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Computational metagenomics in personalized medicine: Defining high resolution microbial genotypes (HILDEBRANDQ20DTP2)

   Graduate Programme

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  Dr F Hildebrand  No more applications being accepted  Competition Funded PhD Project (European/UK Students Only)

About the Project

We are looking for a highly motivated and bioinformatically minded student, to investigate bacterial communities through metagenomics and population genetics.

In the 4-year funded DTP, the candidate will explore bacterial strains and their evolution primarily within the human gut using metagenomics. Metagenomics is the random sequencing of all DNA within a sample; due to the stochastic nature and size of this data, advanced machine learning and data mining techniques can be used to make inferences about which bacteria inhabit a sample, and what they do. However, to identify pathogens harmful to the human, ultra high-resolution metagenomics is required. In this PhD the theory and tools to enable this will be developed.

If you identify yourself as someone interested in developing metagenomic, bacterial genomics, and understanding what a bacterial species is, this PhD project will be right for you. The ideal candidate will have experience in computational biology (Linux environment, one or several programming languages among R/Perl/Python/C++). Knowledge of topics like population genetics, ecology, machine learning, statistics, SNP calling, DNA sequencing, metagenomics and basic wetlab experience are beneficial, but will each be trained during the PhD. The applicant will receive scientific training, can present their work at international conferences and research in a dynamic environment, where young researchers have an impact. Exchanges over several months to close collaborators at EMBL (Heidelberg, Germany) are planned as part of the PhD.

The candidate will be supervised by Dr Falk Hildebrand (metagenomics), Dr Lindsay Hall (infant microbiome) and Prof Rob Kingsley (genetic pathogen tracking) at the Quadram Institute Bioscience, the Earlham Institute and the University of East Anglia (Norwich, UK), a supervisory team that frequently publishes high-impact studies in Nature/Science on the gut microbiome and its impact to human health. Norwich is the leading microbiology and microbiota research centre in the UK and is an excellent platform for starting a scientific career.

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 7th, 8th or 9th January 2020.

The NRP DTP 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

For funding eligibility guidance, please visit our website: Full Studentships cover a stipend (2019/0 rate: £15,009pa), 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. To be eligible students must meet the EU residency requirements.
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