PhD Research Project

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Fully funded PhD studentship in high performance computing for comparative genomics and genome assembly improvement

Institution:

Aberystwyth University

Dept/School/Faculty:

Institute of Biological, Environmental and Rural Sciences (IBERS)

PhD Supervisor:

Prof D Larkin

Co-Supervisor:

Dr M Swain

Application Deadline:

No more applications being accepted

Funding Availability:

Funded PhD Project (European/UK Students Only)

PhD Research Project

This PhD studentship in the area of comparative and computational genomics is funded by Fujitsu and HPC Wales. It will be supervised by Drs. Denis Larkin and Martin Swain and co-supervised by Prof. Jamie Newbold and a supervisor from Fujitsu.

Next-generation sequencing technologies together with de novo assembly algorithms have enabled the reconstruction of mammalian genomes at low cost. This trend will be even more accelerated by the launch of projects like the G10K project that aims to sequence 10,000 vertebrate genomes.

At IBERS we are interested in performing comparative genomic studies on a range of different species. These studies are important for understanding genome evolution, and for applying this knowledge and the associated computational techniques to reducing negative environmental effects from farm animals and crops, and to help with managing neglected tropical diseases such as schistosomiasis and sleeping sickness.

In the first part of this project the Ph.D. student will focus on developing cutting-edge algorithms for comparative genome analysis using the HPC resources provided by HPC Wales, and generate chromosome assemblies for newly sequenced species. In the second part the student will use these genomes to reveal novel lineage-specific features of vertebrate genomes formed during the process of adaptation, speciation, and selection including those that are present in distinct mammalian phylogenetic clades.

More specifically, the Ph.D. applicant will focus on the development of new algorithms for faster alignment of large genomes. The student will also be involved in improving algorithms and reconstruction of chromosomes of several genomes, including the sheep genome, to perform the comparative analysis to detect features of ruminant genomes related to unique adaptive phenotypes. The student will contribute to the detection of polymorphisms from native Welsh sheep breeds to understand their history and genome adaptations.

The student will learn a range of advanced informatics skills that are required for performing sophisticated analyses of Next Generation Sequencing data and other complex data sets.

There will be many opportunities for the student to develop innovative approaches and ideas to exploit the wealth of freely available data. The skills, interests, and imagination of the student will guide the type of analyses performed.

Funding Notes:

An important aspect of this project is to ensure that the bioinformatics pipelines developed will be used in future projects at IBERS and worldwide.
This multidisciplinary PhD would be suitable for graduates with appropriate computational skills and a background in either biology or one of the physical sciences.
This studentship is open to UK/European Economic Area applicants. The studentship covers the full cost of UK/EU fees and a tax free stipend of £13,590 p.a.
There will also be an extra £17,000 available for research expenses and £2,000 for travel.