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Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: YOLOAchievement: StarstruckAchievement: QuickdrawAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: YOLOAchievement: StarstruckAchievement: QuickdrawAchievement: Arctic Code Vault Contributor

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flowuenne/README.md

Hey, I'm Florian 👋

Senior Bioinformatics Engineer @ Seqera — the company behind Nextflow

I help life sciences and biotech teams get their computational workflows running in the cloud. My work sits at the intersection of pipeline development, cloud infrastructure, and making bioinformatics accessible to scientists who'd rather focus on biology than YAML files.

Previously: cardiovascular genetics research (PhD, Université de Montréal) → spatial omics & multiplexed imaging (postdoc, Institute for Computational Biomedicine, Heidelberg).

🔬 What I work on

  • Nextflow pipelines — building, optimizing, and deploying reproducible bioinformatics workflows at scale
  • Cloud infrastructure — AWS Batch, GCP, Nebius, Kubernetes (including GPU workloads with H100s for protein design)
  • nf-core — contributor & maintainer, creator of nf-core/molkart for multiplexed tissue imaging analysis
  • Computational protein design — nf-proteindesign pipeline (Boltz-2, ProteinMPNN, OpenFold3)
  • AI + Bioinformatics — exploring LLM-powered workflow orchestration, MCP integrations, and agentic tooling for scientific computing

🛠️ Tech Stack

Workflow & Orchestration

Nextflow Seqera Platform Snakemake

Languages

Python Groovy R Bash

Cloud & Infrastructure

AWS GCP Kubernetes Docker Terraform

AI & ML

Claude PyTorch Hugging Face

Bioinformatics

nf-core Bioconductor Conda Biocontainers

🌍 Languages I speak

🇩🇪 German · 🇬🇧 English · 🇫🇷 French · 🇪🇸 Spanish (learning)

📫 Get in touch

LinkedIn Google Scholar

Pinned Loading

  1. nf-workdir-size nf-workdir-size Public archive

    A nextflow plugin to calculate the size of files in each task work directory

    Groovy

  2. nf-core/molkart nf-core/molkart Public

    A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

    Nextflow 13 11

  3. bioconda_recipepod bioconda_recipepod Public

    Repository containing gitpod configuration for creating and testing bioconda recipes.

    Dockerfile 11

  4. multimodal_CRISPR_CAD multimodal_CRISPR_CAD Public

    This repository contains all the code for the manuscript: "Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells"

    PostScript

  5. FlorianWuennemann_CV FlorianWuennemann_CV Public

    Up to date CV compiled with the R vitae package

    TeX