The Charite Berlin and the Wellcome Sanger Institute are looking for a post-doctoral researcher to explore the transmission routes of pneumococci by a uniquely vast genomic database of ultra-deep sequenced samples from plate sweeps (following pneumococcal selective growth). The available data was generated from a large cluster-randomised trial run for 7 years in Nha Trang, Vietnam taking annual swabs from about 3000 children. The scope of work will include validation of existing tools, methodological development as well as data analyses. The focus of the work will centre around the inference of spatio, temporal and age dependent transmission (including the inference of direction, making use of within sample diversity). The employment will be via Charite Berlin but the successful candidate is expected to work closely with the Sanger Institute and Nagasaki University (and their research site in Vietnam), including the potential to be based with Sanger Institute for a few months.

The successful candidate will have
A doctoral degree in mathematics, statistics, computer science, epidemiology, or an equivalent degree in a subject with a strong analytical component
Evidence of substantial experience with programming in R, Python or similar
Evidence of experience in the use of phylogenetic methods
Interest in working in inter-disciplinary teams

The successful candidate will likely also have:
Experience with Bayesian statistics and/or math modelling.
Experience in infectious disease research.
Experience in inference of transmission pathways using genomic data.
Experience in the use of version control and collaborative coding (e.g. via GitHub)