Job: Computational PhD position available in the CVR's Virus Genomics and Bioinformatics group at the University of Glasgow
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David Robertson0 wrote:

FUNDED PhD OPPORTUNITY

Mapping the molecular specificity of virus-host interactions Prof David L Robertson, http://www.bioinf.manchester.ac.uk/robertson

A three and a half year PhD project is available in the CVR’s Viral Genomics & Bioinformatics group, http://www.bioinformatics.cvr.ac.uk from September 2017. The project will be computer-based and will train the student in systems virology, evolutionary biology, bioinformatics/computational biology and network biology/modelling. Please direct enquiries to david.robertson@manchester.ac.uk,who will be moving to CVR in 2017. Note, the deadline for applications is 23rd January 2017.

Project description Viruses exploit the molecular system of an infected host in order to replicate. This requires an intricate set of molecular interactions between the virus and the host system, placing a high degree of specificity on the virus-host relationship. The key to better understanding this relationship will be to study the coevolutionary changes between viruses and their host, in particular the precise nature of the interactions involved, i.e., a viruses’ ability to mimic host molecular interactions and events, in the context of the host’s response to infection. Depending on the student’s interests there will be some flexibility in terms of the focus of the project, e.g., a study of HIV/retroviruses versus bacteriophage infections. The aim will be to construct the virus-host interaction network at the species level and for case studies model the virus-host molecular interaction network. These molecular interactions can be represented as a dynamic network by considering both temporal and spatial aspects of infection of a cell. This will be represented as a directed network, and properties of the host proteins investigated, for example, their connectivity, control-status, and functional relationships. Questions to be addressed include: How many host species on average does a virus target? How do viruses so effectively use and control the host system? What changes contribute to host-switching? What constraints do the maintenance of host interactions place on viral evolution? Given the inherently hierarchical and multi-scale nature of function, how should infection be modelled? The project can be tailored to candidates with a background in virology, biology, bioinformatics, computer science, machine learning, statistics or mathematics.

To apply, please follow the steps detailed in ‘How to apply for a research degree’: http://www.gla.ac.uk/research/opportunities/howtoapplyforaresearchdegree/. When applying, please search for "Mapping the molecular specificity of virus-host interactions" in the programme description box.

Interview Process
Following selection for interview, you will be invited to come to Glasgow to visit the CVR in February 2017. The interviews will be held on Friday February 10th 2017 and all interviewees are registered for free and invited to attend the Glasgow Virology Workshop on Saturday February 11th. Reasonable travel expenses will be reimbursed and accommodation made available on the 9th and/or the 10th. Please be available on these dates.

We will consider any UK graduate (meeting the residency requirements) with a minimum 2:1 BSc, or equivalent, degree in a relevant discipline. A Master’s degree and previous experience of computer-based research is advantageous. Candidates with a computer science or mathematics background are encouraged to apply.

We are currently inviting applications for the programme beginning in October 2017. Unfortunately, we cannot consider citizens from outside the EU for this programme. The deadline for applications is 23rd January 2017.

Funding Notes

There are strict eligibility criteria for MRC-funded pre-doctoral studentships. Students from the UK (UK passport holders) are eligible. EU students (EU citizens) are eligible for this programme only if they have been ordinarily resident in the UK for the three years (continuously) prior to the start of the studentship (commencing the first week in October).

References - Dickerson JE, Pinney JW, and Robertson DL (2010) The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Systems Biology 4:80. - MacPherson JI, Dickerson JE, Pinney JW, and Robertson DL (2010) Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Computational Biology 6:e1000863. - Oyeyemi OJ, Davies O, Robertson DL, and Schwartz JM (2015) A logical model of HIV-1 interactions with the T-cell activation signalling pathway. Bioinformatics. 31:1075-83.

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