Stochastic Modelling of DNA methylation Dynamics


Together with the group of Jörn Walter we develop stochastic models that describe epigenetic modifications of the DNA. We focus on DNA methylation which plays an important role during embryogenesis and is linked to certain diseases. We fit hidden Markov models to (oxidative) hairpin bisulfite sequencing data and analyse active and passive demethylation. A central goal is an improved understanding of the role of the Tet enzymes, their interplay with the chromatin structure and other methylation enzymes.


  • J. Arand, D. Spieler, T. Karius, M. R. Branco, D. Meilinger, A. Meissner, T. Jenuwein, G. Xu, H. Leonhardt, V. Wolf, J. Walter: In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases, PLOS Genetics, 2012.
  • C. Kyriakopoulos, P. Giehr, G. Fisz, V. Wolf, J. Walter: The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: a HMM approach, PLoS Computational Biology, 2016
  • M. A. Eckersley-Maslin, V. Svensson, C. Krüger, T. Stubbs, P. Giehr, F. Krüger, R. Miragaia, C. Kyriakopoulos, R. Berrens, I. Milagre, J. Walter, S. Teichmann, W. Reik: MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs, Cell Reports, 2016
  • C. Kyriakopoulos, P. Giehr, V. Wolf: H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data, Bioinformatics, 2017
  • A. Lück, P. Giehr, J. Walter, V. Wolf: A Stochastic Model for the Formation of Spatial Methylation Patterns, CMSB 2017.
  • P. Giehr, C. Kyriakopoulos, K. Lepikhov, S. Walner, V. Wolf, J. Walter: Two are better than one: HPoxBS – Hairpin oxidative Bisulfite Sequencing, Nucleic Acids Research, 2018
  • C. Kyriakopoulos, P. Giehr, A. Lück, J. Walter, V. Wolf: A Hybrid HMM Approach for the Dynamics of DNA Methylation, HSB 2019
  • C. Kyriakopoulos, P. Giehr, K. Nordström, S. Abdulrahman, F. Müller, F. von Meyenn, G. Ficz, W. Reik, V. Wolf, J. Walter: Genome-wide single-base resolution efficiency profiling reveals modulation of maintenance and de novo methylation by Tet di-oxygenases, under review