• Foo, Gherman, Zhang, Bates and Denby. (2018) A framework for engineering stress resilient plants using genetic feedback control and regulatory network rewiring. ACS Synthetic Biology online


  • Polanski, Gao, Mason, Brown, Ott, Denby and Wild. (2017) Bringing numerous methods for expression and promoter analysis to a public cloud computing service. Bioinformatics btx692
  • Hickman, Van Verk, Van Dijken, Mendes, Vroegop-Vos, Caarls, Steenbergen, Van der Nagel, Wesselink, Jironkin, Talbot, Rhodes, De Vries, Schuurink, Denby, Pieterse and Van Wees (2017) Architecture and dynamics of the jasmonic acid regulatory network. Plant Cell 29:2086-2105.
  • Buchanan-Wollaston, Wilson, Tardieu, Beynon and Denby. (2017) Harnessing diversity from ecosystems to crops to genes. Food and Energy Security 6(1):19–25


  • Oates, Denby, Myberg, Slippers and Naidoo. (2016). Insect Gallers and their Plant Hosts: from Omics data to systems biology. Int. J. Mol. Sci. 17(11): E1891
  • Bechtold, Penfold, Jenkins, Legaie, Moore, Lawson, Matthews, Vialet-Chabrand, Baxter, Subramaniam, Hickman, Florance, Sambles, Salmon, Feil, Bowden, Hill, Baker, Lunn, Finkenstädt, Mead, Buchanan-Wollaston, Beynon, Rand, Wild, Denby, Ott, Smirnoff, Mullineaux (2016) Time-series transcriptomics reveals that AGAMOUS-LIKE22 affects primary metabolism and developmental processes in drought-stressed Arabidopsis. Plant Cell 28: 345–366
  • Lewis, Polanski, Torres-Zabala, Jayaraman, Bowden, Moore, Penfold, Jenkins, Hill, Baxter, Kulasekaran, Truman, Littlejohn, Prusinska, Mead, Steinbrenner, Hickman, Rand, Wild, Ott, Buchanan-Wollaston, Smirnoff, Beynon, Denby and Grant. (2016) Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae tomato DC3000. Plant Cell 27: 3038-3064


  • Ingle, Stoker, Stone, Adams, Smith, Grant, Carré, Roden and Denby (2015) Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea. The Plant Journal 84:937-948
  • Atwell, Corwin, Soltis, Subedy, Denby and Kliebenstein (2015) Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Frontiers in Microbiology,
  • Brady, Burow, Busch, Carlborg, Denby, Glazebrook, Hamilton, Harmer, Haswell, Maloof, Springer and Kliebenstein (2015) Re-assess the t-test: interact with all your data via ANOVA. Plant Cell 27:2088-2094
  • Patron et al. (2015) Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA. New Phytologist 208(1):13-19
  • Windram and Denby (2015) Modeling signaling networks underlying plant defence. Current Opinion in Plant Biology 27:165-171


  • Carstens, McCrindle, Adams, Diener, Guzha, Murray, Parker, Denby and Ingle. (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 2014 doi:10.1371/journal.pone.0109853
  • Windram, Penfold and Denby (2014) Network Modelling to Understand Plant Immunity. Annual Review of Phytopathology 52:93-111
  • Polanski, Rhodes, Hill, Zhang, Jenkins, Kiddle, Jironkin, Beynon, Buchanan-Wollaston, Ott and Denby. (2014) Wigwams: identifying gene modules co-regulated across multiple biological conditions. Bioinformatics 30(7):962-70


  • Hickman, Hill, Penfold, Breeze, Bowden, Moore, Zhang, Jackson, Cooke, Bewicke-Copley, Mead, Beynon, Wild, Denby, Ott and Buchanan-Wollaston. (2013) A Local Regulatory Network Around Three NAC Transcription Factors in Arabidopsis Stress Responses and Senescence. Plant Journal 75(1):26-39
  • Van der Linden,Bredenkamp,Naidoo,Fouché-Weich,Denby, Genin, Marco and (2013) Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis. MPMI 26(4): 398-406


  • Baxter, Jironkin, Hickman, Moore, Barrington, Krusche, Dyer, Buchanan-Wollaston, Tiskin, Beynon, Denby and Ott. (2012) Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants. Plant Cell 24: 3949-3965
  • Windram, Madhou, McHattie, Hill, Hickman, Cooke, Jenkins, Penfold, Baxter, Breeze, Kiddle, Rhodes, Atwell, Kliebenstein, Kim, Stegle, Borgwardt, Zhang, Tabrett, Legaie, Moore, Finkenstadt, Wild, Mead, Rand, Beynon, Ott, Buchanan-Wollaston, Denby. (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell 24(9): 3530-3557
  • Cevik, Kidd, Zhang, Hill, Kiddle, Denby, Holub, Cahill, Manners, Schenk, Beynon and Kazan. (2012) MED25 Acts as an Integrative Hub for the Regulation of Jasmonate-Responsive Gene Expression in Arabidopsis. Plant Physiology 160(1): 541-555
  • Penfold, Buchanan-Wollaston, Denby and Wild. (2012) Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. Bioinformatics 28: i233-i241


  • Lloyd, Allwood, Winder, Dunn, Heald, Cristescu, Sivakumaran, Harren, Mulema, Denby, Goodacre, Smith and Mur (2011) Metabolomic approaches reveal that cell wall modifications play a major role in ethylene-mediated resistance against Botrytis cinerea. Plant Journal 67(5):852-68
  • Erik Alexandersson, John VW Becker, Dan Jacobson, Eric Nguema-Ona, Cobus Steyn, Katherine J Denby, Melane A Vivier (2011) Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco. BMC Research Notes 2011, 4:493
  • J.M.K. Mulema, P. Okori, K.J. Denby, Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography, Afr. J. Biotechnol. 10 (2011) 17551-17563.
  • Joseph M. K. Mulema and Katherine J. Denby (2011) Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana – Botrytis cinerea interaction. Molecular Biology Reports DOI: 10.1007/s11033-011-1185-4
  • Breeze, Harrison, McHattie, Hughes, Hickman, Hill, Kiddle, Kim, Penfold, Jenkins, Zhang, Morris, Jenner, Jackson, Thomas, Tabrett, Legaie, Moore, Wild, Ott, Rand, Beynon, Denby, Mead, Buchanan-Wollaston. (2011) High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation. Plant Cell 23(3):873-94.
  • Edward R. Morrissey, Miguel A. Juarez, Katherine J. Denby and Nigel J. Burroughs. (2011) Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression 
Biostatistics; doi: 10.1093/biostatistics/kxr009
  • Naidoo, J. Fouche-Weich, P. Law, K. J. Denby, Y. Marco, and D. K. Berger. (2011) An Eucalyptus bacterial wilt isolate from South Africa is pathogenic on Arabidopsis and manipulates host defences. Forest Pathology 41(2):101-113


  • R.Morrissey, M. A. Juárez, K. J. Denby and N. J. Burroughs (2010) “On reverse engineering of gene interaction networks using time course data with repeated measurements” Bioinformatics. 26(18):2305-2312
  • Stegle, E. Cooke, K. Denby, D. L. Wild, Z. Ghahramani and K. M. Borgwardt. (2010) “A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series” Journal of Computational Biology 17(3), 355-367
  • Kiddle, S.J., Windram, O.P.F., McHattie, S., Mead, A., Beynon, J., Buchanan-Wollaston, V., Denby, K.J. and Mukherjee, S.N. (2010) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics 26(3):355-362


  • Zou C, Denby, K. and Feng J. (2009) “Granger causality vs. dynamic Bayesian network inference: a comparative study” BMC Bioinformatics, 10:401. Correction of authorship of BMC Bioinformatics 2009,10:122
  • Richard Savage, Katherine Heller, Yang Xu, Zoubin Ghahramani, William M. Truman, Murray Grant, Katherine Denby and David L. Wild. (2009) “R/BHC: Fast Bayesian Hierarchical Clustering for Microarray Data” BMC Bioinformatics 10:242
  • Lindsay N. Petersen, Robert A. Ingle, Marc R. Knight and Katherine J. Denby. (2009) “OXI1 protein kinase is required for plant immunity against Pseudomonas syringae in Arabidopsis” 
Journal of Experimental Botany 60(13):3727-3735
  • Oliver Stegle, Katherine Denby, David L. Wild, Zoubin Ghahramani and Karsten M. Borgwardt. (2009) “A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series” in Research in Computational Molecular Biology, ed. Batzoglou (Springer Berlin, Heidelberg, 2009), Book Series: Lecture Notes in Computer Science 5541:201-216


  • Murray, S., Ingle, R., Petersen, L. and Denby, K.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 20(11):1431-8
  • Naidoo S, Murray SL, Denby KJ and Berger DK. (2007) “Microarray analysis of the Arabidopsis thaliana cir1 (constitutive induced resistance 1) mutant reveals candidate defence response genes against Pseudomonas syringae pv tomato DC3000” South African Journal of Botany. 73(3): 412-421

2006 and earlier:

  • Ingle, R., Carstens, M. and Denby, K.J. (2006) “PAMP recognition and the plant-pathogen arms race” Bioessays 28(9): 880-889
  • Daniel J. Kliebenstein, Heather C. Rowe and Katherine J. Denby (2005) ”Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity” Plant Journal 44: 25-36
  • Katherine Denby and Chris Gehring (2005) “Engineering drought and salinity tolerance in plants: lessons from genome-wide expression profiling in Arabidopsis” Trends in Biotechnology 23(11): 547-552
  • Katherine J. Denby, Laure J.M. Jason, Shane L. Murray, and Robert L. Last (2005) “ups1, an Arabidopsis thaliana camalexin accumulation mutant defective in multiple defence signalling pathways” Plant Journal 41:673-684
  • Shane L. Murray, Nicolette Adams, Daniel J. Kliebenstein, Gary J. Loake and Katherine J. Denby (2005) “A constitutive PR-1::luciferase expression screen identifies Arabidopsis mutants with differential disease resistance to both biotrophic and necrotrophic pathogens” Molecular Plant Pathology 6(1): 31-41
  • Illing, N, Denby, K.J., Collett, H., Shen, A. and Farrant, J.M. (2005) “The signature of seeds in resurrection plants: a molecular and physiological comparison of desiccation tolerance in seeds and vegetative tissues” Integrative and Comparative Biology 45: 771-787
  • Naidoo S, Denby KJ and Berger DK (2005). “Microarray experiments: considerations for experimental design” South African Journal of Science, 101: 347-354.
  • Donaldson, L.E., Ludidi, N., Knight, M.R., Gehring, C. and Denby, K.J. (2004) “Salt and osmotic stress cause rapid increases in Arabidopsis thaliana cGMP levels.” FEBS Letters. Vol 569/1-3 pp 317-320
  • Collett, H., Shen A., Gardner M., Farrant J.M., Denby K.J. and Illing N. (2004) Towards transcript profiling of desiccation tolerance in Xerophyta humilis: Construction of a normalised 11 k humilis cDNA set and microarray expression analysis of 424 cDNAs in response to dehydration. Physiologia Plantarum 122:39-53
  • Denby, K.J., Kumar, P. and Kliebenstein, D.J. (2004) “Identification of Botrytis cinerea susceptibility loci in Arabidopsis thaliana” Plant Journal. 38(3):473-486