Denis Puthier
Professor In Genomics And Bioinformatics
Marseille, Provence-Alpes-Côte d'Azur, France
Summary
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Rockstar🎓
Top SchoolDenis Puthier is a Full Professor in Genomics and Bioinformatics at Aix-Marseille Université with over 11 years of experience leading research and training in transcriptomics, epigenomics, spatial transcriptomics and non-coding RNA biology. He co-heads the TGML sequencing platform and serves as Deputy Director for Education at the MarMaRa Institute, combining hands-on sequencing operations with academic leadership. Denis develops practical bioinformatics tools—most notably the Python GTF toolkit (pygtftk) and the Scigenex R package—for reproducible functional annotation and single-cell/spatial analyses, reflecting his emphasis on usable software for genomics. Trained from bench to computation (PhD and postdoc in molecular biology/immunology, HDR in transcriptome bioinformatics), he blends wet-lab insight with engineering of workflows (Snakemake, Nextflow, Galaxy) and teaches a broad range of programming and statistical methods. An underappreciated strength is his focus on quality management in core facilities (ISO-certified TGML), ensuring that large-scale sequencing projects meet rigorous standards.
11 years of coding experience
18 years of employment as a software developer
Postdoc, Molecular biology, Immunology, Bioinformatics, Postdoc, Molecular biology, Immunology, Bioinformatics at TAGC/INSERM U928Habilitation à diriger des recherches (HDR), Bioinformtics and genomics, Titre: Analyse moléculaire et bioinformatique du transcriptome, Habilitation à diriger des recherches (HDR), Bioinformtics and genomics, Titre: Analyse moléculaire et bioinformatique du transcriptome at Aix-Marseille UniversitéPhD, Expression and regulation of the Bcl-2 family proteins in human myeloma cells, PhD, Expression and regulation of the Bcl-2 family proteins in human myeloma cells at EPHE
English
Stackoverflow
774reputation
47kreached
5answers
19questions
Github Skills (89)
package-management10
cds10
gtk10
transcript10
genomics10
par10
bedtools10
minhash10
rna-seq10
pygobject10
bioconda10
r-package10
conda10
tss10
des10
Programming languages (7)
Github contributions (5)
dputhier/libgtftk
Nov 2018 - Feb 2022
gtftk C Library and program
Contributions:1 PR, 1 push, 1 branch in 3 years 3 months
c-library
dputhier/pygtftk
May 2018 - Dec 2022
A python package and a set of shell commands to handle GTF files
Contributions:33 releases, 999 commits, 7 PRs in 4 years 7 months
bedpythonbioinformaticsshelltts
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