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

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