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Research Engineer / Postdoctoral Researcher (M/F) – NGS Data Generation and Analysis of the Respiratory Microbiome in Environmental Health University of Rouen Normandy in France
Degree Level
Postdoc
Field of study
Computer Science
Funding
Available
Deadline
Dec 31, 2026
Country
France
University
University of Rouen
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About this position
Research Engineer / Postdoctoral Researcher (M/F) is available for 12 months at the University of Rouen Normandy within INSERM U1311 DYNAMICURE, a multidisciplinary research unit spanning Rouen and Caen. The position is part of the MICROBIOPOL project, which investigates how chronic exposure to urban air pollution (PM2.5, PM10, NO2) influences the structure and functional profile of the respiratory microbiota in the Rouen metropolitan area.
The successful candidate will be based on the Rouen campus and will work in a highly collaborative environment with microbiologists, bioinformaticians, air quality specialists, geomatics experts, and partners from public health and health economics. The unit combines expertise in respiratory and urinary tract infections, host–microorganism interactions, microbiomes, genomics, immunology, bioinformatics, and clinical research.
The role is strongly experimental, with a focus on NGS data generation and an interest in downstream bioinformatics analysis. Main tasks include DNA/RNA extraction from low-biomass respiratory samples, preparation of shotgun metagenomic libraries, operation of Illumina sequencing runs on the university’s Asgard platform, quality control of raw sequencing data, and running bioinformatics workflows on an HPC/Slurm cluster. The project also includes R-based analysis of alpha/beta diversity and identification of dysbiosis signatures linked to the urban exposome.
The post offers access to state-of-the-art sequencing infrastructure and regional high-performance computing resources. The selected person will have scientific autonomy, contribute to publications and conference presentations, and may co-supervise master’s students or interns.
Eligibility highlights: PhD or equivalent in Microbiology, Genomics, Molecular Biology, or a related field; strong practical laboratory experience in molecular biology and NGS library preparation; familiarity with Linux/Unix, Bash, SLURM, R, and microbiome/shotgun metagenomic tools. Experience with low-biomass samples, microbiome analysis, and environmental health topics will be especially valued. Very good English or French is required.
Funding: Funding has already been secured for this fixed-term 12-month contract.
Application deadline: 31 December 2026, 23:59 (Europe/Paris).
How to apply: Send a detailed CV, cover letter, and optional academic references by email to Dr. Chervin Hassel at [email protected].
Funding details
Available
What's required
PhD or equivalent in Microbiology, Genomics, Molecular Biology, or a related field. Required: solid hands-on experience in molecular biology techniques including DNA/RNA extraction, PCR/qPCR, NGS library preparation (ideally shotgun), and Illumina sequencer operation; strong attention to sample traceability, management, and good laboratory practice; processing of shotgun metagenomic data; basic Linux/Unix knowledge, Bash shell scripting, and command-line use; ability to use bioinformatics tools and pipelines on an HPC cluster with SLURM; R programming for data manipulation and visualization; familiarity with common microbiomics tools. Particularly valued: experience with low microbial biomass samples, microbiome or shotgun metagenomic analyses, and interest in environmental health, dysbiosis, or the exposome. Very good English or French is required.
How to apply
Prepare a detailed CV and a cover letter. Include contact information for two academic references if available. Send the application by email to Dr. Chervin Hassel at [email protected].
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