Characterising the structure of the plant defence gene expression network (MACLEAN_S17DTP)

University of East Anglia - School of Computing Sciences

Start Date:  1st October 2017

No. of positions available: 1

Supervisor: Dr Dan MacLean 

Project description: 
The long-term objective of this project is to facilitate the discovery of novel sources of plant resistance to disease by understanding the control of gene expression and the structure of the response network.

A major biological question is how plants control the expression of genes to defend against infection. The central hypothesis of this research project is that modular transcriptional regulatory networks integrate varied signals and that the structure of these networks creates a computational layer that is a central mechanism in the control of gene expression.  This layer can ultimately be manipulated to improve resistance.

The overall aims of the project are:

1) Identify the major co-regulating transcription factors and their candidate binding sites and targets during the defence response

2) Develop a predicted in silico network of regulation and predict likely useful TF candidates for future in vivo and in planta experiments including direct binding site and methylation status.

3) To further characterise the temporal granularity of structural changes in the Arabidopsis transcriptional network and reveal the coarse structure of the system.

In this project you will work in a bioinformatics team closely with experienced Post Docs, learn or apply programming and data science skills including Python, Javascript and Unix to mine large gene expression data sets and databases. You will use the latest bioinformatics tools for gene expression estimates and learn to cross-reference online databases in a computational way using the latest web programming techniques. You will apply statistical and mathematical approaches to integrating different data sources into a single network and apply graph theoretical approaches to study a large network.

Person specification:  Minimum entry 2:1

Funding notes: Full Studentships cover a stipend (RCUK rate: £14,296pa – 2016/7), research costs and tuition fees at UK/EU rate, and are available to UK and EU students who meet the UK residency requirements.

Students from EU countries who do not meet the UK residency requirements may be eligible for a fees-only award. Students in receipt of a fees-only award will be eligible for a maintenance stipend awarded by the NRPDTP Bioscience Doctoral Scholarships, which when combined will equal a full studentship. To be eligible students must meet the EU residency requirements.

Details on eligibility for funding on the BBSRC website:

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South East England