Bioinformatics Research Engineer in Comparative Genomics, Multi-Omics, and Method Development to Characterize the Evolution of Mammalian Innate Immunity M/F

Job Description

Missions

The FUNEVO project aims to elucidate the FUNctional EVOlution of mammalian innate immunity. Funded by a 5-year ERC Consolidator Grant, FUNEVO seeks to identify multi-scale innovations (genomic, genetic, transcriptomic, and proteomic) in immunity. The project includes a specific focus on the antiviral immunity of bats—a key model organism for which the team has multi-omics data and novel cellular and virological models. Bats are particularly interesting as they carry numerous viruses, often without developing symptoms, and some of these viruses are the origin of zoonoses. They also exhibit remarkable genomic adaptations at virus-host interfaces.
To understand the role of gene duplications/losses and protein domain rearrangements (recombination) in the diversification of the immune system, particularly against pathogenic viruses, the FUNEVO project involves:
• Integrating genomics and evolutionary biology to characterize innovations in innate immunity;
• Identifying domain rearrangements and their functional consequences;
• Experimentally testing associated cellular and antiviral activities.
Responsibilities:
Design and develop bioinformatics pipelines; analyze results; characterize the genomic, transcriptomic, and proteomic evolution of innate immunity in mammals.

Activity

The research engineer will play a central role in the FUNEVO project, working closely with the team's scientific and experimental axes. They will collaborate directly with other project members, including bioinformaticians, virologists, and cell biologists. Supervision will be provided by Lucie ETIENNE, CNRS Research Director and co-head of the LP2L/HIVE team, as well as Carine REY, an expert in bioinformatics and comparative genomics, and head of the BIBS bioinformatics and biostatistics platform at CIRI.
Main Activities:
• Develop robust and reproducible bioinformatics methods and pipelines to identify and characterize multi-scale innovations (genomic, genetic, transcriptomic, and proteomic) in mammalian innate immunity;
• Collaborate with team members (bioinformaticians, virologists, cell biologists) on comparative and phylogenetic analyses of immunity genes, focusing on gene duplications/losses and protein domain rearrangements (including AI-based protein structure prediction methods);
• Provide methodological support for the team's bioinformatics analyses;
• Conduct active methodological monitoring and evaluate published tools and methods;
• Contribute to the writing of scientific articles and the dissemination of research work.

Your Profil

Skills

The candidate must demonstrate successful experience in:
• Multi-omics data analysis,
• Comparative genomics approaches,
• Development and use of bioinformatics pipelines.
Experience or training in AI-predicted protein structures or imaging data analysis would be a plus.
Experience or training in immunology across the tree of life is also a plus.
Excellent English communication skills (written and oral) are required.

Your Work Environment

The missions will be carried out at the CIRI (Centre International de Recherche en Infectiologie), which brings together over 400 researchers in Lyon and Saint-Étienne in the fields of immunology, bacteriology, and virology. CIRI is primarily under the supervision of Université Lyon 1, Inserm, CNRS, and ENS de Lyon. Its goal is to better understand microbes, the immune system, and their interactions to combat infectious and immune diseases.
The hosting team is "Host Interactions with Viruses and Evolution" (HIVE/LP2L), located on the ENS de Lyon campus. All necessary resources to carry out the missions and activities will be provided.

Web:
- HIVE/LP2L Team: https://ciri.ens-lyon.fr/teams/lp2l
- BIBS Platform: https://ciri.ens-lyon.fr/la-recherche-au-ciri/plateformes-et-equipements/bibs

References of the team:
- Vazquez JM & Lauterbur ME, Mottaghinia S, et al. Insights into longevity and virus-driven adaptation from Myotis bat genomes. Nature. 2026 Aug 26. doi: 10.1038/s41586-026-10932-7. https://www.nature.com/articles/s41586-026-10932-7
- Le Corf A, et al. Genomic and functional adaptations in the guanylate-binding protein GBP5 highlight specificities of bat antiviral innate immunity. PLoS Biol. 2026 Apr 21;24(4):e3003760. doi: 10.1371/journal.pbio.3003760. PMID: 42013170. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003760
- Legrand A, et al. Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations. Nat Ecol Evol. 2025 Dec;9(12):2206-2222. doi: 10.1038/s41559-025-02845-x. PMID: 41219459. https://www.nature.com/articles/s41559-025-02845-x
- Picard L, et al. DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes. Nucleic Acids Res. 2020 Oct 9;48(18):e103. doi: 10.1093/nar/gkaa680. PMID: 32941639. https://academic.oup.com/nar/article/48/18/e103/5907962

Compensation and benefits

Compensation

from €3,175 gross per month, depending on experience

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions