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yersim/README.md

Hi there, welcome on my GitHub

I'm Simon, a computational microbiologist and bioinformatician currently based in Lausanne, Switzerland working in the group of Prof. Pascale Vonaesch. I hold a PhD in Life Science from the University of Lausanne. I analyse metagenomic, 16S and whole-genome sequencing data from large paediatric cohorts, mainly on gut microbiome and children undernutrition.

What I work with

  • Languages and tools: R, Bash (advanced); Python, Snakemake, C++ (basic)
  • Methods: shotgun metagenomics, strain tracking, AMR gene profiling, 16S amplicon analysis, differential abundance, regression modelling
  • Environment: HPC clusters, conda, Git/GitHub

Selected work

  • Satellite_project: code for our Gut Microbes (2026) paper on strain-level translocation of oral bacteria in stunted children
  • Pastobiome: gut microbiota of agropastoral children in Ethiopia (Sci Rep, 2023)
  • Lab pipeline: shotgun metagenomics workflow (VonaeschLabUNIL) - built and maintained reproducible workflows on HPC cluster

Contact

LinkedIn · ORCID · simon.yersin@gmail.com

Looking for

  • Open to postdoc, data analyst and epidemiologist roles in Göteborg, Sweden, summer 2027.

Pinned Loading

  1. Satellite_project Satellite_project Public

    Scripts and code used for the Satellite project

    Shell

  2. VonaeschLabUNIL/Afribiota VonaeschLabUNIL/Afribiota Public

    Code related to the Afribiota project and associated publications

    R

  3. Bioinformatic-scripts Bioinformatic-scripts Public

    BioInformatic script for microbiome study

    Shell

  4. Pastobiome Pastobiome Public

    Pastobiome project: the gut microbiota of agro-pastoralist and pastoralist children from the Somali Regional State of Ethiopia.

    Shell