Peer-Reviewed Publication
PLoS Comput Biol2025;21(8):e1013358.August 1, 2025Journal Article
The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.
Jędrzej Kubica1,2, Sevastianos Korsak1,3, Krzysztof H Banecki1,3, Dvir Schirman4, Anurupa Devi Yadavalli5, Ariana Brenner Clerkin6,7, David Kouřil8, Michał Kadlof3, Ben Busby9, Dariusz Plewczynski1,3
1Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland.
2Univ. Grenoble Alpes, CNRS, UMR, TIMC/ MAGe, Grenoble, France.
3Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
4Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
5Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut, United States of America.
6Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, New York, United States of America.
7Tri-Institutional PhD Program in Computational Biology and Medicine, New York, New York, United States of America.
8Department of Biomedical Informatics, Harvard Medical School, Boston, Maryland, United States of America.
9DNAnexus, Mountain View, California, United States of America.
Abstract
The computational modeling of chromatin structure is highly complex due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. Chromatin structure modeling can be based on diverse approaches and assumptions, making it essential to determine how different methods influence the modeling outcomes.…
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