Yusen Ye

BandHiC reduces memory usage for Hi-C matrices by 99% using a banded storage strategy while enabling efficient analysis of ultra-high-resolution data.

CellLoop identifies single-cell chromatin loops using a density-based framework, improving accuracy in mouse brain and embryogenesis data.

The paper develops HiCS, a method to identify hierarchical chromatin domains in single-cell Hi-C maps, revealing multiple factors and retrotransposons involved in boundary formation in mouse embryonic stem cells.

The paper introduces MSTD, a method to detect multi-scale topological domains from 3D genomic maps, showing its effectiveness in identifying promoter-anchored interaction domains and improving accuracy over existing methods.