Portrait of Pierre-Edouard Guerin Bioinformatician Data Scientist
Pierre-Edouard Guerin

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 breeders in the analysis and interpretation of omics 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

Processed DNA sequence data for population genetics studies of various fish species, enabling marine biologists to assess their conservation status.

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 software 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

Training



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

Other activities