, Greece, Vol. II. p. 182-191 10 p.

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

  225. Published

    Ridge Regression learning algorithm in dual variables

    Saunders, C., Gammerman, A. & Vovk, V., 1998, Proceedings of the Fifteenth International Conference on Machine Learning. San Francisco, CA: Morgan Kaufmann, p. 515-521 7 p.

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

  226. Published

    Safe Portfolio Optimization

    Watkins, C. & Macrae, R., 1999, Proc. IX Int. Symp. of Applied Stochastic Models and Data Analysis: Quantitative Methods in Business and Industry Society.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  227. 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

  228. Published

    Sea quark effects on quarkonia

    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., 1 Dec 2000, In: Physical Review D . 6211, 11, p. - 13 p.

    Research output: Contribution to journalArticlepeer-review

  229. 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

  230. 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

  231. Published

    Sequential decision problems and neural networks

    Barto, AG., Sutton, RS. & Watkins, C., 1990, p. 693.

    Research output: Contribution to conferenceOtherpeer-review

  232. 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

  233. 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

  234. Published

    Social Technologies for Community Response to Epidemics

    Cole, J. & Watkins, C., Aug 2013, Tackling Antimicrobial Resistance - Identifying Future Research Themes: Proceedings of the Conference Tackling Antimicrobial Resistance, 6 February 2013. London: Royal United Services Institute, p. 65-73 9 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  235. Published

    Somatic hyper mutagenesis in immunoglobulin genes. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection

    Rogozin, I. B., Solovyev, V. & Kolchanov, N. A., 1991, In: Biochim. Biophys. Acta. 1089, p. 175-182

    Research output: Contribution to journalArticlepeer-review

  236. 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

  237. Published

    Special issue editorial - Kolmogorov complexity

    Gammerman, A. & Vovk, V., 1999, In: The Computer Journal. 42, 4, p. 251-251 1 p.

    Research output: Contribution to journalEditorialpeer-review

  238. 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

  239. 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

  240. 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

  241. Published

    Spin effects in heavy hybrid mesons on an anisotropic lattice

    Drummond, I. T., Goodman, N. A., Horgan, R. R., Shanahan, H. P. & Storoni, L. C., 6 Apr 2000, In: Physics Letters B. 478, 1-3, p. 151-160 10 p.

    Research output: Contribution to journalArticlepeer-review

  242. Published

    SpliceDB: database of canonical and non-canonical mammalian splice sites

    Burset, M., Seledtsov, I. A. & Solovyev, V. V., 1 Jan 2001, In: Nucleic Acids Research. 29, 1, p. 255-259 5 p.

    Research output: Contribution to journalArticlepeer-review

  243. 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

  244. Published

    Statistical applications of algorithmic randomness

    Vovk, V. & Gammerman, A., 1999, Bulletin of the International Statistical Institute. Proceedings of the Fifty Second Session: Contributed Papers. book 3 ed. Vol. 58. p. 469-470 2 p.

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

  245. 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

  246. Published

    Statistical significance of ungapped sequence alignments.

    Alexandrov, N. N. & Solovyev, V. V., 1998, p. 463-472. 10 p.

    Research output: Contribution to conferenceAbstract

  247. Published

    Stoss — A stochastic simulation system for Bayesian belief networks

    Luo, Z. & Gammerman, A., 1991, Uncertainty in Knowledge Bases: Lecture Notes in Computer Science. Bouchon-Meunier, B., Yager, R. R. & Zadeh, L. A. (eds.). Springer, Vol. 521. p. 97-105

    Research output: Chapter in Book/Report/Conference proceedingChapter

  248. Forthcoming

    Structural Pattern Discovery in Protein-Protein Interaction Networks

    Nepusz, T. & Paccanaro, A., 2012, (Accepted/In press) Handbook of Bio- and Neuroinformatics. Springer

    Research output: Chapter in Book/Report/Conference proceedingChapter

  249. 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

  250. Published

    Structuring Time Series Data to Gain Insight into Agent Behaviour

    Al-Baghdadi, N., Wisniewski, W., Lindsay, D., Lindsay, S., Kalnishkan, Y. & Watkins, C., 24 Feb 2020, Proceedings of the 3rd International Workshop on Big Data for Financial News and Data. IEEE, p. 5480-5490 11 p.

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

  251. Published

    Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates

    Webster, P., Dawes, J., Dewchand, H., Takacs, K., Iadarola, B., Bolt, B., Caceres Silva, J., Kaczor, J., Dharmalingam, G., Dore, M., Game, L., Adejumo, T., Elliott, J., Naresh, K., Karimi, M., Rekopoulou, K., Tan, G., Paccanaro, A. & Uren, A., 9 Jul 2018, In: Nature Communications. 9, p. 1-14 14 p., 2649.

    Research output: Contribution to journalArticlepeer-review

  252. Published

    Support Vector density estimation

    Weston, J., Gammerman, A., Stitson, M., Vapnik, V., Vovk, V. & Watkins, C., 1999, Advances in Kernel Methods: Support Vector Learning. Scholkopf, B., Burghes, C. J. C. & Smola, A. J. (eds.). Cambridge, MA: MIT Press, p. 293-305 13 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  253. Published

    Support vector machines for multi-class pattern recognition

    Weston, J. & Watkins, C., 1999.

    Research output: Contribution to conferenceOtherpeer-review

  254. Published

    Support Vector regression with ANOVA decomposition kernels

    Stitson, M., Gammerman, A., Vapnik, V., Vovk, V., Watkins, C. & Weston, J., 1999, Advances in Kernel Methods: Support Vector Learning. Scholkopf, B., Burghes, C. J. C. & Smola, A. J. (eds.). Cambridge, MA: MIT Press, p. 285-291 7 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  255. Published

    SVM Venn Machine with k-Means Clustering

    Zhou, C., Nouretdinov, I., Luo, Z. & Gammerman, A., 2014, Artificial Intelligence Applications and Innovations: AIAI2014 Workshops. Rhodes, Greece, p. 251-260 10 p.

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

  256. Published

    Systems Metagenomics: Profiling short-read microbiome data using population-based k-mer identification

    Shanahan, H. & Radwan, G., 6 Jul 2018.

    Research output: Contribution to conferencePosterpeer-review

  257. Published

    Systems Metagenomics

    Shanahan, H. & Radwan, G., 15 Jul 2018.

    Research output: Contribution to conferencePosterpeer-review

  258. Published

    Teaching Data Science and Cloud Computing in Low and Middle Income Countries

    Shanahan, H., Harrison, A. & May, S., 23 Nov 2015, In: Advanced Techniques in Biology & Medicine. 3, 3, p. 1-5 5 p., 1000150.

    Research output: Contribution to journalArticlepeer-review

  259. Submitted

    Teaching FAIR

    Shanahan, H., 4 May 2019, (Submitted) In: Data Intelligence.

    Research output: Contribution to journalArticlepeer-review

  260. 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

  261. Published

    Testing Exchangeability On-line

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

    Research output: Working paper

  262. Published

    Testing the Gauss linear assumption for on-line predictions

    Fedorova, V., Nouretdinov, I. & Gammerman, A., 2012, In: Progress in Artificial Intelligence. 1, 3, p. 205-213 9 p.

    Research output: Contribution to journalArticlepeer-review

  263. 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

  264. Published

    The application of Hadoop in structural bioinformatics

    Alnasir, J. & Shanahan, H., 20 Nov 2018, In: Briefings in Bioinformatics. p. 1-10 10 p., bby106.

    Research output: Contribution to journalArticlepeer-review

  265. Published

    The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Bhat, P., Torres Bobadilla, M., Paccanaro, A., Yang, H. & Romero, A. E., 19 Nov 2019, In: Genome Biology. 20, p. 1-23 23 p., 244 (2019).

    Research output: Contribution to journalArticlepeer-review

  266. 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

  267. Published

    The Chern-Simons number as an order parameter: classical sphaleron transitions for SU(2)-Higgs field theories for m(H)approximate to 120 GeV

    Shanahan, H. P. & Davis, A. C., 9 Jul 1998, In: Physics Letters B. 431, 1-2, p. 135-140 6 p.

    Research output: Contribution to journalArticlepeer-review

  268. Published

    The cluster of the point mutations predetermined by the quasipalindromic sequences of the nucleotide in the DNA

    Salganik, R. I., Dianov, G. L., Medvedev, O. A. & Solovyev, V., 1986, In: Proceedings of the USSR Academy of Science (Russ). 291, p. 1499-1502

    Research output: Contribution to journalArticlepeer-review

  269. Published

    The Corrected Gene Proximity map for analyzing the 3D genome organization using Hi-C data

    Ye, C., Paccanaro, A., Gerstein, M. & Yan, K-K., 29 May 2020, In: BMC Bioinformatics. 21, p. 1-18 18 p., 222.

    Research output: Contribution to journalArticlepeer-review

  270. 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

  271. Published

    The effect of mutation deletion and insertion of single amino acids on the three-dimensional structure of globins

    Kolchanov, N. A., Solovyev, V. & Zharkikh, A. A., 1983, In: FEBS Letters. 161, p. 65-70

    Research output: Contribution to journalArticlepeer-review

  272. Published

    The Gene-Finder computer tools for analysis of human and model organisms genome sequences

    Solovyev, V. & Salamov, A., 1 Jan 1997, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology. Vol. 5. p. 294-302 9 p.

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

  273. 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

  274. 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

  275. 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

  276. Published

    The identification of Transcription Factor Binding Sites using string kernels

    Shanahan, H., 10 Sep 2010.

    Research output: Contribution to conferenceOther

  277. Published

    The Isgur-Wise function from the lattice

    BOOTH, S. P., BOWLER, K. C., HAZEL, N. M., HENTY, D. S., HOEBER, H., KENWAY, R. D., RICHARDS, D. G., SHANAHAN, H. P., SIMONE, J. N., SIMPSON, A. D., LELLOUCH, L., NIEVES, J., SACHRAJDA, C. T. & WITTIG, H., 24 Jan 1994, In: Physical Review Letters. 72, 4, p. 462-465 4 p.

    Research output: Contribution to journalArticlepeer-review

  278. 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

  279. Published

    The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

    Solovyev, V. V., Salamov, A. A. & Lawrence, C. B., 1 Jan 1994, In: Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 2, p. 354-62 9 p.

    Research output: Contribution to journalArticlepeer-review

  280. 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

  281. Published

    The static quark potential in full QCD

    Aoki, S., Boyd, G., Burkhalter, R., Ejiri, S., Fukugita, M., Hashimoto, S., Iwasaki, Y., Kanaya, K., Kaneko, T., Kuramashi, Y., Nagai, K., Okawa, M., Shanahan, H. P., Ukawa, A., Yoshie, T. & CP-PACS Collaboration, Mar 1999, In: Nuclear Physics B - Proceedings Supplements. 73, p. 216-218 3 p.

    Research output: Contribution to journalArticlepeer-review

  282. Published

    The template RNAs of RNA polymerases can have compact secondary structure formed by long double helices with partial violation of the complementarities

    Solovyev, V., Zharkikh, A. A. & Kolchanov, N. A., 1984, In: FEBS Letters. 165, p. 72-78

    Research output: Contribution to journalArticlepeer-review

  283. Published

    There are no R3 x S1 Gravitational Instantons

    Shanahan, H. & O'Murachadha, N., Mar 1993, In: Physical Review Letters. 70, 11, p. 1576 2 p.

    Research output: Contribution to journalArticlepeer-review

  284. 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

  285. Published

    Transatlantic Perspectives on the Use of Data Science in Museums and Heritage

    Platts, H., Howard, D., Dalton, P. & Watkins, C., Jul 2020, UK Research and Innovation.

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

  286. Published

    Transcriptomics: Quantifying Non-Uniform Read Distribution Using MapReduce

    Alnasir, J. & Shanahan, H., 27 Dec 2018, In: International Journal for the Foundations of Computer Science. 29, 8, 20 p.

    Research output: Contribution to journalArticlepeer-review

  287. Published
  288. Published
  289. Published

    Transduction with confidence and credibility

    Saunders, C., Gammerman, A. & Vovk, V., 1999, Proceedings of the Sixteenth International Joint Conference on Articial Intelligence. Dean, T. (ed.). San Francisco, CA: Morgan Kaufmann, Vol. 2. p. 722-726 5 p.

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

  290. 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

  291. Published

    Universal portfolio selection

    Vovk, V. & Watkins, C. J. H. C., 1998, Proceedings of the Eleventh Annual Conference on Computational Learning Theory. New York: ACM Press, p. 12-23 12 p.

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

  292. 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

  293. Published

    Valid prediction with confidence estimation in air pollution problem

    Ivina, O., Nouretdinov, I. & Gammerman, A., Jul 2011, p. 45. 1 p.

    Research output: Contribution to conferenceAbstract

  294. Published

    Valid predictions with confidence estimation in an air pollution problem.

    Ivina, O., Nouretdinov, I. & Gammerman, A., 17 Jun 2012, In: Progress in Artificial Intelligence. 1, p. 235-243 9 p.

    Research output: Contribution to journalArticlepeer-review

  295. Published

    Valid Probabilistic Prediction of Life Status after Percutaneous Coronary Intervention procedure

    Volkhonskiy, D., Nouretdinov, I., Gammerman, A. & Lim, P., Jun 2017, 6th Symposium on Conformal and Probabilistic Prediction with Applications (COPA 2017).

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

  296. Published

    What is semantic diversity and why does it facilitate visual word recognition?

    Cevoli, B., Watkins, C. & Rastle, K., 14 Jul 2020, In: Behavior Research Methods. p. 1-17 17 p.

    Research output: Contribution to journalArticlepeer-review

  297. Published

    Y spectrum from NRQCD with improved action

    Manke, T., Drummond, I. T., Horgan, R. R. & Shanahan, H. P., 11 Sep 1997, In: Physics Letters B. 408, 1-4, p. 308-314 7 p.

    Research output: Contribution to journalArticlepeer-review