Michael Stadler
FMI Computational Biology Group
Friedrich Miescher Institute, Basel
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What do we do?

Our FMI Computational Biology Group is located at the Friedrich Miescher Institute in Basel. We study gene regulation through the analysis and modeling of genome-wide datasets. We collaborate closely with experimental researchers on various biological topics including cancer progression and cellular differentiation. Using statistical approaches, we aim to gain a better understanding on how the different layers of epigenetic, transcriptional and post-transcriptional regulation interact and contribute to the control of gene expression. The great majority of our projects measure various aspects of gene expression including DNA methylation, single cell transcription, protein-binding to DNA, and translation using high-throughput sequencing.

Highlights 2016

In most cells, the DNA is packaged around histone proteins. However, mammalian sperm cells have a highly compacted genome, and during maturation they evict the large majority of their histone proteins from the DNA. Whether the histones that are left carry epigenetic marks and could therefore serve as a carrier for epigenetic information across generations remains an open question. In a re-analysis of published datasets, we were able to clarify former contradicting reports on the subject, which associated retained histones with repeat elements, although open questions still remain in this intriguing research field.
For more information see “Royo et al., Dev Cell, 2016

Main publications 2016

  • Habacher C, Guo Y, Venz R, Kumari P, Neagu A, Gaidatzis D, Harvald EB, Færgeman NJ, Gut H, Ciosk R. Ribonuclease-Mediated Control of Body Fat. Dev Cell. 2016; 39(3):359-369.
  • Miki TS, Carl SH, Stadler MB, Großhans H. XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans. PLoS Genet. 2016; 12(9):e1006313.
  • Eymery A, Liu Z, Ozonov EA, Stadler MB, Peters AH. The methyltransferase Setdb1 is essential for meiosis and mitosis in mouse oocytes and early embryos. Development. 2016; 143(15):2767-79.
  • Royo H, Stadler MB, Peters AH. Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa. Developmental Cell. 2016; 37(1):98-104.
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 (

Our research topics: