Computational biologist at the Functional Genomics Center Zurich (ETH / UZH).
I work on single-cell and spatial transcriptomics — helping labs across ETH and UZH get from raw sequencing data to biology. My day-to-day is split between running analyses for collaborators, writing and maintaining shared infrastructure (B-Fabric, SUSHI, ezRun), and building open-source tools when the existing ones don’t fit.
Before FGCZ I did a postdoc at UNIL on cancer immunology, a stint in industry at Mnemo Therapeutics on CAR-T, and a PhD at Institut Curie on tumor-infiltrating CD8 T cells. I like problems where the computational choices actually change the biological conclusion.
A PyTorch reimplementation of RCTD for deconvolving spatial transcriptomics spots (Visium, Xenium, MERFISH, Slide-seq) into cell-type proportions. Drop-in replacement for the R spacexr package, 4–40× faster on GPU with 99.7% concordance on benchmarks. Works on CPU when a GPU isn’t available.
A curated, opinionated index of the spatial transcriptomics tooling landscape — segmentation, cell-type annotation, deconvolution, differential expression, benchmarks, datasets, foundation models. Started as my own working notes; now community-maintained with regular updates as the field moves.
Reproducible analysis notebooks accompanying my Science Immunology paper on tumor-infiltrating CD8 T cells in non-small-cell lung cancer. End-to-end from count matrices to the figures in the paper.
Läderach F, Piteros I, Fennell É, … Gueguen P, et al.
López-Cobo S, Fuentealba JR, Gueguen P, et al.
Andreatta M, Hérault L, Gueguen P, Carmona SJ, et al.
Andreatta M, Gueguen P, Borcherding N, Carmona SJ.
Timperi E, Gueguen P, et al.
Gueguen P, Metoikidou C, Dupic T, et al.
Gueguen P. Université Paris Cité.
Pace L, Goudot C, Zueva E, Gueguen P, et al.
Single-cell and spatial analysis for collaborators; pipelines and infrastructure on B-Fabric, SUSHI, ezRun.
Cancer immunology; reference maps for human tumor-infiltrating T cells.
Pre-clinical CAR-T analysis — scRNA-seq and TCR repertoire.
Single-cell dissection of CD8 T-cell states in human lung cancer.