Computational methods for analyzing and modeling genome structure and organization

Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Dejun LinWilliam S Noble

Abstract

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.

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Citations

Sep 6, 2019·Scientific Reports·Shay Ben-ElazarZohar Yakhini
Sep 29, 2019·Development·Elizabeth Ing-Simmons, Juan M Vaquerizas
Mar 27, 2020·PLoS Computational Biology·Zhaleh GhaemiZaida Luthey-Schulten
Feb 9, 2021·Frontiers in Genetics·Polina Belokopytova, Veniamin Fishman
Feb 15, 2021·The FEBS Journal·Andrea M ChiarielloMario Nicodemi
Mar 19, 2021·Frontiers in Genetics·Alessandro Bertero
May 7, 2021·Nature Reviews. Molecular Cell Biology·Ivana Jerkovic, Giacomo Cavalli
May 9, 2021·Nature Methods·Luca FiorilloMario Nicodemi
Jul 15, 2021·Computational and Structural Biotechnology Journal·Jing LiMingzhou Li
Aug 31, 2019·Methods : a Companion to Methods in Enzymology·Dario Meluzzi, Gaurav Arya

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