A postdoctoral fellow is sought for a position working with Marc Lipsitch and Bill Hanage at the Center for Communicable Disease Dynamics (CCDD), within the Department of Epidemiology at Harvard T.H. Chan School of Public Health. The successful applicant will have responsibility for a set of studies to analyze the factors maintaining genomic diversity in Streptococcus pneumoniae (pneumococcus) and the response of Streptococcus pneumoniae populations to vaccination. This will be a extension of recent work including cross-sectional and longitudinal population comparisons (references below) and will focus on defining the selective forces underlying observed population dynamics. The work will involve collaboration with other fellows and potentially students within the research group, to combine theoretical insights with detailed analysis of populations of genome sequences.

Applicants should have a PhD and some publications in bioinformatics, evolutionary biology, population genomics or related fields. As the position will involve large amounts of sequence data, the successful candidate will ideally have experience with bioinformatic analyses on large genomic data sets and should be proficient at programming in R, Python, or equivalent. Enthusiasm for collaborative work is essential, as this project will involve not only a highly interactive team here but important collaborations with CDC and with colleagues in the UK and Europe. More broadly, working at CCDD (at the Harvard Chan School in Boston, MA, USA), offers opportunities for interaction and collaboration with a wide range of colleagues working on diverse topics in quantitative infectious diseases. The post is for two years in the first instance, with the possibility of extension.

To apply, please send a letter, a CV and names of references to Marc Lipsitch mlipsitc@hsph.harvard.edu.

Recent work in this area:

Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M. The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathog. 2018 Apr 4;14(4):e1006966.
Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol. 2017 Dec;1(12):1950-1960.
Azarian T, Martinez PP, Arnold BJ, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC, Bentley SD, O’Brien KL, Lipsitch M*, Hanage WP*. Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies https://www.biorxiv.org/content/early/2018/09/18/420315