Curriculum Vitae




Contact

Experience

Software Development engineer (Bioinformatics)

CNRS UMR 5175, Center of Functional Ecology and Evolution, Montpellier

I develop softwares for the analysis and visualization of data from high-throughput DNA sequencing (genomics, metagenomics, environmental DNA). I also ensure technology watch to implement new data processing methods and optimize scientific reproducibility.

python R C++ Singularity Docker SGE SLURM Snakemake Nextflow Jupyter notebook

Bioinformatics engineer internship

INSERM UMR S598, Genetics of Diabetes, Paris

I developed and integrated a functionnality and its graphical interface to a medical software. It aims to detect and annotate rare genetic variants related to diabetes on human genome sequence data.

python Qt mySQL Docker

Bioinformatics engineer internship

INSERM UMR S1134, Dynamics of Structures and Interactions of Macromolecules in Biology, Paris

Implementation of an algorithm to predict 3D-modelisation of protein structure at atomic resolution.

C C++ postgreSQL HTML CSS Javascript

Education


Projects

Genbar 2
I programmed a software to identify genetic boundaries between populations from individual spatial coordinates and genetic variants data.
(C, C++, htslib)

From may 2019 to february 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)

From january 2019 to present WIP
Benchmarking of metabarcoding workflows
I did a modularized workflow in order to process metabarcoding data with different combination of softwares. Then we designed the workflow with the best performances.
(obitools, vsearch, cutadapt, bash, python, singularity, Univa Grid Engine)

From march 2018 to present WIP
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)

From june 2017 to october 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)

From may 2017 to 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)

From may 2017 to february 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)

From february 2017 to march 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)

From january 2017 to novembrer 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)

From january 2016 to july 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 )

From february 2015 to june 2015

Softwares


Publications

Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification

Laetitia Mathon, Alice Valentini, Pierre-Edouard Guerin, Eric Normandeau, Cyril Noel, Clément Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stephanie Manel

Molecular Ecology Resources. 2021 May 18. DOI 10.1111/1755-0998.13430

Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences

Virginie Marques, Pierre‐Edouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, David Mouillot, Tony Dejean

Ecography. 2020 Aug 04. DOI: 10.1111/ecog.05049

New genomic ressources for three exploited Mediterranean fishes

Katharina Fietz, Elena Trofimenkoa, Pierre-Edouard Guerin, Veronique Arnal, Montserrat Torres-Oliva, Stephane Lobreaux,Angel Perez-Ruzafa, Stephanie Manel, Oscar Puebla

Genomics. 2020 July 03. DOI: 10.1016/j.ygeno.2020.06.041

Global determinants of freshwater and marine fish genetic diversity

Stephanie Manel, Pierre-Edouard Guerin, David Mouillot, Simon Blanchet, Laure Velez, Camille Albouy & Loic Pellissier

Nature communications. 2020 Feb 10. DOI: 10.1038/s41467-020-14409-7

Predicting genotype environmental range from genome–environment associations

Stephanie Manel, Marco Andrello, Karine Henry, Daphne Verdelet, Aude Darracq, Pierre‐Edouard Guerin, Bruno Desprez, Pierre Devaux

Molecular Ecology. 2018 May 17. DOI: 10.1111/mec.14723

ORION : a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

Yassine Ghouzam, Guillaume Postic, Pierre-Edouard Guerin, Alexandre G. de Brevern & Jean-Christophe Gelly

Scientific Reports. 2016 Jun 20. DOI: 10.1038/srep28268


Other activities

Sciences

Personnal projects

Triathlon

I'm an active member of the USN-MONTPELLIER sportive club since 2017. Join us !