Items where Research Group is "Computational Biology

B

Bignell, Graham R., Greenman, Chris D., Davies, Helen, Butler, Adam P., Edkins, Sarah, Andrews, Jenny M., Buck, Gemma, Chen, Lina, Beare, David, Latimer, Calli, Widaa, Sara, Hinton, Jonathon, Fahey, Ciara, Fu, Beiyuan, Swamy, Sajani, Dalgliesh, Gillian L., Teh, Bin T., Deloukas, Panos, Yang, Fengtang, Campbell, Peter J., Futreal, P. Andrew and Stratton, Michael R. (2010) Signatures of mutation and selection in the cancer genome. Nature, 463 (7283). pp. 893-898. ISSN 1476-4687

Byrka, Jaroslaw, Gawrychowski, Pawel, Huber, Katharina T. and Kelk, Steven (2010) Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. Journal of Discrete Algorithms, 8 (1). pp. 65-75. ISSN 1570-8667

C

Cameron, Peter J. and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2010) The complexity of the weight problem for permutation and matrix groups. Discrete Mathematics, 310 (3). pp. 408-416. ISSN 1872-681X

Cawley, G. C. ORCID: https://orcid.org/0000-0002-4118-9095 and Janacek, G. J. (2010) On allometric equations for predicting body mass of dinosaurs. Journal of Zoology, 280 (4). pp. 355-361. ISSN 0952-8369

Cawley, Gavin ORCID: https://orcid.org/0000-0002-4118-9095 (2010) Some Baseline Methods for the Active Learning Challenge. In: 13th International Conference on Artificial Intelligence and Statistics, 2010-05-16.

Cawley, Gavin C. ORCID: https://orcid.org/0000-0002-4118-9095 and Talbot, Nicola L. C. (2010) On over-fitting in model selection and subsequent selection bias in performance evaluation. Journal of Machine Learning Research, 11 (70). pp. 2079-2107. ISSN 1533-7928

D

Dalgliesh, Gillian L., Furge, Kyle, Greenman, Chris, Chen, Lina, Bignell, Graham, Butler, Adam, Davies, Helen, Edkins, Sarah, Hardy, Claire, Latimer, Calli, Teague, Jon, Andrews, Jenny, Barthorpe, Syd, Beare, Dave, Buck, Gemma, Campbell, Peter J., Forbes, Simon, Jia, Mingming, Jones, David, Knott, Henry, Kok, Chai Yin, Lau, King Wai, Leroy, Catherine, Lin, Meng-Lay, McBride, David J., Maddison, Mark, Maguire, Simon, McLay, Kirsten, Menzies, Andrew, Mironenko, Tatiana, Mulderrig, Lee, Mudie, Laura, O'Meara, Sarah, Pleasance, Erin, Rajasingham, Aarjunan, Shepherd, Rebecca, Smith, Raffaella, Stebbings, Lucy, Stephens, Philip, Tang, Gurpreet, Tarpey, Patrick S., Turrell, Kelly, Dykema, Karl J., Khoo, Sok Kean, Petillo, David, Wondergem, Bill, Anema, John, Kahnoski, Richard J., Teh, Bin Tean, Stratton, Michael R. and Futreal, P. Andrew (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature, 463 (7279). pp. 360-363. ISSN 1476-4687

Dress, Andreas, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2010) Species, clusters and the ‘Tree of life’: A graph-theoretic perspective. Journal of Theoretical Biology, 265 (4). pp. 535-542.

Dress, Andreas W. M., Huber, Katharina T., Koolen, Jacobus, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Spillner, Andreas (2010) An algorithm for computing cutpoints in finite metric spaces. Journal of Classification, 27 (2). pp. 158-172.

Dress, Andreas W. M., Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 and Xu, XiaoMing (2010) A note on single-linkage equivalence. Applied Mathematics Letters, 23 (4). pp. 432-435.

G

Greenman, Chris D., Bignell, Graham, Butler, Adam, Edkins, Sarah, Hinton, Jon, Beare, Dave, Swamy, Sajani, Santarius, Thomas, Chen, Lina, Widaa, Sara, Futreal, P. Andy and Stratton, Michael R. (2010) PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics, 11 (1). pp. 164-175. ISSN 1465-4644

Guyon, Isabelle, Cawley, Gavin ORCID: https://orcid.org/0000-0002-4118-9095, Dror, Gideon and Lemaire, Vincent (2010) Design and Analysis of the WCCI 2010 Active Learning Challenge. In: IEEE/INNS International Joint Conference on Neural Networks, 2010-07-18 - 2010-07-23.

Guyon, Isabelle, Saffari, Amir, Dror, Gideon and Cawley, Gavin ORCID: https://orcid.org/0000-0002-4118-9095 (2010) Model selection: Beyond the Bayesian/frequentist divide. Journal of Machine Learning Research, 11. pp. 61-87. ISSN 1533-7928

H

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Kitao, Akio (2010) Effect of end constraints on protein loop kinematics. Biophysical Journal, 98 (9). pp. 1976-1985.

Huber, Katharina T., van Iersel, Leo, Kelk, Steven and Suchecki, Radosław (2010) A practical algorithm for reconstructing level-1 phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (3). pp. 635-649. ISSN 1557-9964

L

Laycock, S. D., Stocks, M. B. and Hayward, S. ORCID: https://orcid.org/0000-0001-6959-2604 (2010) Navigation and exploration of large data-sets using a haptic feedback device. In: ACM Siggraph: Posters, 2010-01-01.

M

MacLean, Daniel, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Studholme, David J. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11. ISSN 1471-2105

Martin, Darren P., Lemey, Philippe, Lott, Martin, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Posada, David and Lefeuvre, Pierre (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26 (19). pp. 2462-2463. ISSN 1367-4803

N

Nguyen, Binh, Spillner, Andreas, Emerson, Brent C. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity. Algorithms for Molecular Biology, 5. ISSN 1748-7188

Nicolas, Francisco Esteban, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, de Haro, Juan P., Calo, Silvia, Grigoriev, Igor V., Torres-Martinez, Santiago, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Ruiz-Vazquez, Rosa M. and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Research, 38 (16). pp. 5535-5541. ISSN 0305-1048

P

Pais, H, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. In: Non-coding RNA networks. Landes Bioscience. ISBN 978-1-4614-0331-9

Pais, Helio, Nicolas, Francisco Esteban, Soond, Surinder M., Swingler, Tracey E., Clark, Ian M., Chantry, Andrew, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA, 16 (3). pp. 489-494. ISSN 1355-8382

Pantaleo, Vitantonio, Szittya, György, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Miozzi, Laura, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Burgyan, Jozsef (2010) Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis. The Plant Journal, 62 (6). pp. 960-976. ISSN 1365-313X

Pleasance, Erin D., Cheetham, R. Keira, Stephens, Philip J., Mcbride, David J., Humphray, Sean J., Greenman, Christopher, Varela, Ignacio, Lin, Meng-Lay, Ordóñez, Gonzalo R., Bignell, Graham R., Ye, Kai, Alipaz, Julie, Bauer, Markus J., Beare, David, Butler, Adam, Carter, Richard J., Chen, Lina, Cox, Anthony J., Edkins, Sarah, Kokko-Gonzales, Paula I., Gormley, Niall A., Grocock, Russell J., Haudenschild, Christian D., Hims, Matthew M., James, Terena, Jia, Mingming, Kingsbury, Zoya, Leroy, Catherine, Marshall, John, Menzies, Andrew, Mudie, Laura J., Ning, Zemin, Royce, Tom, Schulz-Trieglaff, Ole B., Spiridou, Anastassia, Stebbings, Lucy A., Szajkowski, Lukasz, Teague, Jon, Williamson, David, Chin, Lynda, Ross, Mark T., Campbell, Peter J., Bentley, David R., Futreal, P. Andrew and Stratton, Michael R. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463 (7278). pp. 191-196. ISSN 1476-4687

Pleasance, Erin D., Stephens, Philip J., O’Meara, Sarah, McBride, David J., Meynert, Alison, Jones, David, Lin, Meng-lay, Beare, David, Lau, King Wai, Greenman, Christopher, Varela, Ignacio, Nik-Zainal, Serena, Davies, Helen R., Ordoñez, Gonzalo R., Mudie, Laura J., Latimer, Calli, Edkins, Sarah, Stebbings, Lucy, Chen, Lina, Jia, Mingming, Leroy, Catherine, Marshall, John, Menzies, Andrew, Butler, Adam, Teague, Jon W., Mangion, Jonathon, Sun, Yongming A., Mclaughlin, Stephen F., Peckham, Heather E., Tsung, Eric F., Costa, Gina L., Lee, Clarence C., Minna, John D., Gazdar, Adi, Birney, Ewan, Rhodes, Michael D., Mckernan, Kevin J., Stratton, Michael R., Futreal, P. Andrew and Campbell, Peter J. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463 (7278). pp. 184-190. ISSN 1476-4687

S

Santarius, Thomas, Bignell, Graham R., Greenman, Christopher, Widaa, Sara, Chen, Lina, Mahoney, Claire L., Butler, Adam, Edkins, Sarah, Waris, Sahar, Thornalley, Paul J., Futreal, P. Andrew and Stratton, Michael R. (2010) GLO1-A novel amplified gene in human cancer. Genes, Chromosomes & Cancer, 49 (8). pp. 711-725. ISSN 1045-2257

Szittya, Gyorgy, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pantaleo, Vitantonio, Toth, Gabor, Rusholme Pilcher, Rachel L., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Burgyan, Jozsef and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Structural and functional analysis of viral siRNAs. PLoS Pathogens, 6 (4). ISSN 1553-7374

T

Tyler, Kevin M. ORCID: https://orcid.org/0000-0002-0647-8158, Wagner, Gerd K., Wu, Qiong and Huber, Katharina T. (2010) Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins. Journal of Molecular Evolution, 70 (4). pp. 395-402. ISSN 1432-1432