PhD Project – Engineering – Development of Novel Algorithms and Tools for Integration of Metagenomics and Metabolomics

The School of Engineering of the University of Glasgow is seeking a highly motivated graduate to undertake an exciting 3.5-year PhD project entitled ‘DEVELOPMENT OF NOVEL ALGORITHMS AND TOOLS FOR INTEGRATION OF METAGENOMICS AND METABOLOMICS’ within the Infrastructure and Environment Division.

Microorganisms are ubiquitous and play a primary role in regulating biochemical systems at both geographic and mesoscopic scales. There is considerable potential in ‘omic technologies and bioinformatics to reveal a wealth of insights on uncultivated microbial species and how the living microbes operate as a system. Whilst the large-scale whole genome metagenomic sequencing is useful for assessment of taxonomic and functional diversity of microbial communities, to fully delineate the metabolic potential of microbial community, chemical fingerprinting is often employed through the use of metabolomics.
Thus the prospective candidate, ideally with a strong computational background, will be supervised by Dr Umer Zeeshan Ijaz to advance the existing metagenomic workflows (both 16S rRNA and whole-genome shotgun sequencing: http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics) and will implement a rich software infrastructure to integrate the datasets originating from metabolomics by focusing on algorithm development, ecological statistics, and numerical ecology. For algorithm development, the candidate will be jointly-supervised by Dr Christopher Quince, an expert in Bayesian statistics. The developed tools will then be used as a test bed to understand the gut ecosystem although they will be general enough to cover the macroecology of microbes. In this regard, the student will work closely with Dr Konstantinos Gerasimidis. Data from gut bacterial 16s rRNA, whole genome sequencing, targeted and untargeted metabolites from past and ongoing projects will be made available to the prospective candidate to understand the impact of dietary interventions and artificial nutritional therapy on the gut microbiota in healthy individuals and others with chronic disease. These encompass conditions such as Crohn’s disease, coeliac disease, obesity as well as experiments in-vitro in batch and continuous models of the large bowel. The student will first explore how changes in microbiome correlate with changes in metabolome measured in a variety of biological samples (urine, faeces, blood) and how these associate with dietary interventions or associate with response to clinical treatment or outcomes. The interdisciplinary nature of this project will enable the selected candidate to get trained on cutting edge technologies in molecular microbiology, DNA sequencing, bioinformatics tools, and laboratory methods and the project will provide a merging of expertise between the Environments, School of Engineering, Glasgow; Human Nutrition, School of Medicine, Glasgow; and Warwick Medical School.
Project Team:
Dr Umer Zeeshan Ijaz, NERC Independent Research Fellow & Lord Kelvin Smith Fellow, School of Engineering, University of Glasgow (1st supervisor)
Dr Konstantinos Gerasimidis, Lecturer (Human Nutrition), School of Medicine, University of Glasgow (2nd Supervisor)
Dr Christopher Quince, MRC Fellow, Warwick Medical School, University of Warwick (3rd Supervisor)
Drs Richard Hansen and Richard Russell, Consultant Paediatric Gastroenterologists, Yorkhill Hospital (Clinical Supervisors)

How to Apply: Please refer to the following website for details on how to apply:
http://www.gla.ac.uk/research/opportunities/howtoapplyforaresearchdegree/.