Jean Monlong
Permanent Researcher CRCN at IRSD Institut de Recherche en Santé Digestive
Toulouse, Occitania, France
Summary
🤩
Rockstar🎓
Top SchoolJean Monlong is a computational genomics researcher and software engineer with 11 years of experience, currently a permanent CRCN researcher at IRSD in Toulouse. He develops and maintains bioinformatics workflows and back-end tools for variation and genome graph analysis, contributing to notable open-source projects such as the Cactus genome aligner. With a PhD in Bioinformatics and postdoctoral experience at UC Santa Cruz, he combines rigorous statistical training and applied software engineering to optimize variant-calling pipelines (BWA, DeepVariant) and data-analysis tooling. His background spans algorithmic graph models for genomes and practical WDL workflow engineering, reflecting a blend of theoretical insight and reproducible pipeline development. An often-overlooked strength is his cross-disciplinary track record—from Bayesian cancer screening models to production-grade genomics workflows—bridging clinical questions and scalable computational solutions.
11 years of coding experience
5 years of employment as a software developer
Engineer Diploma, Bioinformatique, Engineer Diploma, Bioinformatique at Ecole Nationale Supérieure d'Informatique et de Mathématiques Appliquées de Grenoble / ENSIMAGHigh School, Scientific; Mathematics, High School, Scientific; Mathematics at Lycéè de NavarreDoctor of Philosophy (PhD), Bioinformatics, Doctor of Philosophy (PhD), Bioinformatics at McGill UniversityUPC Universitat Politècnica de CatalunyaPrépa, Mathématiques, Physique, Prépa, Mathématiques, Physique at Lycée Michel-Montaigne
English, French, Spanish
Github Skills (7)
bioinformatics10
work-flow10
workflow-engine10
wdl10
variants9
r8
python8
Programming languages (14)
Github contributions (5)
ComparativeGenomicsToolkit/cactus
Oct 2022 - Oct 2022
Official home of genome aligner based upon notion of Cactus graphs
Role in this project:
Back-end Developer
Back-end DeveloperContributions:8 commits, 3 PRs, 4 comments in 1 month
Contributions summary:Jean primarily contributed to the development and maintenance of a workflow written in WDL (Workflow Description Language) for genomic analysis, specifically for BWA and DeepVariant variant calling. Their contributions involved modifying an existing WDL workflow, incorporating different indexing files, and adjusting parameters for mapping and variant calling processes. The user also made changes related to the analysis of genomic data, including scripts for plotting and analyzing genomic data. This indicates a focus on bioinformatics workflows and data processing.
genomenotioncactusalignergenomics
jmonlong/docker-vg
Jun 2020 - Jul 2024
Contributions:1 release, 2 pushes, 1 branch in 4 years 2 months
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