PhD student in bioinformatics (M/F)

CNRS; France; Sur place; EUR 30 000 - 45 000; Plein temps

Résumé du poste

A leading research organization in France is looking for a Researcher specialized in phage genomics. The role involves conceptualizing and executing research projects, developing AI tools, and conducting data analysis. Candidates should possess expertise in phage biology, bioinformatics, and programming skills in Bash and Python. Excellent English communication skills are essential. This full-time temporary position starts on February 1, 2026, with a deadline for applications on December 10, 2025.

Qualifications

• In-depth knowledge of phage biology, evolutionary biology, and structural bioinformatics.
• Proficiency in Bash and Python.
• Excellent written and oral communication skills in English.

Responsabilités

• Conceptualize and carry out a research project in phage genomics.
• Use and develop new AI tools for the study of phages.
• Development of code in Bash and Python.
• Genomics data analysis.
• Scientific monitoring.
• Writing scientific articles.
• Oral presentation of work.

Connaissances

In‑depth knowledge of phage biology

Evolutionary biology

Structural bioinformatics

Proficiency in Bash

Proficiency in Python

Excellent written communication skills in English

Excellent oral communication skills in English

Description du poste

Organisation/Company CNRS Department Centre International de Recherche en Infectiologie Research Field Biological sciences Medical sciences Pharmacological sciences Researcher Profile First Stage Researcher (R1) Country France Application Deadline 10 Dec 2025 - 23:59 (UTC) Type of Contract Temporary Job Status Full-time Hours Per Week 35 Offer Starting Date 1 Feb 2026 Is the job funded through the EU Research Framework Programme? Horizon Europe - ERC Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The thesis will be supervised by François Rousset and carried out at CIRI in the Rosalind Franklin building on the Gerland campus. The candidate will have access to the ENS Lyon computing cluster.

Like other living organisms, bacteria are also susceptible to viral infections. Bacterial viruses, called phages, are the most abundant biological entities on our planet. In order to resist phages, bacteria have developed an arsenal of defense systems that form natural barriers against infection, thus defining bacterial immunity. Dozens of defense systems have recently been discovered in bacteria, highlighting an immense diversity of molecular mechanisms, some of which are conserved in eukaryotic immunity. In turn, phages have evolved so-called anti‑defense proteins to counter bacterial immunity and restore infection. Knowledge of these anti‑defence proteins and their mechanisms would make it possible to better predict interactions between phages and bacteria, and more generally to improve our understanding of virus‑host interactions across the tree of life. However, few anti‑defence proteins are known to date, in contrast to the 250 families of bacterial defence systems that have now been identified.

The Molecular Genomics of Microorganisms team led by François Rousset at CIRI studies the molecular mechanisms of phage‑bacteria interactions and their evolution in the eukaryotic domain. This thesis project aims to develop computational approaches to comparative genomics and structural bioinformatics in order to improve our understanding of anti‑defence strategies in phages and their mode of action. This bioinformatics project will be carried out in collaboration with the experimental part of the laboratory.

Tasks

• Conceptualize and carry out a research project in phage genomics
• Use and develop new AI tools for the study of phages

Activities

• Development of code in Bash and Python
• Genomics data analysis
• Scientific monitoring
• Writing scientific articles
• Oral presentation of work

Required Skills

• In‑depth knowledge of phage biology, evolutionary biology, and structural bioinformatics.
• Proficiency in Bash, Python, and computing clusters
• Excellent written and oral communication skills in English