Defra/N8 AgriFood/BSPP undergraduate summer studentships in Plant Health

Defra, N8 AgriFood and British Society of Plant Pathology are funding 9 undergraduate summer studentships for 8-10 weeks working on key plant health challenges identified by Defra. The studentships are open to students from any University in the middle years of their degree. See for more information and to apply. 

Spend a happy summer working on plant health!



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1st International Plant Systems Biology Conference

The first International Plant Systems Biology conference will be held in Roscoff, France 10th – 14th Sept 2018. See the website for details on the programme and this fantastic venue. Look forward to seeing you there!

FLYER iPSB2018.v2

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Gatsby PhD studentship to investigate how the circadian clock impacts plant immunity

An opportunity for a Gatsby-funded enhanced 4-year PhD studentship to investigate how the circadian clock is impacting plant disease resistance. This studentship is open to UK and international graduates – further details can be found here.  Please contact me with any questions.

Applications due by 3rd February 2018.


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Making gene expression tools easily accessible

Applications note with 14 easy to use gene expression data tools integrated into the public cloud computing service CyVerse.

During our systems biology project on Arabidopsis responses to environmental stress we (Universities of Warwick, Exeter and Essex) developed multiple tools to analyse and mine gene expression data, particularly time series gene expression data. Many of these tools have been published in papers highlighting our biological findings and insight but usually as Matlab code, or R code:

  • Bechtold et al. (2016) Time-series transcriptomics reveals that AGAMOUS-LIKE22 affects primary metabolism and developmental processes in drought-stressed Arabidopsis. Plant Cell 28: 345–366
  • Lewis et al. (2016) Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae tomato DC3000Plant Cell 27: 3038-3064
  • Polanski et al. (2014) Wigwams: identifying gene modules co-regulated across multiple biological conditions. Bioinformatics 30(7):962-70
  • Hickman et al. (2013) A Local Regulatory Network Around Three NAC Transcription Factors in Arabidopsis Stress Responses and Senescence. Plant Journal 75(1):26-39
  • Baxter et al. (2012) Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants. Plant Cell 24: 3949-3965
  • Windram et al. (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell 24(9): 3530-3557
  • Penfold et al. (2012) Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks.Bioinformatics 28: i233-i241
  • Breeze et al. (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.

Now we have put 14 tools onto the easy to use, powerful CyVerse infrastructure (grouping them as an output of the CyVerse UK project) and written tutorials to accompany the tools and make them easy to use and understand. The applications note describing the tools is here – Hope you have fun using them!

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Three PhD projects available for start Oct 2018

Three PhD projects are available in my lab or in collaboration with my lab funded by the White Rose BBSRC Mechanistic Biology Doctoral Training Partnership. See the links below for more details and information on how to apply, and please contact me with any queries.

Come and join us and explore plant – environment interactions!

How does the circadian clock regulate disease resistance?

Dynamics of the soil microbiome during drought

Dissecting quantitative variation in the plant circadian clock


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CyVerse UK

GARNet and CyVerseUK are organising a workshop to provide hands-on training for the software tools that the CyVerseUK grant has developed (

These tools are designed to be used with data from any experimental system so researchers who work in any organism are encouraged to attend.

The new software tools are for the analysis of RNAseq, GWAS, gene expression and imaging data. The workshop has a training-focus so each attendee will be provided with datasets to work with so that they gain hands-on experience in using these software tools. The workshop is designed for new users so no prior knowledge is required.

The workshop is on March 20th-21st at the University of York and costs just £35!
The registration deadline is Wednesday March 1st but places are limited.

Registration and more information can be found here:

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Sainsbury PhD Studentship opportunity

We are recruiting for a Sainsbury PhD Studentship which will be competitively awarded for entry in Octobber 2017. These studentships are prestigious and well-funded and enable excellent students to undertake a PhD in plant science. Proposals for PhD work in the DenbyLab should fall under the title “Tricking plant pathogens: exploiting pathogen effectors to develop durable disease resistance“.

If you are interested please contact Katherine to discuss the opportunity and potential projects further. The deadline for applications is Feb 24th 2017 with interviews on March 10th 2017.

See details at Nature.

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