2016: Master's degree of Bioinformatics, Université Paris Diderot Paris 7, France
- Landscape genomics approach to assess genetic populations of mediteranean fishes for the european mission RESERVEBENEFIT
- Program to process metabarcoding marine eDNA data for the world oceanographic mission of Monaco
- Genome assembly
- Human genomes DNA high throughput sequencing data analysis
- Program to detect and annotate rare genetic variants
- Graphical interface
- Dynamics of Structures and Interactions of Macromolecules in Biology Paris, FR
- 3D-modelisation of protein structure at atomic resolution
- Optimization of a method of fold recognition in protein structure
- New algorithm to predict protein structure
One of the most promising genetic techniques for improving biodiversity assessments is the metabarcoding of environmental DNA. I did a state of the Art of available methods and developed serveral workflows to process and manage metabarcoding data from the Monaco Marine Scientific Exploration.
Overview: the necessity to assess marine biodiversity
Marine environments, both coastal and offshore, are being severely impacted by traditional and emerging human activities. This is translated into habitat losses, pollution and overexploitation which treats marine >biodiversity. It compromises the sustainability of marine ecosystems and services.
As a response to the environmental degradation, initiatives aims to protect marine ecosystems. Development of reliable marine biodiversity assessment methods is necessary. One of the most promising genetic techniques for >improving biodiversity assessments is the metabarcoding of environmental DNA.
What is Metabarcoding
Indeed, all organisms shed cells containing DNA in their environment, as intra or extra-cellular material for up to a few days. The amplification and high-throughput eDNA sequencing followed by bioinformatic analyses >produces a list of sequences with the ultimate goal to assess species diversity in a given site.
Assess marine biodiversity all over the world with metabarcoding
eDNA samples were collected by Monaco Scientific Exploration Yersin in Guadeloupe, Lengguru, Malpelo Fakarava and Mediteranean sea. Sequencing were performed by SPYGEN company and I was in charge of the bioinformatics processing of sequencing data.
My contribution as a computational biologist
I did a state of the Art of available methods and developed serveral workflows to process metabarcoding data in order to assess marine biodiversity all over the world. Source codes are available as git repositories on the Montpellier server dedicated to eDNA analysis.
Genotyping by sequencing
02.2017 - current
Overview: the necessity to produce whole genome sequence
What is a genome ?
Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of As, Cs, Gs, and Ts that make up an organism's DNA. For instance, the human genome is made up of over 3 billion of these genetic letters.
Sequencing the genome
New genomes available for three species of mediterranean fishes
Global determinants of freshwater and marine fish genetic diversity
Predicting genotype environmental range from genome–environment associations
- Genbar2: identify genetic boundaries between populations using individual spatial coordinates and genetic variants
- DEMORT: a DEmultiplexing MOnitoring Report Tool
- EXAM: a whole exome sequencing analysis and its graphical interface
- COAT: a COverage Analysis Tool for exome sequencing data
- ORION: a sensivitve method for protein template detection
- New genomic ressources for three exploited Mediterranean fishes (submitted to Molecular Ecology Ressources in november 2019)
- Global determinants of freshwater and marine fish genetic diversity (submitted to Nature Communications in februrary 2019)
- Predicting genotype environmental range from genome–environment associations (Molecular Ecology in may 2018)
- ORION : a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles (Scientific Reports in june 1016)
- My scientific blog
- Member of the association of Young French Bioinformaticians Jebif
- Author on french bioinformatics participative blog bioinfo-fr
- fromdnatomusic: convert DNA sequences into MIDI track and listen to it
- Nos data ont du talent: a youtube channel dedicated to data visualisation
I'm an active member of the USN-MONTPELLIER sportive club since 2017. Join us !