Bioinformatician based in Zurich. I build analysis pipelines, data tools, and scientific software — with a research background in functional genomics, chromatin biology, and multi-omics that keeps the biology honest.
Currently at the Functional Genomics Center Zurich (FGCZ).
bulk_rna_explorer — Interactive Shiny app for exploring bulk RNA-seq DESeq2/edgeR results. Dynamic column mapping for any SummarizedExperiment, volcano and PCA plots, click-to-plot expression barplots, PNG/PDF export. testthat suite, GitHub Actions CI on Ubuntu + Windows.
mismap-qc — Python package for visualising missing-data patterns in RNA-Seq and proteomics QC. Hierarchical clustering, multi-level annotations, interactive Plotly export. Published on PyPI, conda-forge submission in review. pytest suite, GitHub Actions CI across Python 3.10–3.13 on Linux and macOS.
Task Tracker — Full-stack productivity app in Flask + HTMX with CSV-backed persistence, workout tracking, Bring! API integration, and a macOS app bundle. 77 passing tests, GitHub Actions CI.
nd2_export — Streaming ND2 → OME-TIFF exporter for microscopy files too large for Fiji/ImageJ. Lazy reading, incremental writing, CLI + GUI, Windows .exe build via PyInstaller.
MSLc_Gene_Priming_public — Reproducible analysis for Foertsch et al., Science Advances (2025) — MSLc-mediated epigenetic priming of neurodevelopmental genes during early neurogenesis. Single-cell multiomics, enhancer-promoter contacts, directed differentiation models. Data deposited at GEO (GSE298000–GSE298010) and Zenodo.
bruenneli — Finds the nearest public drinking fountain in Switzerland and gives walking directions to it. Next.js/TypeScript, build-time data pipeline covering Basel, Zürich, and OpenStreetMap (~15,000 fountains), fully offline-capable PWA, no runtime API. Deliberate design sibling of scooterino.
scooterino — Finds the nearest reachable shared scooter/bike in Basel, Zürich, and the Glattal, ranked by real OSRM walking time (not straight-line) across 9 aggregated GBFS operator feeds. Flask + vanilla JS/CSS, no paid APIs, a weekly GitHub Action that discovers new operator feeds automatically, 67-test pytest suite, GitHub Actions CI. Deliberate design sibling of bruenneli.
Languages: R, Python, Bash
Software engineering: Python packaging (PyPI / conda-forge), pytest, GitHub Actions CI, Flask, HTMX, CLI tools
Bioinformatics: Seurat, DESeq2, edgeR, Signac, MOFA2, clusterProfiler, SnakePipes, deepTools, SAMtools, BEDTools
Data & ML: Pandas, NumPy, SciPy, scikit-learn, XGBoost, SHAP
Visualization: ggplot2, matplotlib, Plotly