Description du sujet de thèse

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-defense 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-defense proteins are known to date, in contrast to the 250 families of bacterial defense 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-defense 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

Contexte de travail

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.

Contraintes et risques

Affiliation with the E2M2 doctoral school