Curriculum Vitae

October 21th, 2021. Pierre-Edouard GUERIN

Computational Biologist

FLORIMOND DESPREZ GROUP

Contact

Mail: pierre.edouard.guerin [at] gmail.com
Phone: (+33) 04 67 61 32 35

Experience

Computational biologist

FLORIMOND DESPREZ Research Unit Applied Genetics and Biometry, Cappelle-en-Pevele

I bring my skills and support to the field crops selection department by improving or designing methods to process omics data.

python R C++ rust Singularity Docker SLURM Nextflow Jupyter notebook

Software Development engineer (Bioinformatics)

CNRS Research Unit 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 Jupyter notebook

Bioinformatics engineer internship

INSERM Research Unit 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 Research Unit 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

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

Publications

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Virginie Marques, Paul Castagne, Andréa Polanco Fernandez, Giomar Helena Borrero-Perez, Regis Hocde, Pierre-Edouard Guerin, Jean-Baptiste Juhel, Laure Velez, Nicolas Loiseau, Tom Bech Letessier, Sandra Bessudo, Alice Valentini, Tony Dejean, David Mouillot, Loïc Pellissier, Sébastien Villéger

Conservation Biology. 2021 July 18. DOI: 10.1111/cobi.13802

Restricted dispersal in a sea of gene flow

Laura Benestan, Nicolas Loiseau, Pierre-Edouard Guerin, Katarina Fietz, Elena Trofimenko, Siren Rühs, Willi Rath, Arne Biastoch, Angel Perez-Ruzafa, Pilar Baixauli, Aitor Forcada, Philippe Lenfant, Sandra Mallol, Rachel Goni, Laure Velez, Marc Höppner, Stuart Kininmonth, David Mouillot, Oscar Puebla, Stephanie Manel

Proceedings of the Royal Society B. 2021 May 18. DOI: 10.1098/rspb.2021.0458

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 17. 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 Trofimenko, 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

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.

Personnal projects

speckyman: a platform game developed in JavaScript
fromdnatomusic: convert DNA sequences into MIDI track and listen to it
Nos data ont du talent: a youtube channel dedicated to data visualisation

Triathlon

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