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MRC DiMeN Doctoral Training Partnership: Are microbes the hidden influencers? Unravelling the genomic network of host-microbe interactions

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  • Full or part time
    Dr D Rico
    Prof S Hambleton
    Dr C Lamb
    Prof R Hirt
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Background and hypotheses

Each of us has a genome. The genome is the same in every cell of our organism but its three-dimensional (3D) structure is different in every cell type. Genes, enhancers and other genomic regions interact with each other forming different networks in different cells.

These 3D genome networks are now available thanks to the recent development of chromosome capture techniques. We exploit graph theory computational approaches to analyse their properties, their sub-communities or fluxes of information, as we do with social networks.

Recent data suggest that genetic variants associated with inflammatory bowel disease (IBD) may be associated with microbial mishandling or aberrant/exaggerated responses to commensal or pathogenic microbes. However, a large fraction of these variants are in non-coding regions and remain unexplored. Here, we hypothesize that:

A) Many diseases with an immune component could be triggered by inappropriate host responses to commensal or pathogenic microbes.
B) Defective immune response in IBD patients can be linked to mutations in non-coding enhancers.

In this project, the student will investigate the role of microbes as “hidden influencers” of variation in these non-coding genomic sequences associated with IBD.


1. To identify communities of genes and non-coding enhancers activated in immune cells in response to microbes by integrating 3D genome networks and gene expression data from healthy donors and patients with microbial infections.

2. To develop Artificial Intelligence (AI) methods to uncover mechanistic associations between IBD-associated variants and enhancers that regulate the transcriptional response to pathogens/resident microbiota.

3. To explore the predictive value of these genomic regions in the onset and progression of the disease, opening new avenues for diagnosis and prevention.

Novelty and timeliness

Current technologies allow to map thousands of DNA interactions. However, we have little understanding about how this information is utilized by different immune cells in response to microbes. We propose a revolutionary analytical approach to fill this gap: modelling genome folding as a communication network of genetic elements.

Experimental Approach

We will develop and apply graph theory and AI methods to understand information processing in the 3D genome networks of immune cells, integrating gene expression data and genetic data. The primary supervisor (Daniel Rico) will provide training in quantitative skills (mathematics, statistics, computation, data analytics and informatics, machine learning and Artificial Intelligence). The other members of the supervisory team are experts in immunodeficiencies and infections (Sophie Hambleton), inflammatory bowel disease (Chris Lamb) and evolution of microbes (Robert Hirt), offering interdisciplinary training opportunities at the interface of computational and systems biology, microbiology and translational medicine.

More information about the supervisory team

Daniel Rico

Chris Lamb

Robert Hirt

Sophie Hambleton

Benefits of being in the DiMeN DTP

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:

Further information on the programme can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs.
- Stipend at national UKRI standard rate
- Tuition fees
- Research training and support grant (RTSG)
- Travel allowance

Studentships commence: 1st October 2020.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here:

Good luck!

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