Items where Research Group is "Computational Biology

Beckers, Matthew, Mohorianu, Irina-Ioana, Stocks, Matthew, Applegate, Christopher, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2017) Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. RNA, 23 (6). pp. 823-835. ISSN 1355-8382

Bücherl, Christoph A, Jarsch, Iris Katharina, Schudoma, Christian, Segonzac, Cécile, Mbengue, Malick, Robatzek, Silke, MacLean, Daniel ORCID: https://orcid.org/0000-0003-1032-0887, Ott, Thomas and Zipfel, Cyril (2017) Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains. eLife, 6. ISSN 2050-084X

Collins, David H., Mohorianu, Irina, Beckers, Matthew, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Bourke, Andrew F. G. ORCID: https://orcid.org/0000-0001-5891-8816 (2017) MicroRNAs associated with caste determination and differentiation in a primitively eusocial insect. Scientific Reports, 7. ISSN 2045-2322

Fishwick, Carl, Higgins, Janet, Percival-Alwyn, Lawrence, Hustler, Arianna, Pearson, Joanna, Bastkowski, Sarah, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Swarbreck, David, Greenman, Chris D. and Southgate, Jennifer (2017) Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium. Cell Death and Differentiation, 24. pp. 809-818. ISSN 1350-9047

Gambette, Philippe, Huber, K. T. ORCID: https://orcid.org/0000-0002-6368-7511 and Kelk, S. (2017) On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. Journal of Mathematical Biology, 74 (7). 1729–1751. ISSN 0303-6812

Gambette, Philippe, Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 and Scholz, Guillaume E. (2017) Uprooted phylogenetic networks. Bulletin of Mathematical Biology, 79 (9). 2022–2048. ISSN 0092-8240

Greenman, Christopher (2017) A path integral approach to age dependent branching processes. Journal of Statistical Mechanics: Theory and Experiment, 2017 (March). ISSN 1742-5468

Greenwood, David, Laycock, Stephen and Matthews, Iain (2017) Predicting Head Pose from Speech with a Conditional Variational Autoencoder. In: Proceedings of Interspeech 2017. ISCA, pp. 3991-3995.

Greenwood, David, Laycock, Stephen and Matthews, Iain (2017) Predicting Head Pose in Dyadic Conversation. In: International Conference on Intelligent Virtual Agents. Intelligent Virtual Agents, 10498 . Springer, pp. 160-169. ISBN 978-3-319-67400-1

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Milner-White, E. James (2017) Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments. Proteins: Structure, Function, and Bioinformatics, 85 (10). 1866–1881. ISSN 0887-3585

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Milner-White, E.J. (2017) Cover Image, Volume 85, Issue 10 (page C1). Wiley, Proteins: Structure, Function and Bioinformatics.

Huber, Katharina ORCID: https://orcid.org/0000-0002-6368-7511, van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Scornavacca, Celine and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77 (1). pp. 173-200. ISSN 0178-4617

Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2017) Minimum triplet covers of binary phylogenetic X-trees. Journal of Mathematical Biology, 75 (6-7). 1827–1840. ISSN 0303-6812

Iakovou, Georgios, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Laycock, Stephen (2017) Virtual environment for studying the docking interactions of rigid biomolecules with haptics. Journal of Chemical Information and Modeling, 57 (5). 1142–1152. ISSN 1549-9596

Lamprinaki, Dimitra, Beasy, Gemma, Zhekova, Aleksandra, Wittmann, Alexandra, James, Steve, Dicks, Jo ORCID: https://orcid.org/0000-0003-1300-5233, Iwakura, Yoichiro, Saijo, Shinobu, Wang, Xiaomin, Chow, Chung-Wai, Roberts, Ian, Korcsmaros, Tamas, Mayer, Ulrike ORCID: https://orcid.org/0000-0003-2328-0052, Wileman, Thomas and Kawasaki, Norihito (2017) LC3-associated phagocytosis is required for dendritic cell inflammatory cytokine response to gut commensal yeast Saccharomyces cerevisiae. Frontiers in Immunology, 8. ISSN 1664-3224

Matthews, Nick, Easdon, Robert, Kitao, Akio, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Laycock, Stephen (2017) High quality rendering of protein dynamics in space filling mode. Journal of Molecular Graphics and Modelling, 78. pp. 158-167. ISSN 1093-3263

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L., Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus U., Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X and Grigoriev, Igor V. (2017) Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus. Nature, 541. 536–540. ISSN 0028-0836

Mohammed, Rekar O. and Cawley, Gavin C. ORCID: https://orcid.org/0000-0002-4118-9095 (2017) Over-Fitting in Model Selection with Gaussian Process Regression. In: Machine Learning and Data Mining in Pattern Recognition. Lecture Notes in Computer Science, 10358 (1). Springer, pp. 192-205. ISBN 978-3-319-62415-0

Mohorianu, Irina, Stocks, Matthew Benedict, Applegate, Christopher Steven, Folkes, Leighton and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2017) The UEA small RNA workbench:A suite of computational tools for small RNA analysis. In: MicroRNA Detection and Target Identification. Methods in Molecular Biology . Springer, pp. 193-224. ISBN 978-1-4939-6864-0

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Oldman, James and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) A cubic-time algorithm for computing the trinet distance between level-1 networks. Information Processing Letters, 123. 36–41. ISSN 0020-0190

Paicu, Claudia, Mohorianu, Irina-Ioana, Stocks, Matthew, Xu, Ping, Coince, Aurore, Billmeier, Martina, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 (2017) miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics, 33 (16). 2446–2454. ISSN 1367-4803

Ryalat, Mohammad Hashem, Laycock, Stephen and Fisher, Mark (2017) Automatic Removal of Mechanical Fixations from CT Imagery with Particle Swarm Optimisation. In: Bioinformatics and Biomedical Engineering. Lecture Notes in Computer Science . Springer, ESP, pp. 419-431. ISBN 978-3-319-56147-9

Ryalat, Mohammad Hashem, Laycock, Stephen and Fisher, Mark (2017) A fast and automatic approach for removing artefacts due to immobilisation masks in X-ray CT. In: 2017 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). The Institute of Electrical and Electronics Engineers (IEEE), USA.

Van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, de Swart, Eveline and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5). 1135–1154. ISSN 0092-8240

Wainer, Jacques and Cawley, Gavin ORCID: https://orcid.org/0000-0002-4118-9095 (2017) Empirical evaluation of resampling procedures for optimising SVM hyperparameters. Journal of Machine Learning Research, 18 (15). pp. 1-35. ISSN 1532-4435

Wu, Jia, Elliston, Adam, Le Gall, Gwenaelle ORCID: https://orcid.org/0000-0002-1379-2196, Colquhoun, Ian J., Collins, Samuel R. A., Dicks, Jo ORCID: https://orcid.org/0000-0003-1300-5233, Roberts, Ian N. and Waldron, Keith W. (2017) Yeast diversity in relation to the production of fuels and chemicals. Scientific Reports, 7. ISSN 2045-2322