{"title":"Pierre-Edouard Guerin","subtitle":"Bioinformatician","link":[{"@attributes":{"rel":"self","type":"application\/atom+xml","href":"https:\/\/guerinpe.com\/atom.xml"}},{"@attributes":{"rel":"alternate","type":"text\/html","href":"https:\/\/guerinpe.com"}}],"generator":"Zola","updated":"2025-10-07T00:00:00+00:00","id":"https:\/\/guerinpe.com\/atom.xml","entry":[{"title":"Research Tax Credit","published":"2025-10-07T00:00:00+00:00","updated":"2025-10-07T00:00:00+00:00","author":{"name":"\n \n Unknown\n \n "},"link":{"@attributes":{"rel":"alternate","type":"text\/html","href":"https:\/\/guerinpe.com\/articles\/research-tax-credit\/"}},"id":"https:\/\/guerinpe.com\/articles\/research-tax-credit\/","summary":"

The Research Activities Tax Credit<\/strong> is a tax credit that incentivizes private companies to increase their Research and Development (R&D). Within my company, I have been tasked with writing the Research Tax Credit (CIR) justification report<\/strong> for France. Here, the method for writing such a report.<\/p>"},{"title":"Turing Complete: From Logical Gates to CPU Architecture","published":"2025-09-17T00:00:00+00:00","updated":"2025-09-17T00:00:00+00:00","author":{"name":"\n \n Unknown\n \n "},"link":{"@attributes":{"rel":"alternate","type":"text\/html","href":"https:\/\/guerinpe.com\/articles\/turing-complete-from-logical-gates-to-cpu-architecture\/"}},"id":"https:\/\/guerinpe.com\/articles\/turing-complete-from-logical-gates-to-cpu-architecture\/","summary":"

In 2021, LevelHead published Turing Complete<\/a>, a game about computer science. My friend Christophe Georgescu<\/strong> recommended me to play it. Unfortunately, I took his advice and now I can not stop to play this game! The game challenges you to design an entire computer from scratch. You start with basic logic gates, then move on to components, memory, CPU architecture, and finally assembly programming. By the way, the game is neat and present all these concepts in a playful and intuitive way.<\/p>"},{"title":"Portfolio","published":"2025-08-12T00:00:00+00:00","updated":"2025-08-12T00:00:00+00:00","author":{"name":"\n \n Unknown\n \n "},"link":{"@attributes":{"rel":"alternate","type":"text\/html","href":"https:\/\/guerinpe.com\/portfolio\/"}},"id":"https:\/\/guerinpe.com\/portfolio\/","content":"

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\n\n
Genbar 2 <\/div>\n
I programmed a software to identify genetic boundaries between populations from individual spatial coordinates and genetic variants data.<\/div>\n
(C, C++, htslib)<\/div>\n
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May 2019 - Feb 2020 <\/div>\n<\/div>\n
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Metabarcoding<\/div>\n
I programmed several workflow to process metabarcoding environmental DNA data from MONACO MARINE WORLDWIDE EXPEDITION.<\/div>\n
(obitools, vsearch, swarm, cutadapt, bash, python, singularity, snakemake)<\/div>\n
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Jan 2019 - Jul 2021<\/div>\n<\/div>\n
\n\n
Benchmarking of metabarcoding workflows<\/div>\n
We tested some combinations of softwares to improve performances of metabarcoding data processing.<\/div>\n
(obitools, vsearch, qiime, python, singularity, Univa Grid Engine)<\/div>\n
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Mar 2018 - Jul 2021<\/div>\n<\/div>\n
\n\n
Population genomics<\/div>\n
I genotyped 1200 individuals belonging to 3 fish species. I worked with restriction enzyme-based data such as RAD-seq.<\/div>\n
(illumina paired-end, STACKS, vcftools, bedtools, bwa, python, snakemake, singularity, Univa Grid Engine, bash)<\/div>\n
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Jun 2017 - Oct 2019 <\/div>\n<\/div>\n
\n\n
Beets genome metrics<\/div>\n
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.<\/div>\n
(R, python, genpop)<\/div>\n
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May 2017 - May 2018 <\/div>\n<\/div>\n
\n\n
First Global Map of Fish Genetic Diversity<\/div>\n
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.<\/div>\n
(julia, python, R, singularity, MUSCLE, UGENE, geonames, BOLD, shiny)<\/div>\n
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May 2017 - Feb 2020 <\/div>\n<\/div>\n
\n\n
Landscape genomics<\/div>\n
I processed low-coverage RAD-seq data from 1800 individuals belonging to 2 fish species collected from all over the Mediterranean sea.<\/div>\n
(dDocent, freebayes, vcftools, samtools, trimmomatic, bash, python, singularity, snakemake)<\/div>\n
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Feb 2017 - Mar 2021 <\/div>\n<\/div>\n
\n\n
Genome assembly<\/div>\n
I did the sequencing and assembly of 3 new fish species nuclear and mitochondrial genomes.<\/div>\n
(illumina paired-end, mate-pair, 10X genomics chromium, Abyss, Platanus, QUAST, SLURM, bash)<\/div>\n
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Jan 2017 - Nov 2019 <\/div>\n<\/div>\n
\n\n
Report bad quality region of coding sequences from genome sequencing data<\/div>\n
I developped a software able to detect human genomic variations with low coverage. Graphical Interface. <\/div>\n
(Illumina paired-end, samtools, bedtools, variation annotation, python, mySQL, qt4)<\/div>\n
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Jan 2016 - Jul 2016 <\/div>\n<\/div>\n
\n\n
Optimization of a method of fold recognition in protein structure<\/div>\n
I added a new algorithm to predict 3D-modelisation of protein structure at atomic resolution <\/div>\n
(PDB, pymol, C, C++, python, R, html, css )<\/div>\n
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Feb 2015 - Jun 2015 <\/div>\n<\/div>\n<\/div>\n"},{"title":"Activity","published":"2025-06-25T00:00:00+00:00","updated":"2025-06-25T00:00:00+00:00","author":{"name":"\n \n Unknown\n \n "},"link":{"@attributes":{"rel":"alternate","type":"text\/html","href":"https:\/\/guerinpe.com\/activity\/"}},"id":"https:\/\/guerinpe.com\/activity\/","content":"

Bioinformatics?<\/h2>\n

Using computers and data to answer biological questions. The Bioinformatician collects, analyses, and interprets the large amounts of data generated by life science research or clinical studies through computing.<\/p>\n

It is multidisciplinary, bringing together biologists, computer scientists, mathematicians, statisticians, and physicists. By turning vast raw data into useful information, this approach helps researchers better understand complex systems and diseases, make diagnoses, and develop new medicines.<\/p>\n

Missions<\/h2>\n

In Florimond Desprez Group, the missions of the bioinformatician are the following:<\/p>\n

Implement bioinformatics solution<\/h3>\n