Postdoc in evolution and public health

interactions, experimental evolution, fieldwork, theory in ecology and evolution and data analysis. People in the team are involved in organizing several community activities such as a quantitative journal club and the Reading group for Equity, Diversity, and Inclusion.

You will work directly with Dr Pleuni Pennings, an evolutionary biologist, specialized in population genetics as applied to drug resistance evolution in viruses, bacteria and malaria. Dr Pennings joined ISEM in 2025 after having worked in the USA for 15 years. She has a strong interest in inclusion and diversity in science, open science, and science communication. Montpellier is a great place to work on evolution and infectious disease.

- main mission: This job is part of a project led by Pleuni Pennings and supported by the region Occitanie. The goal of the project is to uncover the rules that determine the dynamics of drug resistance in different pathogens. We use modeling techniques from ecology, evolution and epidemiology and publicly available data from surveillance programs and genomic databases. We work on various pathogens (HIV, E. coli and P. falciparum) to be able to compare and contrast. The project consists of three subprojects and the person we hire will be able to work on two subprojects of their choice.

- activities:

Subproject 1: Resistance to antimalarials in P. falciparum

This subproject focuses on resistance to mefloquine which is caused by a gene amplification of the Pfmdr-1 gene which is known to occur recurrently. However, despite the high rate of de novo evolution of resistance, resistance had not reached fixation in the population. The goal of this subproject is to determine the fitness cost of the amplification and determine whether this cost explains why it is not fixed. We will use publicly available sequencing data, determine amplification breakpoints to identify independently evolved resistance alleles and infer the fitness cost of carrying the resistance alleles using phylogenetic approaches.

Subproject 2. Diversity of resistance in E. coli populations

It is known that for many drug-bacteria pairs, consumption levels of drugs correlate with resistance levels. We hypothesize that higher levels of resistance in countries with higher treatment levels are caused by more origins of resistant strains. We plan to test this hypothesis by determining diversity of resistant bacterial strains in different countries and at different time points using subsets of the Enterobase database which contains several hundred thousand E. coli genomes.

Subproject 3: Reusable machine learning models to predict drug resistance

Machine learning models to predict antibiotic resistance phenotypes are usually specific to one particular dataset. This limits their practical usefulness. We propose here to align genomes to a standardized reference pan-genome to capture information on SNPs and gene presence-absence in a standardized way. This means that a model that was trained on one dataset can be tested on new genomic data which will allow us to determine how generalizable the models are.

The net monthly salary is between €2,200 and €2,380

The contract duration is 24 months

Where to apply

E-mail: pleunie.pennings@umontpellier.fr

Requirements

Research Field: Biological sciences

Education Level: PhD or equivalent

Skills/Qualifications

We are looking for a curious and motivated candidate with a PhD in biology or bioinformatics with skills in bioinformatics and sequence analysis and experience coding in Python or R or related languages. Other useful (not required) skills and interests would be modeling, simulations, evolutionary / population genetics, statistics, writing, reading primary literature, and public health.

Additional Information

Work Location(s)

Number of offers available: 1

Company/Institute: Institut des Sciences de l'Evolution de Montpellier (ISEM)

Country: France

Contact

City: Montpellier

Website: http://www.umontpellier.fr/

Street: 163 rue Auguste Broussonnet

Postal Code: 34000