Items where Research Group is "Computational Biology

Article

Dress, Andreas W. M., Huber, Katharina T. 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. (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, 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.

Herrmann, Sven, Huber, Katharina T., 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

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

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 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. 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

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

Book Section

Gruenewald, S and Huber, Katharina T. (2012) Identifying and defining trees. In: Reconstructing evolution: New Mathematical and computational advances. UNSPECIFIED.

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

Conference or Workshop Item

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

Huber, Katharina T., 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.