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.
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 DC3000. Plant 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!
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
GARNet and CyVerseUK are organising a workshop to provide hands-on training for the software tools that the CyVerseUK grant has developed (http://cyverseuk.org/).
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:
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.
A competitively funded PhD studentship is available in the Denby group. This project – Keeping time on immunity – will be funded through the BBSRC White Rose Mechanistic Biology DTP and is a 4 year studentship.
Please contact Katherine if you are interested in this project and would like more information or want to discuss the project in more detail. The deadline for applications is Sunday January 8th 2017.
We look forward to hearing from motivated scientists looking to learn a range of skills and contribute to a productive and friendly research group.
We have moved to the Biology Department at the University of York. We have unpacked the lab in our new home and are ready to go. If you are nearby please come and say hello.
Katherine has also taken on a new exciting role as Academic Director of the N8 AgriFood programme; the launch event on 21st -22nd June in Manchester promises to be a fantastic event so hope to see you there!