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Number of items: 54.
Alan Turing Institute
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
Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)
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.
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.
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.
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.
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.
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
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.
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.
Cambridge Gates Trust
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.
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
EU Marie-Curie IRG Fellowship
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
Engineering and Physical Sciences Research Council (EPSRC)
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
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.
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.
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.
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.
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.
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
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.
European Commission (EC)
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.
European Research Area Network (ERA-NET)
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.
European Union (EU)
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.
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
L'OrΓ©al (Firm)
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.
Leverhulme Trust (LT)
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.
Marie Curie Fellowship Association (MCFA)
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.
Medical Research Council (Great Britain) (MRC)
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.
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.
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.
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.
Monash University
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.
National Institutes of Health
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.
National Institutes of Health (U.S.) (NIH)
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.
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
National Science Foundation (U.S.) (NSF)
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.
Norges forskningsrΓ₯d [Norwegian Research Council]
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.
Norges forskningsrΓ₯d [Research Council of Norway] (NF)
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.
Unesco
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.
University of Warwick. MOAC Doctoral Training Centre
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
University of Warwick. Molecular Organisation and Assembly in Cells
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.
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.
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.
This list was generated on Fri Apr 19 12:32:03 2024 BST.