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Number of items: 34.
Journal Article
Cunningham, Nathan, Griffin, Jim E. and Wild, David L. (2020) ParticleMDI - Particle Monte Carlo methods for the cluster analysis of multiple datasets with applications to cancer subtype identification. Advances in Data Analysis and Classification, 14 . pp. 463-484. doi:10.1007/s11634-020-00401-y ISSN 1862-5347.
Penfold, Christopher A., Gherman, Iulia, Sybirna, Anastasiya and Wild, David L. (2018) Inferring Gene Regulatory Networks from Multiple Datasets. Gene Regulatory Networks, 1883 . pp. 251-282. doi:10.1007/978-1-4939-8882-2_11 ISSN 1064-3745.
PolaΕski, Krzysztof , Gao, Bo, Mason, Sam, Brown, Paul E., Ott, Sascha, Denby, Katherine J. and Wild, David L. (2018) Bringing numerous methods for expression and promoter analysis to a public cloud computing service. Bioinformatics, 34 (5). pp. 884-886. doi:10.1093/bioinformatics/btx692 ISSN 1367-4803.
VΓ‘rnai, Csilla, Burkoff, Nikolas S. and Wild, David L. (2017) Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs. PLoS One, 12 (2). e0169356. ISSN 1932-6203.
Burkoff, Nikolas S., Baldock, Robert J.N., VΓ‘rnai, Csilla, Wild, David L. and Csanyi, Gabor (2016) Exploiting molecular dynamics in Nested Sampling simulations of small peptides. Computer Physics Communications, 201 . pp. 8-18. doi:10.1016/j.cpc.2015.12.005 ISSN 0010-4655.
Bechtold, Ulrike, Penfold, Christopher A., Jenkins, Dafyd J., Legaie, Roxane, Moore, Jonathan D., Lawson, Tracy, Matthews, Jack S.A., Vialet-Chabrand, Silvere R. M., Baxter, Laura, Subramaniam, Sunitha et al.
(2016)
Time-series transcriptomics reveals that AGAMOUS-LIKE22 affects primary metabolism and developmental processes in drought-stressed Arabidopsis.
The Plant Cell, 28
(2).
pp. 345-366.
doi:10.1105/tpc.15.00910
ISSN 1040-4651.
Mason, Sam, Sayyid, Faiz, Kirk, Paul, Starr, Colin and Wild, David L. (2016) MDI-GPU : accelerating integrative modelling for genomic-scale data using GP-GPU computing. Statistical Applications in Genetics and Molecular Biology, 15 (1). pp. 83-86. doi:10.1515/sagmb-2015-0055 ISSN 1544-6115.
Lewis, Laura, Polanskia, Krzysztof, de Torres-Zabala, Marta, Jayaraman, Siddharth, Bowden, Laura, Moore, Jonathan D., Penfold, Christopher A., Jenkins, Dafyd J., Hills, Claire E., Baxter, Laura et al.
(2015)
Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with pseudomonas syringae pv tomato DC3000.
The Plant Cell, 27
(11).
pp. 3038-3064.
doi:10.1105/tpc.15.00471
ISSN 1040-4651.
Penfold, Christopher A., Shifaz, Ahmed, Brown, Paul E., Nicholson, Ann and Wild, David L. (2015) CSI : A nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data. Statistical Applications in Genetics and Molecular Biology, Volume 14 (Number 3). pp. 307-310. doi:10.1515/sagmb-2014-0082 ISSN 1544-6115.
Penfold, Christopher A., Millar, Jonathan B. A. and Wild, David L. (2015) Inferring orthologous gene regulatory networks using interspecies data fusion. Bioinformatics, 31 (12). i97-i105. doi:10.1093/bioinformatics/btv267 ISSN 1367-4803.
Hickman, Richard J., Hill, C., Penfold, Christopher A., Breeze, Emily, Bowden, Laura, Moore, Jonathan D., Zhang, Peijun, Jackson, Alison C., Cooke, Emma J., Bewicke-Copley, Findlay, Mead, A. (Andrew), Beynon, Jim, Wild, David L., Denby, Katherine J., Ott, Sascha and Buchanan-Wollaston, Vicky (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. The Plant Journal, Volume 75 (Number 1). pp. 26-39. doi:10.1111/tpj.12194 ISSN 0960-7412.
Darkins, Robert, Cooke, Emma J., Ghahramani, Zoubin, Kirk, P. (Paul), Wild, David L. and Savage, Richard S. (2013) Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm. PLoS One, 8 (4). e59795. doi:10.1371/journal.pone.0059795 ISSN 1932-6203.
Burkoff, Nikolas S., VΓ‘rnai, Csilla and Wild, David L. (2013) Predicting protein : sheet contacts using a maximum entropy-based correlated mutation measure. Bioinformatics, Volume 29 (Number 5). pp. 580-587. doi:10.1093/bioinformatics/btt005 ISSN 1367-4803.
VΓ‘rnai, Csilla, Burkoff, Nikolas S. and Wild, David L. (2013) Efficient parameter estimation of generalizable coarse-grained protein force fields using contrastive civergence : a maximum likelihood approach. Journal of Chemical Theory and Computation, Volume 9 (Number 12). pp. 5718-5733. doi:10.1021/ct400628h ISSN 1549-9618.
Windram, Oliver P., Madhou, Priyadharshini, McHattie, Stuart, Hill, Claire, Hickman, Richard J., Cooke, Emma J., Jenkins, Dafyd J., Penfold, Christopher A., Baxter, Laura, Breeze, Emily et al.
(2012)
Arabidopsis defense against Botrytis cinerea : chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
The Plant Cell, Vol.24
(No.9).
pp. 3530-3557.
doi:10.1105/tpc.112.102046
ISSN 1040-4651.
Burkoff, Nikolas S., VΓ‘rnai, Csilla, Wells, Stephen A. and Wild, David L. (2012) Exploring the energy landscapes of protein folding simulations with Bayesian computation. Biophysical Journal, Vol.102 (No.4). pp. 878-886. doi:10.1016/j.bpj.2011.12.053 ISSN 0006-3495.
Kirk, Paul, Griffin, Jim E., Savage, Richard S., Ghahramani, Zoubin and Wild, David L. (2012) Bayesian correlated clustering to integrate multiple datasets. Bioinformatics, Volume 28 (Number 4). pp. 3290-3297. doi:10.1093/bioinformatics/bts595 ISSN 1367-4803.
Penfold, Christopher A., Buchanan-Wollaston, Vicky, Denby, Katherine J. and Wild, David L. (2012) Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. Bioinformatics, Vol.28 (No.12). i233-i241. doi:10.1093/bioinformatics/bts222 ISSN 1367-4803.
Cooke, Emma J., Savage, Richard S., Kirk, Paul, Darkins, Robert and Wild, David L. (2011) Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. BMC Bioinformatics, Vol.12 (No.1). p. 399. doi:10.1186/1471-2105-12-399 ISSN 1471-2105.
Breeze, Emily, Harrison, Elizabeth, McHattie, Stuart, Hughes, Linda Karen, Hickman, Richard J., Hill, Claire, Kiddle, Steven J., Kim, Youn-sung, Penfold, Christopher A., Jenkins, Dafyd J. et al.
(2011)
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.
Plant Cell, The, Vol.23
(No.3).
pp. 873-894.
doi:10.1105/tpc.111.083345
ISSN 1040-4651.
Savage, Richard S., Ghahramani, Zoubin, Griffin, Jim E., De la Cruz, Bernard J. and Wild, David L. (2010) Discovering transcriptional modules by Bayesian data integration. Bioinformatics, Vol.26 (No.12). pp. 158-167. doi:10.1093/bioinformatics/btq210 ISSN 1367-4803.
Stegle, Oliver, Denby, Katherine J., Cooke, Emma J., Wild, David L., Ghahramani, Zoubin and Borgwardt, Karsten M. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. Journal of Computational Biology , Volume 17 (Number 3). pp. 355-367. doi:10.1089/cmb.2009.0175 ISSN 1066-5277.
Nieselt, Kay, Battke, Florian, Herbig, Alexander, Bruheim, Per, Wentzel, Alexander, Jakobsen, Γyvind M., Sletta, HΓ₯vard, Alam, Mohammad T., Merlo, Maria E., Moore, Jonathan D. et al.
(2010)
The dynamic architecture of the metabolic switch in Streptomyces coelicolor.
BMC Genomics, Vol.11
(Article 10).
doi:10.1186/1471-2164-11-10
ISSN 1471-2164.
Nieselt, Kay, Battke, Florian, Herbig, Alexander, Bruheim, Per, Wentzel, Alexander, Jakobsen, Γyvind M, Sletta, HΓ₯vard, Alam, Mohammad Tauqee, Merlo, Maria E., Moore, Jonathan et al.
(2010)
The dynamic architecture of the metabolic switch in Streptomyces coelicolor.
BMC Genomics, 11
.
p. 10.
doi:DOI: 10.1186/1471-2164-11-10
ISSN 1471-2164.
Rasmussen, Carl Edward, De la Cruz, Bernard J., Ghahramani, Zoubin and Wild, David L. (2009) Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures. IEEE - ACM Transactions on Computational Biology and Bioinformatics, Vol.6 (No.4). pp. 615-628. doi:10.1109/TCBB.2007.70269 ISSN 1545-5963.
Savage, Richard S., Heller, K. (Katherine), Xu, Yang, Ghahramani, Zoubin, Truman, William M., Grant, Murray, Denby, Katherine J. and Wild, David L. (2009) R/BHC : fast Bayesian hierarchical clustering for microarray data. BMC Bioinformatics, 10 . 242. doi:10.1186/1471-2105-10-242 ISSN 1471-2105.
Podtelezhnikov, Alexei A. and Wild, David L. (2009) Reconstruction and stability of secondary structure elements in the context of protein structure prediction. Biophysical Journal, Vol.96 (No.11). pp. 4399-4408. doi:10.1016/j.bpj.2009.02.057 ISSN 0006-3495.
Saqi, Mansoor, Dobson, Richard J B, Kraben, Preben, Hodgson, D. A. and Wild, David L. (2009) An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching. Journal of Integrative Bioinformatics, Vol.6 (No.1). p. 107. doi:10.2390/biecoll-jib-2009-107 ISSN 1613-4516.
Podtelezhnikov, Alexei A. and Wild, David L. (2008) CRANKITE: a fast polypeptide backbone conformation sampler. Source Code for Biology and Medicine, Vol. 3 (No. 12). doi:10.1186/1751-0473-3-12 ISSN 1751-0473.
Podtelezhnikov, Alexei A., Ghahramani, Zoubin and Wild, David L. (2007) Learning about protein hydrogen bonding by minimizing contrastive divergence. Proteins: Structure, Function, and Bioinformatics, Vol.66 (No.3). pp. 588-599. doi:10.1002/prot.21247 ISSN 0887-3585.
Book Item
Cunningham, Nathan, Griffin, Jim E., Wild, David L. and Lee, Anthony (2019) particleMDI : a Julia Package for the Integrative Cluster Analysis of Multiple Datasets. In: Argiento, R. and Durante, D. and Wade, S., (eds.) Bayesian Statistics and New Generations. BAYSM 2018. Springer Proceedings in Mathematics & Statistics, 296 . Cham: Springer, pp. 65-74. ISBN 9783030306106
Stegle, Oliver, Denby, Katherine J., Cooke, Emma J., Wild, David L., Ghahramani, Zoubin and Borgwardt, Karsten M. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. In: Research in Computational Molecular Biology : Proceedings of the 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Lecture Notes in Computer Science, Volume 5541 . Berlin Heidelberg: Springer, pp. 201-216. ISBN 9783642020087
Journal Item
Cooke, Emma J., Savage, Richard S. and Wild, David L. (2009) Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks. Seminars in Cell and Developmental Biology, Vol.20 (No.7). pp. 863-868. ISSN 1084-9521 doi:10.1016/j.semcdb.2009.08.004
Podtelezhnikov, Alexei A. and Wild, David L. (2008) Comment on "Efficient Monte Carlo trial moves for polypeptide simulations" [J. Chem. Phys. 123, 174905 (2005)]. Journal of Chemical Physics, Volume 129 (Number 2). Article No. 027103 . ISSN 0021-9606 doi:10.1063/1.2953326
This list was generated on Fri Apr 19 12:32:03 2024 BST.