We are seeking a postdoctoral research assistant/associate to make a leading contribution to the project “A novel targeted sequencing approach for untangling the epidemiology of endemic anthrax, a neglected zoonosis”, funded by the Academy of Medical Sciences within the remit of the Global Challenges Research Fund. The successful candidate will work with Dr Taya Forde and other collaborators at the University of Glasgow, as well as with University of Oxford's Big Data Institute and the French National Institute for Agricultural Research (INRA).

The aim of this study is to develop a framework for applying culture-independent targeted sequencing approaches for the epidemiological study of anthrax. Little is known about the epidemiology of anthrax, including how the causative bacterium Bacillus anthracis is transmitted within and between outbreaks. We have shown that targeted sequence capture - wherein DNA of the pathogen of interest is enriched from clinical samples - can be used to obtain high-depth genomic sequence data. This approach holds great promise for improving inference about
bacterial pathogen transmission through the unbiased capture of mixed strains from a single host. However, to successfully apply these techniques for epidemiological inference, data analytical methods require further development. Specific objectives of this project are to: 1. Develop methods for quantifying the within-host diversity of B. anthracis using targeted sequence data; 2. Adapt existing tools to leverage the genetic diversity captured by this approach for improved phylogenetic and epidemiological inference; and 3. Apply the validated data analytical methods to a large collection of anthrax-positive samples to gain an improved understanding of the epidemiology of B. anthracis in endemic settings. Ultimately, this will help inform decisions about where and when to focus livestock vaccination efforts to limit pathogen spread in a multi-host environment.

The successful candidate will be expected to contribute to the formulation and submission of research publications and research proposals as well as help manage and direct this complex and challenging project. Essential required skills in bioinformatics, particularly related to high-throughput genetic sequence data, demonstrated ability to analyse genetic sequence data sets using state-of-the-art bioinformatic and/or phylogenetic approaches, and quantitative skills including use of computer programming and statistics.

This position has funding for up to 20 months in the first instance. Flexible start date, could easily be started remotely.