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Detecting hierarchical genome folding with network modularity #MMPMID29334377
Norton HK; Emerson DJ; Huang H; Kim J; Titus KR; Gu S; Bassett DS; Phillips-Cremins JE
Nat Methods 2018[Feb]; 15 (2): 119-22 PMID29334377show ga
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.