What we do

We study gene regulation through the analysis and modelling of genome-wide datasets. We collaborate closely with experimental researchers on various biological topics, including cancer progression, chromatin biology and cellular differentiation, using data from various aspects of gene expression, such as DNA methylation and RNA transcription in single cells, measured by high-throughput sequencing. Our aim is to better understand how the different layers of epigenetic, transcriptional and post-transcriptional regulation interact and contribute to the control of gene expression.

Find out about the Group’s activities

Core facility activities

We help FMI scientists to exploit large data efficiently, depending on their specific needs, through collaboration, a bioinformatics helpdesk and relevant training. We focus on providing solutions based on free and open-source software, allowing the scientists to continue their own bioinformatics research even after leaving the FMI.

Here are some of the key services we provide (also see here):

  • High-throughput data analysis, from experiment design to result interpretation;
  • Training (one-on-one, lectures, workshops);
  • Bioinformatics helpdesk;
  • Software tool development.

Main publication 2021

  • Iurlaro M et al.
    Mammalian SWI/SNF continuously restores local accessibility to chromatin
    Nat Genet, 10.1038/s41588-020-00768-w
  • Kitazawa T et al.
    A unique bipartite Polycomb signature regulates stimulus-response transcription during development
    Nat Genet, 10.1038/s41588-021-00789-z
  • Olivieri D et al.
    Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells
    EMBO J, 10.15252/embj.2020106818

Find out more about the Group’s activities


Epigenesys - European Community-funded Network of Excellence in the fields of epigenetics and systems biology.
MetastasiX - Systems Biology of Breast Cancer, MRD project of the Swiss Initiative for Systems Biology (SystemsX.ch)


University basel

Michael Stadler
FMI Computational Biology Group
Friedrich Miescher Institute, Basel
Group Webpage


Domain(s) of activity:

  • Genes and genomes
  • Systems biology
  • Epigenetics
  • Functional genomics
  • Gene regulation
  • Machine learning
  • Next generation sequencing
  • Single-cell biology
  • Software engineering
  • Transcriptomics

Domain(s) of application:

  • Basic research
  • Medicine and health