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PhD Studentship in Bioinformatics – ref 2008-8

Summary

Description

In silico prediction of the genes and pathways involved in pathogenicity, virulence and host-specificity during bacterial infection of farm animals.

Elucidating the genes and pathways involved in virulence, pathogenicity and host specificity during bacterial infection remains a complex and challenging problem. However, due to the emergence of genomic and post-genomics techniques, a huge body of data now exists on the molecular make-up of a number of bacterial pathogens of interest to the IAH; the genomes of several Salmonella, E coli and Mycobacterium species have been sequenced and published, and data from functional genomics experiments are available both in the public domain and from experiments carried out at, or through collaboration with, the IAH. Accurate prediction and analysis of the genes involved in virulence, pathogenicity and host-specificity requires that the most up-to-date annotation of genes is integrated with quantitative data from functional genomics experiments to allow a systems biology approach to be adopted, integrating bioinformatics tools with post-genomic datasets. The questions which will be asked are: can we predict/identify the genes and pathways involved in the above processes? Are there common pathways that undergo gene decay in host-restricted strains? Are there genes commonly lost or gained in host-specific vs host-restricted strains? Are there common mutations? Can we use the above information to predict the behaviour of some of the currently unsequenced strains of bacteria held at IAH? And finally, can we use this information to predict threats to animal and human health? This is an interesting and challenging problem in bioinformatics.

This project will involve the development of skills in bioinformatics, sequence analysis and statistics, though candidates with training and experience in these areas are particularly encouraged.

For a full description of the project, please see http://www.iah.ac.uk/students/project/2008-8.pdf

TO APPLY - go to http://www.iah.ac.uk/students/ for applications forms and guidance

An enhanced stipend (in line with the recommendations of the Roberts Review and further supplemented by the IAH) is offered. For 2007/08 the student stipend is £16,800 (£19,450 for veterinary graduates) but is currently under review.

1. Pruitt et al Nucleic Acid Res (2007) 35:D61
2. Hinton Mol Microbiol (1997) 26(3):417
3. Watson M BMC Bioinformatics (2005) 6:98.

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