Mots-Clés
Comparative transcriptomic
Comparative genomic
Nematode
Programmed-DNA Elimination
Description
12-months contract for a computational biologist/bioinformatic scientist at LBMC/Lyon
CV, cover letter and references to Marie Delattre (in French or English) to marie.delattre@ens-lyon.fr
http://www.ens-lyon.fr/LBMC/NematodeCell/
The Laboratory of Biology and Modeling of the Cell (LBMC) is a research center on the campus of Ecole Normale
Supérieure in Lyon, France. We are looking for a computational biologist/bioinformatic scientist to apply
comparative transcriptomic and genomic analysis for the study of Programmed-DNA Elimination in animals.
In most eukaryotes, all cells of an organism have an identical genome. However, for a hundred species
(found in insects, nematodes, birds and even mammals), somatic cells are subjected to the systematic elimination
of specific DNA sequences. The process is extensively studied in unicellular ciliates but has been overlooked in
animals. We discovered a group of nematode species which undergo programmed-DNA elimination. In contrast
to the other species described so far, these worms offer many experimental advantages, as well as a small genome
(that we already assembled de novo), to at last elucidate the mechanisms of elimination.
Using genomic data (Illumina, Nanopore, Pacbio and HiC data) we characterized the eliminated
sequences and the nature of the breakpoints. With comparative transcriptomic (RNAseq from multiple tissues and
isolated cells) we started to identify the genes involved in this mechanism. One species has been described so far
(manuscript in preparation) and other species will be analyzed with the same strategy.
Although hosted in a biology wet-lab, the candidate will benefit from the bioinformatic hub of LBMC,
which foster interactions between all bioinformaticians within the institute (http://www.ens-lyon.fr/LBMC/pole-
bioinformatique )
Required qualifications:
• PhD or Master’s degree in bioinformatics, computer/data sciences or related discipline
• The candidate should be able to work both independently and in collaboration with the team members
(for the experimental validation of the results). A good background in biology will be an asset.
• Strong experience in the area of NGS data analyses, with background in comparatives genomics, and
the analysis of large data sets
• Experience with working with various biological databases and bioinformatics tools (e.g. BLAST,
samtools, IGV)
• Knowledge & confident handling of at least one programming/scripting language in the NGS
environment (e.g., R, Python)
• Experience with Linux and writing shell scripts is required
• Experience with workflow languages (ideally Nextflow) is preferred
• Experience working with cloud environments is preferred.