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BMC Genomics|November 29, 2024
DeCGR: an interactive toolkit for deciphering complex genomic rearrangements from Hi-C dataJunping Li, Minghui Sun, Yusen Ye, et al.Plos Computational Biology|January 6, 2023
HiSV: A control-free method for structural variation detection from Hi-C dataJunping Li, Lin Gao, Yusen YeBMC Genomics|May 7, 2026
BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolutionWeibing Wang, Junping Li, Yusen Ye, et al.Advanced Science (Weinheim, Baden-Wurttemberg, Germany)|December 14, 2019
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C MapsYusen Ye, Lin Gao, Shihua ZhangNucleic Acids Research|April 4, 2019
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic mapsYusen Ye, Lin Gao, Shihua ZhangMethods in Molecular Biology (Clifton, N.J.)|January 22, 2020
MSTD for Detecting Topological Domains from 3D Genomic MapsYusen Ye, Lin Gao, Shihua ZhangFrontiers in Genetics|October 17, 2017
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization ApproachYusen Ye, Lin Gao, Shihua ZhangBriefings in Bioinformatics|July 14, 2024
Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinderWeibing Wang, Yusen Ye, Lin GaoBioinformatics (Oxford, England)|July 21, 2021
CCIP: predicting CTCF-mediated chromatin loops with transitivityWeibing Wang, Lin Gao, Yusen Ye, et al.Plos One|May 13, 2016
Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate GenesFei Xiao, Lin Gao, Yusen Ye, et al.Pageof 188