Consensus clustering of single-cell RNA-seq data by enhancing network affinity. - Yaxuan Cui; Shaoqiang Zhang; Ying Liang; Xiangyun Wang; Thomas N. Ferraro; Yong Chen 031 (Briefings Bioinform., 2021)

Deciphering hierarchical organization of topologically associated domains through change-point testing. - Haipeng Xing; Yingru Wu; Michael Q. Zhang; Yong Chen 031 (BMC Bioinform., 2021)

Decoding brain memory formation by single-cell RNA sequencing. - Atlas M. Sardoo; Shaoqiang Zhang; Thomas N. Ferraro; Thomas M. Keck; Yong Chen 031 (Briefings Bioinform., 2022)

Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations. - Tianyuan Lei; Ruoyu Chen; Shaoqiang Zhang; Yong Chen 031 (Briefings Bioinform., 2023)

Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencoders. - Liang Chen; Madison Dautle; Ruoying Gao; Shaoqiang Zhang; Yong Chen 031 (Briefings Bioinform., 2025)