Comparing 3D genome organization in multiple species using Phylo-HMRF

We developed a continuous-trait probabilistic model to identify genome-wide evolutionary patterns of 3D genome structures based on multi-species Hi-C data. We applied the proposed method to analyzing cross-species Hi-C data from the same cell type in multiple primate species. The results showed that the proposed method enables discovery of distinct Hi-C contact frequency evolutionary patterns across species. Overall design: Comparing Hi-C contact frequencies among multiple primate species