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Detection of infectious agents in animal disease from whole genome sequencing data (COOPERU16HDTP)

   School of Health Sciences

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  Prof C Cooper  No more applications being accepted  Competition Funded PhD Project (European/UK Students Only)

About the Project

Infectious agents are known to be involved in the development of a variety of animal diseases. For example, Bovine tuberculosis (TB) is a chronic disease of animals caused by a bacteria called Mycobacterium bovis. In the last decade, next-generation DNA sequencing technology has reduced the cost of sequencing to less than 5p per Mb. This has resulted in a huge increase in whole-genome sequencing of tissue and bloods. It will become commonplace to sequence material from disease-infected animals and screening healthy livestock in risk areas. Samples collected from a host will also contain any infectious agents present and so it is possible to detect and quantify the sample’s microbiome at no additional cost. Our hypotheses are as follows:

1. A pipeline can be developed to efficiently detect and quantify the presence of infectious agents in whole genome sequence data from host material.
2. This tool will be able to provide evidence of a link between infectious agents and disease or the progression of disease in large whole-genome datasets.
3. This tool will be able to provide early warning signs of disease in apparently healthy livestock

The aim of this project is to develop a novel optimised pipeline to detect infectious agents in whole genome sequencing data from a range of vertebrates, package it so that it can be used by the wider research community and apply it to a panel of datasets.

This is a joint proposal between Norwich Medical School and TGAC and you will have the opportunity to benefit from a lively interdisciplinary environment and a large community of bioinformaticians.
This project has been shortlisted for funding by the Norwich Biosciences Doctoral Training Partnership (NRPDTP). Shortlisted applicants will be interviewed as part of the studentship competition. Candidates will be interviewed on either the 16th or 17th March 2016.
The Norwich Biosciences Doctoral Training Partnership (NRPDTP) offers postgraduates the opportunity to undertake a 4 year research project whilst enhancing professional development and research skills through a comprehensive training programme. You will join a vibrant community of world-leading researchers. All NRPDTP students undertake a three month professional internship (PIPS) during their study. The internship offers exciting and invaluable work experience designed to enhance professional development. Full support and advice will be provided by our Professional Internship team. Students with, or expecting to attain, at least an upper second class honours degree, or equivalent, are invited to apply.
For further information and to apply, please visit our website:

Funding Notes

Full Studentships cover a stipend (RCUK rate: £14,057pa - 2015/6), 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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