CCIP: predicting CTCF-mediated chromatin loops with transitivity. - Weibing Wang; Lin Gao 006; Yusen Ye; Yong Gao 001 (Bioinform., 2021)

SpriteHyper2vec: A SCSPRITE Data Completion Method Based on Hypergraph Random Walk. - Yamin Liu; Yusen Ye; Lin Gao 006 (CCIS, 2023)

HiSV: A control-free method for structural variation detection from Hi-C data. - Junping Li; Lin Gao 006; Yusen Ye (PLoS Comput. Biol., 2023)

CellFeature: Cell and Feature Co-Embedding from Single-Cell Multi-Omics with Heterogeneous Graph Model. - Enling Li; Lin Gao 006; Yusen Ye (BIBM, 2024)

Exploring Hierarchical Structures of Cell Types in scRNA-seq Data. - Haojie Zhai; Yusen Ye; Yuxuan Hu 004; Lanying Wang; Lin Gao 006 (ISBRA (2), 2024)

Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder. - Weibing Wang; Yusen Ye; Lin Gao 006 (Briefings Bioinform., 2024)