Curriculum Vitae

Experience

July 2021 to present

Bioinformatician

Florimond Desprez Group Research Unit

Cappelle-en-Pévèle, France

Developed and optimised software, workflows, and databases to support plant and molecular breeders in analyzing and interpreting their data.

Python SQL R C++ Docker Nextflow Azure Databricks Elastic Stack

January 2017 to July 2021

Bioinformatician

CNRS Research Unit 5175, Center of Functional Ecology and Evolution

Montpellier, France

Developed and optimised pipelines and tools to help marine biologists analyze and visualize high-throughput sequencing data (genomics, metagenomics, environmental DNA).

Python R C++ Singularity Snakemake Jupyter SGE SLURM

January to August 2016

Bioinformatics Internship

INSERM Unit S598, Genetics of Diabetes

Paris, France

Developed a module and user interface for a medical app to detect and annotate rare variants in human genome sequences related to diabetes.

SQL Python Qt

January to June 2015

Bioinformatics Internship

INSERM Unit S1134, Macromolecular Biology

Paris, France

Optimised an algorithm to predict protein 3D structure at atomic resolution.

C Python

Education

2016: M.Sc. in Bioinformatics, Paris University, France
2014: Licence in Bioinformatics, Paris University, France

Projects

Florimond Desprez Group

My projects for the company are confidentials. Please contact me for more information.

Public research

Genbar 2

I programmed a software to identify genetic boundaries between populations from individual spatial coordinates and genetic variants data.

(C, C++, htslib)

May 2019 - Feb 2020

Metabarcoding

I programmed several workflow to process metabarcoding environmental DNA data from MONACO MARINE WORLDWIDE EXPEDITION.

(obitools, vsearch, swarm, cutadapt, bash, python, singularity, snakemake)

Jan 2019 - Jul 2021

Benchmarking of metabarcoding workflows

We tested some combinations of softwares to improve performances of metabarcoding data processing.

(obitools, vsearch, qiime, python, singularity, Univa Grid Engine)

Mar 2018 - Jul 2021

Population genomics

I genotyped 1200 individuals belonging to 3 fish species. I worked with restriction enzyme-based data such as RAD-seq.

(illumina paired-end, STACKS, vcftools, bedtools, bwa, python, snakemake, singularity, Univa Grid Engine, bash)

Jun 2017 - Oct 2019

Beets genome metrics

I calculated metrics (nucleotide diversity, Tajima's D) on the beets genome from 14,409 random single nucleotide polymorphisms (SNPs) among 299 accessions of cultivated beets.

(R, python, genpop)

May 2017 - May 2018

First Global Map of Fish Genetic Diversity

I built a database containing over 50,000 DNA sequences representing 3,815 species of marine fish and 1,611 species of freshwater fish. I estimated the average genetic diversity at different geographical scales.

(julia, python, R, singularity, MUSCLE, UGENE, geonames, BOLD, shiny)

May 2017 - Feb 2020

Landscape genomics

I processed low-coverage RAD-seq data from 1800 individuals belonging to 2 fish species collected from all over the Mediterranean sea.

(dDocent, freebayes, vcftools, samtools, trimmomatic, bash, python, singularity, snakemake)

Feb 2017 - Mar 2021

Genome assembly

I did the sequencing and assembly of 3 new fish species nuclear and mitochondrial genomes.

(illumina paired-end, mate-pair, 10X genomics chromium, Abyss, Platanus, QUAST, SLURM, bash)

Jan 2017 - Nov 2019

Report bad quality region of coding sequences from genome sequencing data

I developped a software able to detect human genomic variations with low coverage. Graphical Interface.

(Illumina paired-end, samtools, bedtools, variation annotation, python, mySQL, qt4)

Jan 2016 - Jul 2016

Optimization of a method of fold recognition in protein structure

I added a new algorithm to predict 3D-modelisation of protein structure at atomic resolution

(PDB, pymol, C, C++, python, R, html, css )

Feb 2015 - Jun 2015

Softwares

Florimond Desprez Group

My software developed for the company is confidential. Please contact me for more information.

Public research

WFGD (main contributor): interactive worldmap of fish genetic diversity.
ANVAGE (main contributor): ANnotation Variants GEnome is a python toolkit software to perform routine operations such as detecting synonymous genetic variants from VCF, GFF3 and FASTA genome files.
Rgeogendiv (main contributor): R package for downloading, preparing and aligning georeferenced DNA sequences on Genbank to calculate genetic diversity at different geographical scales
Workflow to process environmental DNA sequencing data (main contributor): this workflow is open-source and was co-developped by the CEFE (main invistigator) and the company SPYGEN (data and tests), including interactions IFREMER, ETH Zurich and the marine explorations of Monaco.
Workflow to genotype reduced genome sequencing data (main contributor): this workflow processed over 3000 fish genomes in the context of the european project RESERVEBENEFIT in collaboration with Helmholtz-Zentrum für Ozeanforschung Kiel and Instituto Español de Oceanografía.
Genbar2 (main contributor): identify genetic boundaries between populations using individual spatial coordinates and genetic variants.
DEMORT (main contributor): a DEmultiplexing MOnitoring Report Tool
EXAM(contributor): a whole exome sequencing analysis and its graphical interface
ORION (contributor): a sensivitive method for protein template detection

Other activities

My scientific blog
Member of the association of Young French Bioinformaticians Jebif
Author on french bioinformatics participative blog bioinfo-fr
My data science skills demo (linear regression, random forest, neural network, bayesian, deep learning) using python ecosystem for machine learning (pandas, numpy, tensorflow, scikit-learn) training on kaggle.