Postdoctoral Fellowship in Bacterial Population Genomics/Bioinformatics

Massachusetts, United States
17 Jan 2019
End of advertisement period
14 Feb 2019
Contract Type
Fixed Term
Full Time


Harvard T.H. Chan School of Public Health


Epidemiology/Center for Communicable Disease Dynamics

Position Description

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 an 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.

The post will be at CCDD (at the Harvard Chan School in Boston, MA, USA), which 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.

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*. Accessory gene frequencies of Streptococcus pneumoniae predict post-vaccine lineage distribution. https://www.biorxiv.org/content/early/2018/09/18/420315

Basic Qualifications

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.

Contact Information

To apply, please send a letter, a CV and names of references to Marc Lipsitch (mlipsitc@hsph.harvard.edu). Applications will be considered as they arrive.

Contact Email


Equal Opportunity Employer

We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law.