EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. - Xiaoyang Chen 007; Shengquan Chen; Rui Jiang 001 (BMC Bioinform., 2020)

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. - Shengquan Chen; Boheng Zhang; Xiaoyang Chen 007; Xuegong Zhang; Rui Jiang 001 (Bioinform., 2021)

SilencerDB: a comprehensive database of silencers. - Wanwen Zeng; Shengquan Chen; Xuejian Cui; Xiaoyang Chen 007; Zijing Gao; Rui Jiang 001 (Nucleic Acids Res., 2021)

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. - Xiaoyang Chen 007; Shengquan Chen; Shuang Song 006; Zijing Gao; Lin Hou; Xuegong Zhang; Hairong Lv; Rui Jiang 001 (Nat. Mach. Intell., 2022)

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. - Chen Li; Xiaoyang Chen 007; Shengquan Chen; Rui Jiang 001; Xuegong Zhang (Bioinform., 2023)

Cofea: correlation-based feature selection for single-cell chromatin accessibility data. - Keyi Li; Xiaoyang Chen 007; Shuang Song 006; Lin Hou; Shengquan Chen; Rui Jiang 001 (Briefings Bioinform., 2024)

Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. - Xuejian Cui; Xiaoyang Chen 007; Zhen Li; Zijing Gao; Shengquan Chen; Rui Jiang 001 (Nat. Comput. Sci., 2024)

CASHeart: A database of single cells chromatin accessibility for the human heart. - Qun Jiang; Xiaoyang Chen 007; Zijing Gao; Jinmeng Jia; Shengquan Chen; Rui Jiang 001 (Quant. Biol., 2025)