2018

Penfold, Christopher A., Sybirna, Anastasiya, Reid, John E, Huang, Yun, Wernisch, Lorenz, Ghahramani, Zoubin, Grant, Murray and Surani, M Azim (2018) Branch-recombinant Gaussian processes for analysis of perturbations in biological time series. Bioinformatics, 34 (17). i1005-i1013. doi:10.1093/bioinformatics/bty603

Penfold, Christopher A., Sybirna, Anastasiya, Reid, John E., Huang, Yun, Wernisch, Lorenz, Ghahramani, Zoubin, Grant, Murray R. and Surani, M. Azim (2018) Branch-recombinant Gaussian processes for analysis of perturbations in biological time series. Bioinformatics, 34 (17). i1005-i1013. doi:10.1093/bioinformatics/bty603

2016

Yang, Jing, Penfold, Christopher A., Grant, Murray R. and Rattray, Magnus (2016) Inferring the perturbation time from biological time course data. Bioinformatics, 32 (19). pp. 2956-2964. doi:10.1093/bioinformatics/btw329

(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

2015

(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

2014

Wang, Ying, Penfold, Christopher A., Hodgson, D. A., Gifford, Miriam L. and Burroughs, Nigel John (2014) Correcting for link loss in causal network inference caused by regulator interference. Bioinformatics, Volume 30 (Number 19). pp. 2779-2786. doi:10.1093/bioinformatics/btu388

Windram, Oliver P., Penfold, Christopher A. and Denby, Katherine J. (2014) Network modeling to understand plant immunity. Annual Review of Phytopathology, Volume 52 (Number 1). pp. 93-111. doi:10.1146/annurev-phyto-102313-050103

Penfold, Christopher A. and Buchanan-Wollaston, Vicky (2014) Modelling transcriptional networks in leaf senescence. Journal of Experimental Botany, Volume 65 (Number 14). pp. 3859-3873. doi:10.1093/jxb/eru054

2013

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

2012

(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

Penfold, Christopher A., Brown, Paul E., Lawrence, Neil (Neil D.) and Goldman, Alastair S. H. (2012) Modeling meiotic chromosomes indicates a size dependent contribution of telomere clustering and chromosome rigidity to homologue juxtaposition. PLoS Computational Biology, Vol.8 (No.5). e1002496. doi:10.1371/journal.pcbi.1002496

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

2011

(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