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Achievements

Achievement: Public SponsorAchievement: YOLOAchievement: QuickdrawAchievement: Pull Shark

Achievements

Achievement: Public SponsorAchievement: YOLOAchievement: QuickdrawAchievement: Pull Shark

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clbenoit/README.md

Hi there! 👋

🎯 What I Do

🤝 Building bridges between biology, software engineering, data engineering and data science.

🔬 Transforming complex biological data into reliable, accessible and reproducible solutions.

⚙️ Designing and operating computational tools used daily by clinicians and biologists across clinical workflows.

I contribute to projects involving:

  • 🧬 Clinical genomics & rare diseases
  • 🧫 Oncology and molecular diagnostics
  • 🦠 Infectious diseases and pathogen analysis
  • 📊 Multi-omics data processing and interpretation

🛠️ How I Do It

🧬 Bioinformatics & Data Engineering

  • Designing and maintaining production-grade bioinformatics pipelines
  • Developing reproducible workflows for large-scale biological data processing
  • Building ETL pipelines and data systems for biomedical applications
  • Automating analysis workflows to improve reliability and scalability
  • Transforming complex biological datasets into actionable insights

💻 Scientific Software Development

  • Designing interactive web applications for researchers, clinicians and platform users
  • Building user-friendly tools that enable non-technical users to explore and analyze complex biological data
  • Developing reliable interfaces and workflows around genomic and multi-omics analyses
  • Deploying scientific applications in production environments

🤖 AI & Automation

  • Designing AI-assisted workflows for scientific and technical applications
  • Developing and integrating LLM-based tools into real-world workflows
  • Building and deploying agentic systems and automation frameworks
  • Evaluating modern AI architectures for productivity and scientific applications

🧪 Personal Infrastructure & Experimentation

  • Maintaining a self-hosted AI/DevOps environment (Debian servers, GPU-accelerated, Docker-based) to experiment with agentic systems, model deployment, and infrastructure automation.

🌱 About Me

Outside of coding: 🛹 skateboarding · 🌿 taking care of plants · 🏔️ exploring the Alps around Grenoble

🔗 Links

Popular repositories Loading

  1. filt3r.shiny filt3r.shiny Public

    R Shiny app encapsulating FilLT3r tool : https://doi.org/10.1186/s12859-022-04983-6

    R 1

  2. CutOneStrand CutOneStrand Public

    This tool is designed to scan all positions on a gene than can be used to specifically cut one DNA strand using a given cas9.

    Shell 1

  3. GermlineVarDBTools GermlineVarDBTools Public

    An R package containing a tool suite to manage a local structured database for germline genomic variants. The resulting database can be then consulted and annotated with https://github.com/clbenoit…

    R 1

  4. GermlineVarDB GermlineVarDB Public

    R Shiny app for germline genomic variants interpretation. The tool suite to deal with the underlying local structured database is provided here : https://github.com/clbenoit/GermlineVarDBTools

    R

  5. SomaVarDB SomaVarDB Public

    R Shiny app for somatic genomic variants interpretation. The tool suite to deal with the underlying local structured database is provided here : https://github.com/clbenoit/SomaVarDBTools

    R

  6. portfolio portfolio Public

    https://clbenoit.github.io/portfolio/

    TypeScript