Landscape of the long non-coding RNA transcriptome in human heart. - Chunjie Jiang; Na Ding; Junyi Li; Xiyun Jin; Lili Li; Tao Pan; Caiqin Huo; Yongsheng Li 001; Juan Xu 001; Xia Li 004 (Briefings Bioinform., 2019)

Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases. - Yongsheng Li 001; Caiqin Huo; Tao Pan; Lili Li; Xiyun Jin; Xiaoyu Lin; Juan Chen; Jinwen Zhang; Zheng Guo 002; Juan Xu 001; Xia Li 004 (Briefings Bioinform., 2019)

Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk. - Yongsheng Li 001; Xiyun Jin; Zishan Wang; Lili Li; Hong Chen; Xiaoyu Lin; Song Yi; Yunpeng Zhang; Juan Xu 001 (Briefings Bioinform., 2019)

Survey of miRNA-miRNA cooperative regulation principles across cancer types. - Tingting Shao; Guangjuan Wang; Hong Chen; Yunjin Xie; Xiyun Jin; Jing Bai 014; Juan Xu 001; Xia Li 004; Jian Huang 004; Yan Jin 007; Yongsheng Li 001 (Briefings Bioinform., 2019)

Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles. - Yan Huang; Pingping Wang; Wenyang Zhou; Meng Luo 001; Zhaochun Xu; Rui Cheng 003; Chang Xu; Xiyun Jin; Yiqun Li; Qinghua Jiang (Briefings Bioinform., 2021)

Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing. - Xiyun Jin; Wenyang Zhou; Meng Luo 001; Pingping Wang; Zhaochun Xu; Kexin Ma 003; Huimin Cao; Chang Xu; Yan Huang; Rui Cheng 003; Lixing Xiao; Xiaoyu Lin; et al. (Briefings Bioinform., 2021)

DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor. - Zhaochun Xu; Meng Luo 001; Weizhong Lin; Guangfu Xue; Pingping Wang; Xiyun Jin; Chang Xu; Wenyang Zhou; Yideng Cai; Wenyi Yang; Huan Nie; Qinghua Jiang (Briefings Bioinform., 2021)

CeRNASeek: an R package for identification and analysis of ceRNA regulation. - Mengying Zhang; Xiyun Jin; Junyi Li; Yi Tian; Qi Wang; Xinhui Li; Juan Xu 001; Yongsheng Li 001; Xia Li 004 (Briefings Bioinform., 2021)

Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development. - Rui Cheng 003; Zhaochun Xu; Meng Luo 001; Pingping Wang; Huimin Cao; Xiyun Jin; Wenyang Zhou; Lixing Xiao; Qinghua Jiang (Briefings Bioinform., 2022)

Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients. - Xiaoyu Lin; Huan Nie; Ran Tang; Pingping Wang; Xiyun Jin; Qinghua Jiang; Fang Han; Na Chen; Yu Li (Comput. Biol. Medicine, 2022)

MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2. - Wenyang Zhou; Chang Xu; Meng Luo 001; Pingping Wang; Zhaochun Xu; Guangfu Xue; Xiyun Jin; Yan Huang; Yiqun Li; Huan Nie; Qinghua Jiang; Anastasia A. Anashkina (Comput. Biol. Medicine, 2022)

DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data. - Wenyi Yang; Pingping Wang; Meng Luo 001; Yideng Cai; Chang Xu; Guangfu Xue; Xiyun Jin; Rui Cheng 003; Jinhao Que; Fenglan Pang; Yuexin Yang; Huan Nie; et al. (Bioinform., 2023)

TriCLFF: a multi-modal feature fusion framework using contrastive learning for spatial domain identification. - Fenglan Pang; Guangfu Xue; Wenyi Yang; Yideng Cai; Jinhao Que; Haoxiu Sun; Pingping Wang; Shuaiyu Su; Xiyun Jin; Qian Ding; Zuxiang Wang; Meng Luo 001; et al. (Briefings Bioinform., 2025)