Bioinformatics Research Engineer M/F: population genetics and comparative genomics in nematodes undergoing programmed DNA elimination

Job Description

Missions

We are studying the process of programmed DNA elimination (PDE) in free-living nematodes of the genus Mesorhabditis. In nematodes, PDE involves the systematic destruction of parts of chromosomes from all somatic cells during early embryonic development. As a consequence, adult individuals have two genomes: one complete genome in germline cells, and one reduced and fragmented genome in somatic cells.
We are characterising PDE in Mesorhabditis nematodes using both genomic and functional approaches. Recently, we have discovered that an intriguing motif precisely specifies the locations at which double-strand breaks are induced during PDE, and that this motif is highly constrained at the sequence level (unpublished). While this motif is present in all Mesorhabditis species tested so far, until recently we lacked the phylogenetic resolution to characterise the selective forces operating on the motif, and on the PDE process itself more generally.

We are now generating data to do this, in the form of population genetic data in one specific species of Mesorhabditis, M. belari, and genomes for closely-related species of M. belari. In this context, we are seeking a bioinformatic research engineer to use these data to finely characterise the selective forces (purifying selection, positive selection, drift) operating on the PDE motif in Mesorhabditis, and on other genomic elements we suspect play a role in the process, namely transposable elements.

Key references
- Rey, C. et al. (2023) 'Programmed DNA elimination in Mesorhabditis nematodes', Current Biology, 33(17), pp. 3711-3721.e5. Available at: https://doi.org/10.1016/j.cub.2023.07.058.
- Launay, C. et al. (2026) 'Somatic Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes', eLife, 15. Available at: https://doi.org/10.7554/eLife.111501.1.
- Duharcourt et al. (2026) 'The mechanistic and evolutionary diversity of programmed DNA elimination'. Nat Rev Genet. 2026 Sep 8. doi: https://doi.org/10.1038/s41576-026-01004-7

Activity

You will play a central role in an ambitious project aimed at characterising the selective forces operating on programmed DNA elimination in nematodes.

Your main tasks will be the following:
- Task 1: Assemble the genomes of 10 strains of one species of Mesorhabditis, M. belari, plus a few closely-related species of M. belari, using long-read PacBio HiFi data + Hi-C for scaffolding, and perform quality control on the resulting assemblies.
- Task 2: Annotate the reference genome of M. belari for repetitive elements: transposable elements and satellites. After this, you will perform manual curation for a number of transposable element families of interest.
- Task 3: Perform variant calling against the M. belari reference genome: you will look for both small (SNPs, small insertions/deletions) variants, and larger, structural variants. For the latter, you will then focus on evidence of transposable element mobility for transposable element families of interest.

Your Profil

Skills

Qualifications: A Masters in Bioinformatics is a minimum requirement. Given the breadth of activities, a PhD in Bioinformatics is additionally strongly recommended.

Technical skills. The candidate should be proficient in (italics for the language we will encourage):
- Development of bioinformatic pipelines (Nextflow, Snakemake, or bash)
- Data analysis in R or equivalent
- Development language: Python, C++, Rust or equivalent

Experience. The candidate should demonstrate solid experience in at least two of the below:
- Comparative genomics and molecular evolution
- Population genetics: variant calling, handling of VCF files
- Genome assembly: long-read assembly, scaffolding with Hi-C, decontamination, haplotypic duplication purging, visualisation of Hi-C contact maps
- Annotation of transposable elements
- Gene prediction in assembled genomes (de novo, using RNA-Seq, using proteins)

Your Work Environment

Starting date: January 2027 (flexible)
Duration Two years
Teams The project is coordinated by two principal investigators: Laurent Duret, head of team BPGE at the LBBE (Laboratoire de Biométrie et Biologie Evolutive, Lyon) and Marie Delattre, head of team WORM at the LBMC (Laboratoire de Biologie et Modélisation de la Cellule, Lyon). Websites: BPGE (https://lbbe-web.univ-lyon1.fr/en/bioinformatics-phylogeny-and-evolutionary-genomics-group) , WORM (https://www.ens-lyon.fr/LBMC/equipes/NematodeCell)
Supervisors You will be supervised by Brice Letcher, postdoc in teams BPGE and WORM, and Laurent Duret, head of team BPGE. Your office will be located at the LBBE, on Campus La Doua, Lyon.

Constraints and risks

none

Compensation and benefits

Compensation

between 3 175€ and 4 864€ gross monthly salary based 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

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