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

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