Items where Research Group is "Computational Biology

Applegate, C. S., Laycock, S. D. and Day, A. M. (2012) A sketch-based system for highway design with user-specified regions of influence. Computers & Graphics, 36 (6). pp. 685-695.

Asque, Christopher T., Day, Andy M. and Laycock, Stephen D. (2012) Cursor Navigation Using Haptics for Motion-Impaired Computer Users. In: Eurohaptics, 2012-01-01.

Asque, Christopher T., Day, Andy M. and Laycock, Stephen D. (2012) Haptic assisted target acquisition in a visual point-and-click task for computer users with motion-impairments. IEEE Transactions on Haptics, 5 (2). pp. 120-130. ISSN 2329-4051

Bailey, S., Powell, C., Laycock, S. and Day, A. (2012) Interactive Exploration of Historic Information via Gesture Recognition. In: International Conference on Virtual Systems and Multimedia (VSMM), 2012-09-01.

Beck, Martina, Zhou, Ji, Faulkner, Christine, MacLean, Daniel ORCID: https://orcid.org/0000-0003-1032-0887 and Robatzek, Silke (2012) Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting. The Plant Cell, 24 (10). pp. 4205-4219. ISSN 1040-4651

Brown, P., Laycock, S. and Day, A. (2012) Vectorising Building Footprints from Historic Maps. In: 13th International Symposium on Virtual Reality, Archaeology and Cultural Heritage, 2012-09-01.

Dorgham, Osama M., Laycock, Stephen D. and Fisher, Mark H. (2012) GPU accelerated generation of digitally reconstructed radiographs for 2D/3D image registration. IEEE Transactions on Biomedical Engineering, 59 (9). pp. 2594-2603.

Dress, Andreas W. M., Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 and Steel, Mike (2012) ‘Lassoing’ a phylogenetic tree I: basic properties, shellings, and covers. Journal of Mathematical Biology, 65 (1). pp. 77-105. ISSN 0303-6812

Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40 (13). ISSN 0305-1048

Gambette, Philippe and Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 (2012) On encodings of phylogenetic networks of bounded level. Journal of Mathematical Biology, 65 (1). pp. 157-180. ISSN 0303-6812

Garnett, Mathew J., Edelman, Elena J., Heidorn, Sonja J., Dastur, Anahita, Lau, King Wai, Greninger, Patricia, Thompson, I. Richard, Luo, Xi, Soares, Jorge, Liu, Qingsong, Iorio, Francesco, Surdez, Didier, Chen, Li, Milano, Randy J., Bignell, Graham R., Tam, Ah T., Davies, Helen, Stevenson, Jesse A., Barthorpe, Syd, Lutz, Stephen R., Kogera, Fiona, Lawrence, Karl, Mclaren-douglas, Anne, Mitropoulos, Xeni, Mironenko, Tatiana, Thi, Helen, Richardson, Laura, Zhou, Wenjun, Jewitt, Frances, Zhang, Tinghu, O'Brien, Patrick, Boisvert, Jessica L., Price, Stacey, Hur, Wooyoung, Yang, Wanjuan, Deng, Xianming, Butler, Adam, Choi, Hwan Geun, Chang, Jae Won, Baselga, Jose, Stamenkovic, Ivan, Engelman, Jeffrey A., Sharma, Sreenath V., Delattre, Olivier, Saez-rodriguez, Julio, Gray, Nathanael S., Settleman, Jeffrey, Futreal, P. Andrew, Haber, Daniel A., Stratton, Michael R., Ramaswamy, Sridhar, Mcdermott, Ultan, Benes, Cyril H. and Greenman, Christopher (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature, 483 (7391). pp. 570-575. ISSN 0028-0836

Greenman, C. D. (2012) Haploinsufficient gene selection in cancer. Science, 337 (6090). pp. 47-48. ISSN 0036-8075

Greenman, Chris D., Pleasance, Erin D., Newman, Scott, Yang, Fengtang, Fu, Beiyuan, Nik-Zainal, Serena, Jones, David, Lau, King Wai, Carter, Nigel, Edwards, Paul A. W., Futreal, P. Andrew, Stratton, Michael R. and Campbell, Peter J. (2012) Estimation of rearrangement phylogeny for cancer genomes. Genome Research, 22 (2). pp. 346-361. ISSN 1088-9051

Greenman, Christopher, Pleasance, Erin D., Newman, Scott, Yang, Fengtang, Fu, Beiyuan, Nik-Zainal, Serena, Jones, David, Lau, King Wai, Carter, Nigel, Edwards, Paul A. W., Futreal, P. Andrew, Stratton, Michael R. and Campbell, Peter J. (2012) Estimation of rearrangement phylogeny in cancer. Genome Research, 22. pp. 346-361. ISSN 1549-5469

Gruenewald, S and Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 (2012) Identifying and defining trees. In: Reconstructing evolution: New Mathematical and computational advances. UNSPECIFIED.

Gruenewald, Stefan, Koolen, Jack H., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2012) The size of 3-compatible, weakly compatible split systems. Journal of Applied Mathematics and Computing, 40 (1-2). pp. 249-259.

Hernandez-Rosales, M, Hellmuth, M, Wieseke, N, Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Stadler, PF (2012) From event-labeled gene trees to species trees. In: UNSPECIFIED.

Herrmann, Sven, Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Recognizing treelike k-dissimilarities. Journal of Classification, 29 (3). pp. 321-340.

Herrmann, Sven and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) Trees, tight-spans and point configurations. Discrete Mathematics, 312 (16). pp. 2506-2521. ISSN 1872-681X

Herrmann, Sven and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) The split decomposition of a k-dissimilarity map. Advances in Applied Mathematics, 49 (1). pp. 39-56. ISSN 0196-8858

Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, A, Storandt, S and Suchecki, Radoslaw (2012) Computing a consensus of multilabeled trees. In: Meeting on Algorithm Engineering & Experiments (ALENEX12), 2012-01-16 - 2012-01-16.

Hulse, M, Tam, M, Isherwood, S, Scrase, C, Laycock, S, Mortimore, D, Patman, J, Short, S and Bell, D (2012) Production of 3-D printer-generated radiotherapy shells using DICOM CT, MRI or 3-D surface laser scan – Acquired STL files: Preclinical feasibility studies. In: NCRI Cancer Conference, 2012-11-01.

Kim, Jan, Camargo-Rodriguez, Anyela, Devoto, Alessandra, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Turner, John (2012) Computational modeling of the regulatory network organizing the wound response in Arabidopsis thaliana. Artificial Life, 18 (4). pp. 445-460. ISSN 1530-9185

Koolen, Jack H., Lesser, Alice, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2012) Injective optimal realizations of finite metric spaces. Discrete Mathematics, 312 (10). pp. 1602-1610. ISSN 1872-681X

Laycock, Stephen D., Bell, Graham D., Mortimore, David B., Greco, Mark K., Corps, Nick and Finkle, Irving (2012) Combining X-ray micro-CT technology and 3D printing for the digital preservation and study of a 19th century cantonese chess piece with intricate internal structure. Journal on Computing and Cultural Heritage, 5 (4). 13:1-13:7.

Lopez-Gomollon, Sara, Mohorianu, Irina, Szittya, Gyorgy, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2012) Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta, 236 (6). pp. 1875-1887. ISSN 0032-0935

Martyn, Iain, Kuhn, Tyler S., Mooers, Arne O., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Computing evolutionary distinctiveness indices in large scale analysis. Algorithms for Molecular Biology, 7 (1). ISSN 1748-7188

McBride, David J., Etemadmoghadam, Dariush, Cooke, Susanna L., Alsop, Kathryn, George, Joshy, Butler, Adam, Cho, Juok, Galappaththige, Danushka, Greenman, Christopher, Howarth, Karen D., Lau, King W., Ng, Charlotte K., Raine, Keiran, Teague, Jon, Wedge, David C., Caubit, Xavier, Stratton, Michael R., Brenton, James D., Campbell, Peter J., Futreal, P. Andrew and Bowtell, David D. L. and Australian Ovarian Cancer Study Group (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. The Journal of Pathology, 227 (4). pp. 446-455. ISSN 0022-3417

Mohorianu, Irina, Lopez-Gomollon, Sara, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) FiRePat-finding regulatory patterns between sRNAs and genes. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2 (3). pp. 273-284.

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 (2012) Network analyses for exploring evolutionary relationships. In: The Phylogenetic Handbook 2nd edition. UNSPECIFIED.

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2012) Optimal algorithms for computing edge weights in planar split networks. Journal of Applied Mathematics and Computing, 39 (1-2). pp. 1-13. ISSN 1598-5865

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Steel, Mike (2012) The 'Butterfly effect' in Cayley graphs with applications to genomics. Journal of Mathematical Biology, 65 (6-7). pp. 1267-1284. ISSN 0303-6812

Nik-Zainal, Serena, Alexandrov, Ludmil B., Wedge, David C., Van Loo, Peter, Greenman, Christopher D., Raine, Keiran, Jones, David, Hinton, Jonathan, Marshall, John, Stebbings, Lucy A., Menzies, Andrew, Martin, Sancha, Leung, Kenric, Chen, Lina, Leroy, Catherine, Ramakrishna, Manasa, Rance, Richard, Lau, King Wai, Mudie, Laura J., Varela, Ignacio, McBride, David J., Bignell, Graham R., Cooke, Susanna L., Shlien, Adam, Gamble, John, Whitmore, Ian, Maddison, Mark, Tarpey, Patrick S., Davies, Helen R., Papaemmanuil, Elli, Stephens, Philip J., McLaren, Stuart, Butler, Adam P., Teague, Jon W., Jönsson, Göran, Garber, Judy E., Silver, Daniel, Miron, Penelope, Fatima, Aquila, Boyault, Sandrine, Langerød, Anita, Tutt, Andrew, Martens, John W. M., Aparicio, Samuel A. J. R., Borg, Åke, Vincent Salomon, Anne, Thomas, Gilles, Børresen-Dale, Anne-Lise, Richardson, Andrea L., Neuberger, Michael S., Futreal, P. Andrew, Campbell, Peter J. and Stratton, Michael R. (2012) Mutational processes molding the genomes of 21 breast cancers. Cell, 149 (5). pp. 979-993. ISSN 0092-8674

Nik-Zainal, Serena, Van Loo, Peter, Wedge, David C., Alexandrov, Ludmil B., Greenman, Christopher D., Lau, King Wai, Raine, Keiran, Jones, David, Marshall, John, Ramakrishna, Manasa, Shlien, Adam, Cooke, Susanna L., Hinton, Jonathan, Menzies, Andrew, Stebbings, Lucy A., Leroy, Catherine, Jia, Mingming, Rance, Richard, Mudie, Laura J., Gamble, Stephen J., Stephens, Philip J., McLaren, Stuart, Tarpey, Patrick S., Papaemmanuil, Elli, Davies, Helen R., Varela, Ignacio, McBride, David J., Bignell, Graham R., Leung, Kenric, Butler, Adam P., Teague, Jon W., Martin, Sancha, Jönsson, Göran, Mariani, Odette, Boyault, Sandrine, Miron, Penelope, Fatima, Aquila, Langerød, Anita, Aparicio, Samuel A. J. R., Tutt, Andrew, Sieuwerts, Anieta M., Borg, Åke, Thomas, Gilles, Vincent Salomon, Anne, Richardson, Andrea L., Børresen-Dale, Anne-Lise, Futreal, P. Andrew, Stratton, Michael R. and Campbell, Peter J. (2012) The life history of 21 breast cancers. Cell, 149 (5). pp. 994-1007. ISSN 0092-8674

Popescu, Andrei-Alin, Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511 and Paradis, Emmanuel (2012) ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28 (11). pp. 1536-1537. ISSN 1367-4803

Powell, C., Laycock, S., Day, A., Bailey, S., Rodziewicz, J., Gregory, J. and Williamson, T. (2012) HistOracle: Consolidation and Dissemination of Heritage Information. In: International Conference on Virtual Systems and Multimedia (VSMM), 2012-09-01.

Rhodes, Jeremy D., Lott, Martin C., Russell, Sarah L. ORCID: https://orcid.org/0000-0001-5615-3418, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Sanderson, Julie, Wormstone, I. Michael ORCID: https://orcid.org/0000-0002-6423-7766 and Broadway, David C. (2012) Activation of the innate immune response and interferon signalling in myotonic dystrophy type 1 and type 2 cataracts. Human Molecular Genetics, 21 (4). pp. 852-862. ISSN 1460-2083

Sorefan, Karim, Pais, Helio, Hall, Adam E, Kozomara, Ana, Griffiths-Jones, Sam, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2012) Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence, 3 (1).

Spillner, Andreas, Nguyen, Binh and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) Constructing and drawing regular planar split networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2). pp. 395-407. ISSN 1545-5963

Stephens, Philip J., Tarpey, Patrick S., Davies, Helen, Van Loo, Peter, Greenman, Chris, Wedge, David C., Zainal, Serena Nik, Martin, Sancha, Varela, Ignacio, Bignell, Graham R., Yates, Lucy R., Papaemmanuil, Elli, Beare, David, Butler, Adam, Cheverton, Angela, Gamble, John, Hinton, Jonathan, Jia, Mingming, Jayakumar, Alagu, Jones, David, Latimer, Calli, Lau, King Wai, McLaren, Stuart, McBride, David J., Menzies, Andrew, Mudie, Laura, Raine, Keiran, Rad, Roland, Spencer Chapman, Michael, Teague, Jon, Easton, Douglas, Langerød, Anita, Lee, Ming Ta Michael, Shen, Chen-Yang, Tee, Benita Tan Kiat, Huimin, Bernice Wong, Broeks, Annegien, Vargas, Ana Cristina, Turashvili, Gulisa, Martens, John, Fatima, Aquila, Miron, Penelope, Chin, Suet-Feung, Thomas, Gilles, Boyault, Sandrine, Mariani, Odette, Lakhani, Sunil R., van de Vijver, Marc, van't Veer, Laura, Foekens, John, Desmedt, Christine, Sotiriou, Christos, Tutt, Andrew, Caldas, Carlos, Reis-Filho, Jorge S., Aparicio, Samuel A. J. R., Vincent Salomon, Anne, Børresen-Dale, Anne-Lise, Richardson, Andrea L., Campbell, Peter J., Futreal, P. Andrew and Stratton, Michael R. and The Oslo Breast Cancer Consortium (OSBREAC) (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature, 486 (7403). 400–404. ISSN 0028-0836

Stocks, Matthew B., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Mapleson, Daniel, Woolfenden, Hugh C., Mohorianu, Irina, Folkes, Leighton, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics, 28 (15). pp. 2059-2061. ISSN 1367-4803

Tam, Matthew, Laycock, Stephen, Bell, Duncan and Chojnowski, Adrian (2012) 3-D printout of a DICOM file to aid surgical planning in a 6 year old patient with a large scapular osteochondroma complicating congenital diaphyseal aclasia. Journal of Radiology Case Reports, 6 (1). pp. 31-37. ISSN 1943-0922