2017

Polanski, Krzysztof , Gao, Bo, Mason, Sam (Sam A.), Brown, Paul E., Ott, Sascha, Denby, Katherine J. and Wild, David L. (2017) Bringing numerous methods for expression and promoter analysis to a public cloud computing service. Bioinformatics . doi:10.1093/bioinformatics/btx692 (In Press)

2016

(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

Ingle, Robert A., Stoker, Claire, Stone, Wendy, Adams, Nicolette, Smith, Rob, Grant, Murray, Carré, Isabelle, Roden, Laura C. and Denby, Katherine J. (2015) Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea. The Plant Journal, 84 . pp. 937-948. doi:10.1111/tpj.13050

(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

Windram, Oliver P. and Denby, Katherine J. (2015) Modelling signaling networks underlying plant defence. Current Opinion in Plant Biology, 27 . pp. 165-171. doi:10.1016/j.pbi.2015.07.007

(2015) Standards for plant synthetic biology : a common syntax for exchange of DNA parts. New Phytologist, 208 (1). pp. 13-19. doi:10.1111/nph.13532

Atwell, Susanna, Corwin, Jason A., Soltis, Nicole E., Subedy, Anushryia, Denby, Katherine J. and Kliebenstein, Daniel James (2015) Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Frontiers in Microbiology, 6 . pp. 1-14. 996. doi:10.3389/fmicb.2015.00996

Brady, Siobhan M., Burow, Meike, Busch, Wolfgang, Carlborg, Örjan, Denby, Katherine J., Glazebrook, Jane, Hamilton, Eric S., Harmer, Stacey L., Haswell, Elizabeth S., Maloof, Julin N., Springer, Nathan M. and Kliebenstein, Daniel James (2015) Reassess the t test : interact with all your data via ANOVA. The Plant Cell, 27 (8). pp. 2088-2094. doi:10.1105/tpc.15.00238

2014

Carstens, Maryke, McCrindle, Tyronne K., Adams, Nicolette, Diener, Anastashia, Guzha, Delroy T., Murray, Shane L., Parker, Jane E., Denby, Katherine J. and Ingle, Robert A. (2014) Increased resistance to biotrophic pathogens in the arabidopsis constitutive induced resistance 1 mutant is EDS1 and PAD4-dependent and modulated by environmental temperature. PLoS One, Volume 9 (Number 10). Article number e109853. doi:10.1371/journal.pone.0109853

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

Polanski, Krzysztof , Rhodes, Johanna, Hills, Claire E., Zhang, Peijun, Jenkins, Dafyd J., Kiddle, Steven J., Jironkin, Aleksey, Beynon, Jim, Buchanan-Wollaston, Vicky, Ott, Sascha and Denby, Katherine J. (2014) Wigwams : identifying gene modules co-regulated across multiple biological conditions. Bioinformatics, Volume 30 (Number 7). pp. 962-970. doi:10.1093/bioinformatics/btt728

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., 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

Van der Linden, Liesl, Bredenkamp, Jane, Naidoo, Sanushka, Fouché-Weich, Joanne, Denby, Katherine J., Genin, Stephane, Marco, Yves and Berger, Dave K. (2013) Gene-for-gene tolerance to bacterial wilt in Arabidopsis. Molecular Plant-Microbe Interactions, Vol.26 (No.4). pp. 398-406. doi:10.1094/MPMI-07-12-0188-R

2012

Baxter, Laura, Jironkin, Aleksey, Hickman, R. D. G., Moore, Jonathan D., Barrington, Christopher, Krusche, Peter, Dyer, Nigel, Buchanan-Wollaston, Vicky, Tiskin, Alexander, Beynon, Jim, Denby, Katherine J. and Ott, Sascha (2012) Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. The Plant Cell, Vol.24 (No.10). pp. 3949-3965. doi:10.1105/tpc.112.103010

(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

Cevik, Volkan, Kidd, B. N., Zhang, Peijun, Hills, Claire E., Kiddle, Steven J., Denby, Katherine J., Holub, E. B., Cahill, D. M., Manners, J. M., Schenk, P. M., Beynon, Jim and Kazan, K. (2012) MEDIATOR25 acts as an integrative Hub for the regulation of jasmonate-responsive gene expression in arabidopsis. Plant Physiology, Volume 160 (Number 1). pp. 541-555. doi:10.1104/pp.112.202697

Cevik, Volkan, Kidd, B. N., Zhang, P., Hills, Claire E., Kiddle, Steven J., Denby, Katherine J., Holub, E. B., Cahill, D. M., Manners, J. M., Schenk, P. M., Beynon, Jim and Kazan, K. (2012) MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis. Plant Physiology, Vol.160 (No.1). pp. 541-555. doi:10.1104/pp.112.202697

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

Mulema, Joseph M. K. and Denby, Katherine J. (2012) Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana–Botrytis cinerea interaction. Molecular Biology Reports, Volume 39 (Number 4). pp. 4039-4049. doi:10.1007/s11033-011-1185-4

2011

Morrissey, Edward R., Juárez, Miguel A., Denby, Katherine J. and Burroughs, Nigel John (2011) Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression. Biostatistics, Vol.12 (No.4). pp. 682-694. doi:10.1093/biostatistics/kxr009

(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

Alexandersson, Erik, Becker, John V. W., Jacobson, Dan, Nguema-Ona, Eric, Steyn, Cobus, Denby, Katherine J. and Vivier, Melané A. (2011) Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco. BMC Research Notes, Vol.4 (No.1). p. 493. doi:10.1186/1756-0500-4-493

Lloyd, Amanda J., William Allwood, J., Winder, Catherine L., Dunn, Warwick B., Heald, James K., Cristescu, Simona M., Sivakumaran, Anushen, Harren, Frans J. M., Mulema, Joseph M. K., Denby, Katherine J., Goodacre, Royston, Smith, Aileen R. and Mur, Luis A. J. (2011) Metabolomic approaches reveal that cell wall modifications play a major role in ethylene-mediated resistance against Botrytis cinerea. The Plant Journal, Vol.67 (No.5). pp. 852-868. doi:10.1111/j.1365-313X.2011.04639.x

Mulema, Joseph M. K., Okori, Patrick and Denby, Katherine J. (2011) Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography. African Journal of Biotechnology, Volume 10 (Number 76). pp. 17551-17563. doi:10.5897/AJB10.2558

Naidoo, Sanushka, Fouché-Weich, Joanne, Law, Philip J., Denby, Katherine J., Marco, Yves and Berger, Dave K. (2011) A eucalyptus bacterial wilt isolate from South Africa is pathogenic on Arabidopsis and manipulates host defences. Forest Pathology, Volume 41 (Number 2). pp. 101-113. doi:10.1111/j.1439-0329.2010.00642.x

2010

Morrissey, Edward R., Juárez, Miguel A., Denby, Katherine J. and Burroughs, Nigel John (2010) On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics, Vol.26 (No.18). pp. 2305-2312. doi:10.1093/bioinformatics/btq421

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

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

2009

Kiddle, Steven J., Windram, Oliver P., McHattie, Stuart, Mead, A., Beynon, Jim, Buchanan-Wollaston, Vicky, Denby, Katherine J. and Mukherjee, Sach (2009) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics, Vol.26 (No.3). pp. 355-362. doi:10.1093/bioinformatics/btp673

Petersen, Lindsay N., Ingle, Robert A., Knight, Marc R. and Denby, Katherine J. (2009) OXI1 protein kinase is required for plant immunity against Pseudomonas syringae in Arabidopsis. Journal of Experimental Botany, Vol.60 (No.13). pp. 3727-3735. doi:10.1093/jxb/erp219

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

Zou, Cunlu, Denby, Katherine J. and Feng, Jianfeng (2009) Granger causality vs. dynamic Bayesian network inference: a comparative study. BMC Bioinformatics, Vol.10 . Article number 122. doi:10.1186/1471-2105-10-122

2007

Murray, Shane L., Ingle, Robert A., Petersen, Lindsay N. and Denby, Katherine J. (2007) Basal resistance against pseudomonas syringae in Arabidopsis involves WRKY53 and a protein with homology to a nematode resistance protein. Molecular Plant - Microbe Interactions, Vol.20 (No.11). pp. 1431-1438. doi:10.1094/MPMI-20-11-1431

Illing, N., Walford, S., Shen, A., Van Heerden, J., Immelman, N., Mulder, N. and Denby, Katherine J. (2007) Molecular tools to study desiccation tolerance in the resurrection plant Xerophyta humilis. In: UNSPECIFIED. Published in: South African Journal of Biology, Vol.73 (No.3). p. 487. ISSN 0254-6299. doi:10.1016/j.sajb.2007.04.015