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Genome-wide association studies for gastrointestinal infections

Project Description

Evolution in bacteria, as in humans and other forms of life, is driven by genetic variation and selection. Different forms of a gene, or the presence or absence of a gene can lead to different function or phenotype. For example, bacteria might cause more or less severe disease, or survive better in the environment, or in one host species compared to another according to their genetic make-up. Genome-wide association studies (GWAS) aim to identify the genetic variants responsible for such phenotypic variations. GWAS has been hugely successful in human genetics, but application to bacteria requires to account for the specificities of bacterial genetics, especially in terms of clonality, recombination, population structure and genome plasticity.

This project will work on extensive available genetic data to link genotype with phenotype. This can include predicting antibiotic resistance, measuring survival of infections through the food chain, better survival in one animal host (e.g. cattle) than another (e.g. sheep), transmissibility and severity of infection. The project will involve the development of new bacterial GWAS methodology, comparison of existing methods including model-based and machine learning, and application to multiple simulated and real datasets of interest. This project will be supervised by Dr Xavier Didelot (University of Warwick), Dr Noel McCarthy (University of Warwick), Dr Alistair Darby (University of Liverpool) and/or Dr Tim Dallman (Public Health England).

We invite applications from candidates who have a 2.1 or 1st class degree in a relevant biological science or quantitative science discipline. A Masters degree in a relevant discipline would be an advantage.
Applicants should send a full CV (including the names and email addresses of at least two academic referees), and personal statement to . This should state:
• An outline of how this programme of research and training will benefit from their past experience and impact upon their career aspirations.

The position may be based at either, The University of Liverpool, The University of Warwick or PHE (Colindale/ Porton Down), depending on the project. For some projects, students will be required to work at one of the partner Universities’ and spend time at PHE.

Funding Notes

Thesis studentships cover research costs and tuition fees at the UK/EU rate for students who meet the residency requirements only.

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