Postdoc in evolution and public health

Universite de Montpellier; France; Sur place; EUR 25 000 - 27 000; Plein temps

Résumé du poste

Universite de Montpellier, Institut des Sciences de l'Evolution (ISEM), invites applications for a 24‑month postdoctoral position at the Institut des Sciences de l'Évolution (ISEM) on the Triolet campus, in the EEC team. The project focuses on drug resistance dynamics in pathogens using ecology, evolution and epidemiology.

The successful candidate will work with Pleuni Pennings, contribute to three subprojects (malaria, E. coli, and ML models), and publish open data and results.

Qualifications

• PhD in biology or bioinformatics.
• Experience in bioinformatics and sequence analysis.
• Programming in Python or R.

Responsabilités

• Contribute to three subprojects on drug resistance in malaria, E. coli, and ML models.
• Apply ecological, evolutionary, and epidemiological modeling to public data.
• Collaborate with the ISEM team and supervisor Pleuni Pennings.

Connaissances

bioinformatics

sequence analysis

Python

R

Formation

PhD in biology or bioinformatics

Description du poste

Organisation/Company Universite de Montpellier Department Human Resources Research Field Biological sciences Researcher Profile Recognised Researcher (R2) Positions Postdoc Positions Application Deadline 25 Oct 2026 - 23:59 (Europe/Paris) Country France Type of Contract Temporary Job Status Full-time Is the job funded through the EU Research Framework Programme? Other EU programme Reference Number 2026-R0377 Is the Job related to staff position within a Research Infrastructure? No

Offer Description

- work environment: You will work at the Institut des Sciences de l'Évolution (ISEM, UMR 5554), on the Triolet campus of the University of Montpellier in the EEC team (Ecology & Evolution of Communities). ISEM is a research institute with 250 staff. The EEC team consists of around 20 people including researchers, technical staff, postdocs, PhD students and master students. The team brings together 8 nationalities and meetings are held in English. The research in the team focuses on host-parasite 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 [e-mail]

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 Geofield