M. Damien COURTINE
Ingénieur biologiste en traitement de données (Bio-informaticien)Coordonnées
Activités / CV
The complete list of publications in which I have taken part is available in the open archive HAL.
- Education
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- PhD, Microbiology, Université de Bretagne Occidentale, Brest, France, 2017. Comparative genomics of closely related Thermococcus isolates, a genus of hyperthermophilic Archaea
- MSc Bio-informatics, Université Blaise Pascal, Clermont-Ferrand, France, 2014
- BSc Biology, Université Blaise Pascal, Clermont-Ferrand, France, 2012
- Technical diploma (DUT), Biology laboratory technician, Université d’Auvergne, Clermont-Ferrand, France, 2011
- Work experiences
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- Staff scientist - Bioinformatician, Laboratoire Microorganismes : Génome et Environnement, Clermont-Ferrand, Dec. 2021 – now
Analysis of high-throughput sequencing data from microbial communities; Development of genome analysis tools; support technique en lien avec les méthodes de séquençage.
Permanent position. - Post-doctoral fellow, Centre d’Immunologie de Marseille-Luminy, Marseille, France, 2019 – 2021
Local and global analysis of a parasite's genome towaqrd a better understanding of its virulence; Data analysis of long-read sequencing from the Oxford Nanopore technology - PhD thesis, Laboratoire de Microbiologie des Environnements Extrêmes (ex BEEP), Brest, France, 2014 – 2017
Microbial ecology and adaptations to environments by bio-informatics approaches
- Staff scientist - Bioinformatician, Laboratoire Microorganismes : Génome et Environnement, Clermont-Ferrand, Dec. 2021 – now
- Skills
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Bio-informatics
- Genome assembly and annotation
- Comparative genomics, pan-genome analysis
- Meta-genomics, meta-barcoding, transcriptomics and meta-transcriptomics
- Phylogeny
IT
- Linux
- Work on server and high-performance cluster (SLURM)
- Version control and tool development with git
- SnakeMake pipeline
- Setup Docker or Singularity containers
- Python, R, BASH
Thèmes de recherche
- MEB team
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I work mainly on lake microorganism communities, using metagenomic, metatranscriptomic and metabarcoding approaches. The project that occupies most of my time aims to identify and document the small eukaryotes, generally unicellular, present in Lake Pavin. To this end, I am using DNA sequencing data. Samples were taken at different times of the year, close to the surface and at 80m depth. The data was assembled to produce environmental genomes (MAGs).
My current activity consists of identifying the MAGs as precisely as possible (taxonomy), studying their presence along the year in the lake, and looking for them in lakes across the globe in order to get an idea of their dispersal.
The current team project, ANR DIAMOND (2025-2029) will generate metabarcoding and metatranscriptomic data and collect associated environmental data. My challenge will be to achieve multiple integration of these data.
- IHP team
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I have various assignments within this team. My initial project focused on developing a tool for identifying small genes in the genomes of microsporidia, an obligate unicellular eukaryotic parasite.
I am also involved in the analysis of RNAseq data, mainly to study the transcriptonal response of a host to a stressor (parasite, insecticide).