Rémi Denise
Software Development Engineer at PathoQuest
Paris, Ile-de-France
Summary
🤩
Rockstar🎓
Top SchoolRémi Denise is a software development engineer based in Paris with 10 years of experience at the intersection of bioinformatics and software engineering. He holds a PhD in microbial genomics and has led computational projects that detect and reconstruct viral genomes from highly degraded ancient DNA, combining NGS workflows, Snakemake pipelines, and machine learning. His work spans deep comparative genomics, phylogenetics and large-scale metagenomic analyses, producing published discoveries on bacteriophage diversity and contributing to open-source tools like TaxMyPhage and MacSyFinder. Transitioning from academic data science roles at Institut Pasteur, University of Florida and APC Microbiome Ireland to an engineering role at PathoQuest, he brings both research rigor and production-oriented engineering practices. Colleagues value his ability to translate complex biological questions into reproducible, automated pipelines that scale across thousands of genomes. An unobvious asset: he pairs experimental wet-lab insight with software craftsmanship, enabling pragmatic solutions that respect both data provenance and computational efficiency.
10 years of coding experience
9 years of employment as a software developer
Doctor of Philosophy - PhD, Microbiology, Genomic, Phylogeny, Doctor of Philosophy - PhD, Microbiology, Genomic, Phylogeny at Sorbonne UniversitéMaster of Science (MSc), Bioinformatics and Modelisation, Master of Science (MSc), Bioinformatics and Modelisation at Pierre and Marie Curie University
Github Skills (44)
package-management10
conda10
bioinformatics10
apple-silicon9
genomes9
refined9
bioconda9
genomics8
metagenomics8
mamba8
microbiome8
binning8
predict7
self-supervised-learning7
treeview6
Programming languages (6)
Github contributions (5)
rdenise/similarity_hhsearch
Oct 2016 - Jan 2022
Contributions:4 PRs, 10 pushes, 2 branches in 5 years 4 months
rdenise/color_label
May 2016 - Apr 2018
Contributions:2 PRs, 44 pushes, 2 branches in 1 year 10 months
testing
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