Tongye Shen

The paper develops network-based metrics to visualize interchromosomal interactions at sub-megabase resolution, revealing shared interaction hotspots across chromosomes.

The paper investigates network properties of chromosome structure networks derived from Hi-C data and their connections to genome annotations, finding that semi-local properties better characterize biological features than local or diffusive features.

The paper analyzes single-cell chromosome imaging data to reveal cell-type and region-specific structural variations in chromatin ensembles, linking these variations to epigenetic states.

The paper infers chromosome radial organization from Hi-C data using PCA and force-directed layout algorithms, showing high correlation with microscopy data across different cell types.

The paper integrates multi-omics data to identify coordinated changes in 3D genome structure across cell types and finds that lamina associations and histone marks guide these structural variations.