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

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

Polański, 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

Várnai, 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.

Burkoff, Nikolas S., Baldock, Robert J.N., Várnai, 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

(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

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

(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

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

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

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

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

Burkoff, Nikolas S., Várnai, 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

Várnai, 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

(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

Burkoff, Nikolas S., Várnai, 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

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

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

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

(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

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

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

(2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics, Vol.11 (Article 10). doi:10.1186/1471-2164-11-10

(2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11 . p. 10. doi:DOI: 10.1186/1471-2164-11-10

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

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

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

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

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

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

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. 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 . doi:10.1063/1.2953326