Postdoctoral Fellow on the TROPHIC Project – Bioinformatics

TROPHIC project investigates how the gut microbiome influences intestinal function and nutritional status in patients with cancer, particularly in the context of malnutrition and chemotherapy. The project combines human cohorts, shotgun metagenomics, metabolomics and animal models to identify biomarkers and mechanisms that could ultimately support the development of new microbiome-targeted interventions.
The successful candidate will primarily contribute to TROPHIC, while also being involved in several other funded projects in oncology, infectious diseases and precancerous conditions.

• Analyze microbiome datasets from human cohorts and mouse models, primarily using shotgun metagenomics and 16S rRNA sequencing data, with opportunities to work on other omics datasets through collaborative projects
• Develop, implement and improve reproducible bioinformatics pipelines, including quality control, taxonomic and functional profiling, statistical analysis and data visualization.
• Integrate microbiome, metabolomic and clinical data, and contribute to biostatistical and machine-learning approaches for biomarker discovery.
• Work within a multidisciplinary network bringing together clinicians, bioinformaticians and experimental biologists, contribute to high-impact scientific publications and, depending on experience and interests, take an active role in coordinating the “Post-analytical” working group of GEM Lyon Microbiota.

• Background and skills in bioinformatics, computational biology, biostatistics, life-science data science or a related field.
• Good proficiency in R and/or Python and experience working in a Unix/Linux environment.
• Experience analyzing omics or other high-dimensional biological datasets.
• Previous experience in microbiome research or metagenomics would be an advantage but is not mandatory. We are primarily looking for scientific curiosity, autonomy, rigor and a strong willingness to learn.

• Access to rich datasets that are already available and currently being enriched, with strong potential for publications and opportunities to develop independent scientific questions.
• A highly interdisciplinary and rich scientific environment at the Institute of Functional Genomics of Lyon (IGFL), with access to ENS de Lyon computing resources, methodological support and daily interactions with experimental biologists.
• Integration into the PEPR SAMS / France 2030 national microbiome research network, together with leading French and European collaborations.
• A position offering progressive scientific independence and opportunities for career development, depending on the candidate’s experience and interests.

• Location: IGFL, ENS de Lyon / Université Claude Bernard Lyon 1, Lyon, France
• Contract: 1 year, renewable up to 3 years
• Starting date: Q4 2026 – Q1 2027, flexible
• Salary: According to experience
• Application: Resume, short cover letter and contact details for 2 referees
• Contact: Nicolas Benech – nicolas.benech[at]chu-lyon.fr