Subject: PhD Studentship in Computational Biology/Bioinformatics/Artificial Life

Microbe Wars: Exploring the Maintenance of Microbial Diversity Using Artificial Life

A PhD studentship in computational biology is available at the University of St Andrews in Scotland.

Microbes are the most ubiquitous life form on Earth, found everywhere from exotic locations - black smokers on the ocean bottom - to the inside of every human’s gut. They are essential for nearly all life on the planet, driving nutrient cycling in the environment and contributing to the health of plants and animals. Microbes are also critical to industrial biotechnology, especially for fuel, fine chemical and drug production. Thus, understanding how microbial ecosystems are maintained is essential. Evolutionary processes within microbial communities appear fundamentally different than those at play in macro-organisms, requiring specific understanding.

In this studentship, you will develop artificial life simulations to explore evolution and maintenance of biodiversity in microbial communities. You will use machine learning and mathematical modelling to identify and assess strategies leading to stable communities that also maintain biodiversity. You will explore how communities respond to perturbation, corresponding to phenomena such as provision of antibiotics to a patient, and human intervention in industrial and agricultural systems.

Your work will have applications in many areas. It is increasingly clear that the microbial communities within our bodies are key contributors to health: because the beneficial effects of these communities are in danger from both antibiotics and antibiotic-resistant pathogens, understanding how healthy biodiversity can be maintained in the face of perturbation is essential. Maintenance of soil microbial diversity is important for plant health, and ultimately our food security. Microbial populations in all contexts may share essential features of community assembly, and this project will inform multiple topic areas.

You will gain training in artificial life simulations, genetic algorithms, machine learning, game theory, microbial genomics and metabolism, and mathematical modelling, and will acquire a working knowledge of microbial communities and their importance on our planet.

Your project will take place in St Andrews’ Centre for Biology Diversity (CBD) in the School of Biology, and will be jointly supervised by Dr V Anne Smith from the School of Biology, Dr John Mitchell from the School of Chemistry, and Dr Leighton Pritchard from the James Hutton Institute. All three groups work in complementary areas of computational systems biology and machine learning. For more information on their research please visit:

Dr V Anne Smith’s research pages: http://biology.st-andrews.ac.uk/vannesmithlab/

Dr John Mitchell’s research pages: http://chemistry.st-andrews.ac.uk/staff/jbom/group/

Dr Leighton Pritchard’s research pages: http://www.hutton.ac.uk/staff/leighton-pritchard

EASTBIO - the BBSRC East of Scotland Bioscience Doctoral Training Partnership - is a partnership between the Universities of Aberdeen, Dundee, Edinburgh and St Andrews; the Scottish Universities Life Sciences Alliance (SULSA); and the Scottish Universities Physics Alliance (SUPA). A fully funded 4-year EASTBIO PhD studentship (fees and stipend at the standard rate) is available for Autumn 2016 for candidates with a strong academic record and that satisfy BBSRC studentship eligibility requirements (see http://www.eastscotbiodtp.ac.uk/how-apply-0 if you are unsure - typically UK citizenship required).

If you are interested, please first make an initial informal enquiry, including a covering letter explaining your interest in the studentship and a CV, to anne.smith@st-andrews.ac.uk.

Formal applications should follow to the University following the procedure available at:

http://www.eastscotbiodtp.ac.uk/how-apply-0

using the forms provided and via the link to St Andrews University.

Complete applications must have been received by the University by 14 December 2015.

On 9 Dec 2015, at 09:45, Bert Overduin <Bert.Overduin@ed.ac.uk> wrote:

Forwarding on behalf of a colleague:

Bioinformatics PhD Opportunity: University of St Andrews: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=67780&LID=1374

Bioinformatics PhD Opportunity: University of Dundee: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=67784&LID=1374

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Bert Overduin, PhD

TRAINING AND OUTREACH BIOINFORMATICIAN

Bert.Overduin@ed.ac.uk

EDINBURGH GENOMICS

The University of Edinburgh

Ashworth Laboratories

The King's Buildings

Charlotte Auerbach Road

Edinburgh EH9 3FL

Scotland, United Kingdom

tel. +44(0)1316507403

http://genomics.ed.ac.uk

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Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e: leighton.pritchard@hutton.ac.uk w: http://www.hutton.ac.uk/staff/leighton-pritchard
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