Professor Katherine Denby
Academic Director of the N8 Agrifood Resilience Programme

Profile

Career

 

2016

Professor

Academic Director of the N8 Agrifood Resilience programme 

Department of Biology, University of York
2006 - 2016  Associate Professor (from 2016 Professor)

School of Life Sciences and Warwick Systems Biology Centre, University of Warwick

2005 - 2006 Senior Lecturer

Department of Molecular and Cell Biology, University of Cape Town

1999 - 2004 Lecturer Department of Molecular and Cell Biology, University of Cape Town
1995 - 1998 Postdoctoral research Boyce Thompson Institute for Plant Research, Cornell University
1991 - 1994 D.Phil. Department of Plant Sciences, University of Oxford
1988 - 1991 B.Sc Hons 1st Class in Microbiology University of Bristol

Research

Overview

I am interested in plant disease resistance and plant-pathogen interaction, and in novel approaches for enabling and enhancing breeding of crop varieties tolerant to environmental stress and disease. We use experimental and computational/mathematical tools to elucidate the gene regulatory networks underlying plant defence, and highlight key genes for conferring disease resistance. We also take a synthetic biology approach, using modelling to predict how to re-engineer plant defence networks to enhance disease resistance. A complementary project is investigating how pathogen effectors are targeting the host defence response to facilitate infection and ways to manipulate these pathogen-host interactions.

You can read more about our work and the Denbylab at denbylab.wordpress.com

Projects

A Systems Approach to Disease Resistance Against Necrotrophic Fungal Pathogens. BBSRC Horticulture and Potato Initiative

Collaborative Open Plant Omics (COPO): a community-driven bioinformatics platform for plant science. BBSRC 

The contribution of pathogen effectors to host range and non-host resistance. BBSRC 

Warwick Centre for Integrative Synthetic Biology. BBSRC (was Co-I, now Honorary member of WISB)

Research group(s)

StatusNameProject
Postdoctoral fellow Dr Sarah Harvey The contribution of pathogen effectors to host range and non-host resistance
Postdoctoral fellow Dr Adam Talbot A Systems Approach to Disease Resistance Against Necrotrophic Fungal Pathogens in lettuce.
Postdoctoral fellow Dr Ruth Bastow Collaborative Open Plant Omics (COPO): a community-driven bioinformatics platform for plant science.
PhD student Elspeth Ransom Investigating the lettuce defence response against the fungal pathogen Sclerotinia sclerotiorum
PhD student Maura Di Martino Investigating the role and regulation of two key transcription factors mediating disease resistance
PhD student Iulia Gherman synthetic biology approaches to re-engineer the plant defence network

Publications

Full publications list

 1) 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 In press

2) Lewis, Polanski, Torres-Zabala, Jayaraman, Bowden, Moore, Penfold, Jenkins, Hill, Baxter, Kulasekaran, Truman, Littlejohn,Prusinska, Mead, Steinbrenner, Hickman, Rand, Wild, Ott, Buchanan-Wollaston, Smirnoff, Denby, Beynon and Grant. (2015) Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv. tomato DC3000Plant Cell 27: 3038-3064 

3) 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. Plant Journal 84: 937-948 

4) Atwell, Corwin, Soltis, Subedy, Denby and Kliebenstein (2015) Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Frontiers in Microbiologyhttp://dx.doi.org/10.3389/fmicb.2015.00996 

5) Windram and Denby (2015) Modeling signaling networks underlying plant defence. Current Opinion in Plant Biology 27:165-171 

6) 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 

7) Patron et al. (2015) Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA. New Phytologist 208(1):13-19 

8) 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 9(10):e109853 

9) Windram, Penfold and Denby (2014) Network Modelling to Understand Plant Immunity. Annual Reviews of Phytopathology 52:93-111 

10) 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

11) 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 

12) Van der Linden,Bredenkamp,Naidoo,Fouché-Weich,Denby,Genin,Marco and Berger. (2013) Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis. Molecular Plant Microbe Interactions 26(4): 398-406 

13) 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 

14) 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 

15) 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 

16) Penfold, Buchanan-Wollaston, Denby and Wild. (2012) Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. Bioinformatics 28: i233-i241 

17) 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 Journal67(5):852-68        

18) 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 Notes2011, 4:493 

19) J.M.K. Mulema, P. Okori, K.J. Denby, Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography, African Journal of Biotechnology. 10 (2011) 17551-17563. 

20) 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 

21) 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. 

22) 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 

23) S. 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 

24) E. 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 

25) O. 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 

26) 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 thalianaBioinformatics 26(3):355-362 

27) 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 

28) 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

29) 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 

30) 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 

31) 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 

32) 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 

33) Ingle, R., Carstens, M. and Denby, K.J. (2006) “PAMP recognition and the plant-pathogen arms race” Bioessays 28(9): 880-889 

34) 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 

35) 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 

36) 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 

37) 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 

38) 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 

39) Naidoo S, Denby KJ and Berger DK (2005). “Microarray experiments: considerations for experimental design” South African Journal of Science, 101: 347-354. 

40) 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 

41) 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 X. humilis cDNA set and microarray expression analysis of 424 cDNAs in response to dehydration. Physiologia Plantarum 122:39-53 

42) 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 

43) Murray S.L., Denby K.J., Berger D. and Loake G. (2002) “Disease Resistance Signalling in Arabidopsis: Applications for the Study of Plant Pathology in South Africa.” South African Journal of Science 98: 161-165 

44) Hide W, Mizrahi V, Venkatesh B, Brenner S, Simpson A, Blatch G, Soodyall H, Denby K, Wingfield M, Wingfield B, van Helden P, Ramesar R, Dorrington R, Kelso J, Oppon E, Goyvaerts E, Ramsay M, de Villiers E, van Heerden C, Allsopp B, Seoighe C.  (2001) “A platform for genomics in South Africa” South African Medical Journal 91(12):1006-7 

45) Graham, I.A., Denby K.J. and Leaver, C.J. (1994) “Carbon Catabolite Repression Regulates Glyoxylate Cycle Gene Expression in Cucumber”Plant Cell, 6: 761-772

 

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Contact details

Prof. Katherine Denby
Professor and Academic Director of the N8 AgriFood Resilience Programme
Department of Biology
University of York
Heslington
York
YO10 5DD

Tel: 01904 328751

https://denbylab.wordpress.com

http://n8agrifood.ac.uk/