Computational metagenomics in personalized medicine: Defining high resolution microbial genotypes


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.