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@article{kyriakopoulosAComprehensiveApproachFor2022,
 author = {Charalampos Kyriakopoulos and Karl Nordström and Paula Linh Kramer and Judith Yumiko Gottfreund and Abdulrahman Salhab and Julia Arand and Fabian Müller and Ferdinand von Meyenn and Gabriella Ficz and Wolf Reik and Verena Wolf and Jörn Walter and Pascal Giehr},
 doi = {10.1016/j.crmeth.2022.100187},
 journal = {Cell Reports Methods},
 month = {3},
 number = {3},
 pages = {1-23},
 publisher = {Cell Press},
 title = {A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes},
 volume = {2},
 year = {2022}
}

@inproceedings{kyriakopoulosAHybridHMMApproach2019,
 address = {Cham},
 author = {Kyriakopoulos, Charalampos and Giehr, Pascal and Lück, Alexander and Walter, Jörn and Wolf, Verena},
 booktitle = {Hybrid Systems Biology},
 editor = {Češka, Milan and Paoletti, Nicola},
 isbn = {978-3-030-28042-0},
 pages = {117--131},
 publisher = {Springer International Publishing},
 title = {A Hybrid HMM Approach for the Dynamics of DNA Methylation},
 year = {2019}
}

@article{giehrTwoAreBetterThan2018,
 author = {Pascal Giehr and Charalampos Kyriakopoulos and Konstantin Lepikhov and Stefan Wallner and Verena Wolf and Jörn Walter},
 doi = {10.1093/nar/gky422},
 journal = {Nucleic Acids Research},
 month = {6},
 number = {15},
 pages = {1-10},
 publisher = {Oxford University Press},
 title = {Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing},
 volume = {46},
 year = {2018}
}

@article{kyriakopoulosLumpingOfDegreeBasedMeanField2018,
$ of the network, which is much smaller than the size of the master equation of the underlying stochastic model, yet numerically solving these equations can still be problematic for large $k_{\max}$. In this paper, we consider AME and PA, extended to cope with multiple local states, and we provide an aggregation procedure that clusters together nodes having similar degrees, treating those in the same cluster as indistinguishable, thus reducing the number of equations while preserving an accurate description of global observables of interest. We also provide an automatic way to build such equations and to identify a small number of degree clusters that give accurate results. The method is tested on several case studies, where it shows a high level of compression and a reduction of computational time of several orders of magnitude for large networks, with minimal loss in accuracy},
 author = {Kyriakopoulos, Charalampos and Grossmann, Gerrit and Wolf, Verena and Bortolussi, Luca},
 doi = {10.1103/PhysRevE.97.012301},
 issue = {1},
 journal = {Phys. Rev. E},
 month = {Jan},
 numpages = {15},
 pages = {012301},
 publisher = {American Physical Society},
 title = {Lumping of degree-based mean-field and pair-approximation equations for multistate contact processes},
 url = {https://link.aps.org/doi/10.1103/PhysRevE.97.012301},
 volume = {97},
 year = {2018}
}

@inproceedings{grossmannLumpingTheApproximateMaster2018,
 address = {Cham},
 author = {Großmann, Gerrit and Kyriakopoulos, Charalampos and Bortolussi, Luca and Wolf, Verena},
 booktitle = {Quantitative Evaluation of Systems},
 editor = {McIver, Annabelle and Horvath, Andras},
 isbn = {978-3-319-99154-2},
 pages = {157--172},
 publisher = {Springer International Publishing},
 title = {Lumping the Approximate Master Equation for Multistate Processes on Complex Networks},
 year = {2018}
}

@article{kyriakopoulosHOTAEstimationOfDNA2017,
 author = {Kyriakopoulos, Charalampos and Giehr, Pascal and Wolf, Verena},
 doi = {10.1093/bioinformatics/btx042},
 eprint = {https://academic.oup.com/bioinformatics/article-pdf/33/11/1733/49039968/bioinformatics_33_11_1733.pdf},
 issn = {1367-4803},
 journal = {Bioinformatics},
 month = {06},
 number = {11},
 pages = {1733-1734},
 title = {H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data},
 url = {https://doi.org/10.1093/bioinformatics/btx042},
 volume = {33},
 year = {2017}
}

@article{giehrTheInfluenceOfHydroxylation2016,
 author = {Pascal Giehr and Charalampos Kyriakopoulos and Gabriella Ficz and Verena Wolf and Jörn Walter},
 doi = {10.1371/journal.pcbi.1004905},
 journal = {PLOS Computational Biology},
 month = {5},
 number = {5},
 pages = {1-16},
 publisher = {Public Library of Science},
 title = {The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach},
 volume = {12},
 year = {2016}
}

@article{eckersleymaslinMERVLZscan4NetworkActivationResults2016,
 author = {Mélanie A. Eckersley-Maslin and Valentine Svensson and Christel Krueger and Thomas M. Stubbs and Pascal Giehr and Felix Krueger and Ricardo J. Miragaia and Charalampos Kyriakopoulos and Rebecca V. Berrens and Inês Milagre and Jörn Walter and Sarah A. Teichmann and Wolf Reik},
 doi = {10.1016/j.celrep.2016.08.087},
 issn = {2211-1247},
 journal = {Cell Reports},
 number = {1},
 pages = {179-192},
 title = {MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs},
 url = {https://www.sciencedirect.com/science/article/pii/S2211124716311962},
 volume = {17},
 year = {2016}
}