What we do

Our group is located at the Friedrich Miescher Institute in Basel. 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.

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Highlights 2017

Differentiating cells need to balance plasticity and restriction of pluripotency. For example, a neural crest progenitor cell in the embryonic head needs to repress neuronal programs to avoid differentiating into a neuron, while keeping the potential to become a cartilage or a bone cell, depending on which part of the head the cell is located in. The molecular basis for this restricted yet plastic developmental potential was not known. In a collaboration with the Rijli-lab studying the epigenomes of developing mouse neural crest cells, we were able to show that the polycomb system and specific histone modifications are keeping key regulatory genes in a poised, reversibly repressed state, which are specifically de-repressed in response to environmental signals and determine the cell's fate. For more information, see Minoux et al., Science, 2017.

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Main publication 2017

  • Minoux M et al. Gene bivalency at Polycomb domains regulates cranial neural crest positional identity. Science 355(6332). pii: eaal2913.
  • Horvathova I et al. The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells. Mol Cell. 2017 Nov; 68(3):615-625
  • Krebs AR et al. Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. Mol Cell. 2017 Aug; 67(3):411-422.


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

Domains of activity:

  • Genes and genomes
  • Core facilities and competence centres
  • DNA Microarrays
  • Epigenetics
  • Functional genomics
  • Gene regulatory network analysis
  • Next generation sequencing
  • Oncology
  • Single-cell biology
  • Software engineering
  • Systems biology
  • Transcriptomics

Domain of application:

  • Medicine and health
  • Basic research