Computational methods for analyzing and modeling genome structure and organization

Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S. Noble

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to inte-grate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summa-rize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.

Original languageEnglish (US)
Article numbere1435
JournalWiley Interdisciplinary Reviews: Systems Biology and Medicine
Issue number1
StatePublished - Jan 1 2019
Externally publishedYes


  • 3D genome modeling
  • Chromosome architecture
  • Computational methods
  • Reviews

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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