ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), 2015
The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the availability of chromosome conformation capture (3C) data sets that characterize the 3D organization of chromatin at a genome-wide scale. This organization, also referred to as the 3D nucleome, is not only important for packing the genome into the nucleus but also has significant impact on how the genome functions. In this tutorial, we will present recent tools and methodologies developed for analysis of genome-wide 3C data sets generated using high-throughput sequencing (Hi-C). We will cover computational approaches that span: (i) processing basics and normalization of Hi-C data, (ii) identification of genomic domains with high contact intensity, (iii) extraction of significant contacts, and (iv) inference of 3D models of the chromatin organization from contact count data. This tutorial will be beneficial for researchers in the broad fields of computational systems biology, gene regulation and transcription, next generation sequencing data analysis, and biological network modeling and analysis.
Ay, Ferhat, and William S. Noble. “Analysis methods for studying the 3D architecture of the genome.” Genome biology 16.1 (2015): 1.