Open AccessComputational methods for analyzing and modeling genome structure and organization
Author(s) -
Lin Dejun,
Bonora Giancarlo,
Yardımcı Galip Gürkan,
Noble William S.
Publication year - 2018
Publication title -
wiley interdisciplinary reviews: systems biology and medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.087
H-Index - 51
eISSN - 1939-005X
pISSN - 1939-5094
DOI - 10.1002/wsbm.1435
Subject(s) - computational model , computer science , genome , chromosome conformation capture , computational biology , construct (python library) , focus (optics) , data science , theoretical computer science , artificial intelligence , biology , genetics , gene expression , physics , enhancer , optics , gene , programming language
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 integrate 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 summarize 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