Postdoctoral Fellowship in Bacterial Population Genomics/Bioinformatics

Marc Lipsitch and Bill Hanage, co-supervisors

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.
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.

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

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

Thank you!
Marc

Marc Lipsitch, DPhil
Professor of Epidemiology
Director, Center for Communicable Disease Dynamics
Harvard T.H. Chan School of Public Health
http://www.hsph.harvard.edu/faculty/marc-lipsitch/
http://ccdd.hsph.harvard.edu
(617) 432-4559 <mlipsitc@hsph.harvard.edu>
Office hours: http://mlipsitch.wikispaces.com
Twitter and Skype: mlipsitch