A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings. - Hongru Shen; Xilin Shen; Mengyao Feng; Dan Wu; Chao Zhang; Yichen Yang 004; Meng Yang; Jiani Hu; Jilei Liu; Wei Wang; Yang Li; Qiang Zhang; et al. (Briefings Bioinform., 2022)

Scalable batch-correction approach for integrating large-scale single-cell transcriptomes. - Xilin Shen; Hongru Shen; Dan Wu; Mengyao Feng; Jiani Hu; Jilei Liu; Yichen Yang 004; Meng Yang; Yang Li; Lei Shi; Kexin Chen; Xiangchun Li (Briefings Bioinform., 2022)

Large language model produces high accurate diagnosis of cancer from end-motif profiles of cell-free DNA. - Jilei Liu; Hongru Shen; Kexin Chen; Xiangchun Li (Briefings Bioinform., 2024)

Language model enables end-to-end accurate detection of cancer from cell-free DNA. - Hongru Shen; Jilei Liu; Kexin Chen; Xiangchun Li (Briefings Bioinform., 2024)

A deep learning model for characterizing protein-RNA interactions from sequences at single-base resolution. - Xilin Shen; Yayan Hou; Xueer Wang; Chunyong Zhang; Jilei Liu; Hongru Shen; Wei Wang; Yichen Yang 004; Meng Yang; Yang Li; Jin Zhang; Yan Sun; et al. (Patterns, 2025)