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Updated: Feb 15, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Detecting hierarchical genome folding with network modularity
Heidi K Norton1, Daniel J Emerson1, Harvey Huang1
1Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Abstract:
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease.
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