Bioinformatician – Single-Cell Omics in Vascular & Skeletal Muscle Biology

The Laboratory of Exercise and Health at the Department of Health Sciences and Technology (D-HEST), ETH Zurich, is offering a fixed-term position for a bioinformatician (postdoctoral level) to lead single-cell and spatial transcriptomics analyses. The lab investigates how the muscle microvascular niche, particularly specialized endothelial cell subpopulations, interacts with other niche cells to maintain skeletal muscle homeostasis and how disruptions contribute to muscle dysfunction. The research combines human patient samples, mouse genetic models, single-cell and spatial transcriptomics, and in vivo cell-cell interaction tracing with CRISPR perturbation to dissect EC-niche communication. The lab provides a collaborative, international research environment at the interface of vascular biology, muscle physiology, and metabolism.

• Lead all single-cell and spatial transcriptomics work in the laboratory.
• Design, execute, and interpret scRNAseq analyses of human and mouse skeletal muscle samples, identifying and annotating cell subpopulations.
• Discuss and design follow-up wet lab experiments with colleagues.
• Integrate scRNAseq datasets with other omics data, including spatial transcriptomics, ATAC sequencing, metabolomics, and/or multiplex imaging data.
• Perform cross-species (human–mouse) data integration to identify conserved and divergent cellular and molecular signatures of PAD.
• Apply and further develop computational tools for cell-cell communication analysis and constraint-based metabolic modeling tools (e.g. COMPASS, scFEA) to link transcriptional states to cell metabolism.
• Analyze single-cell datasets from in vivo cell-cell interaction tracing models.
• Perform pseudobulk and differential expression analyses (e.g. edgeR) of scRNAseq/5’ECCITE-seq data from CRISPR perturbation screens.
• Apply in silico perturbation approaches to nominate candidate regulators of cellular crosstalk for downstream functional validation.
• Build, document, and maintain reproducible bioinformatics pipelines, and support other lab members with transcriptomics and genomics data.
• Design Shiny apps for data visualization for internal and possibly external use in publications.
• Contribute to manuscript preparation, data visualization, and project reporting, and stay current with emerging single-cell and spatial genomics methods.