PhD in Proteome Informatics

Proteomics – the science of discovering which proteins are present in a given biological sample, and in what quantities – has become a crucial tool in modern biology. The current method for achieving this is to analyse samples using high throughput mass spectrometry (MS), then use computational tools to determine the identities and abundance of proteins from the acquired spectra. However, the computational interpretation of proteomic spectra is not a solved problem, particularly for variant proteins and in complex samples.

This entirely computer-based PhD will focus on the development of new algorithms and software for the reliable identification and quantitation of proteins (including proteins that differ from a standard reference version due to post translational modifications, splice variance or variations in the genome of the individual under study). Some of this work will make use of a recently developed approach in which RNA-seq transcriptomic data is used to guide the proteomics algorithms. Findings from the PhD will feed into our existing proteomics software offerings, including MRMaid and x-Tracker. More information about these tools can be found via our web site, bessantlab.org.

The ideal applicant will have a sound understanding of molecular biology, biochemistry, data analysis and software development. A good first degree, at least an upper-second class Honours degree (or equivalent qualification) in a relevant scientific subject (e.g. biochemistry, statistics, biotechnology), and a Masters degree in bioinformatics or chemometrics would be a distinct advantage. Proven expertise in Java programming, and experience of working in bioinformatics software development, especially for proteomics, is highly desirable. International students are required to provide evidence of their proficiency in English language skills.

The student will be located in a newly created dedicated bioinformatics laboratory, working alongside other researchers engaged in related projects, with access to new computing equipment including high specification PCs and dedicated servers. There will also be extensive opportunities to collaborate with proteome informatics researchers elsewhere in the UK and around the world.

For more information about this opportunity, feel free to contact the supervisor Prof Conrad Bessant.