Application of individualized differential expression analysis in human cancer proteome. - Yachen Liu; Yalan Lin; Wenxian Yang; Yuxiang Lin; Yujuan Wu; Zheyang Zhang; Nuoqi Lin; Xianlong Wang 002; Mengsha Tong; Rongshan Yu (Briefings Bioinform., 2022)

Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis. - Danni Hong; Hongli Lin; Lifang Liu; Muya Shu; Jianwu Dai; Falong Lu; Mengsha Tong; Jialiang Huang (Briefings Bioinform., 2023)

Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer. - Mengsha Tong; Yuxiang Lin; Wenxian Yang; Jinsheng Song; Zheyang Zhang; Jiajing Xie; Jingyi Tian; Shijie Luo; Chenyu Liang 004; Jialiang Huang; Rongshan Yu (Briefings Bioinform., 2023)

PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation. - Jiajing Xie; Yuhang Song; Hailong Zheng; Shijie Luo; Ying Chen; Chen Zhang; Rongshan Yu; Mengsha Tong (Briefings Bioinform., 2024)

Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia. - Zheyang Zhang; Ronghan Tang; Ming Zhu; Zhijuan Zhu; Jiali Zhu; Hua Li; Mengsha Tong; Nainong Li; Jialiang Huang (Briefings Bioinform., 2024)

SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer. - Mengsha Tong; Shijie Luo; Lin Gu 003; Xinkang Wang; Zheyang Zhang; Chenyu Liang 004; Huaqiang Huang; Yuxiang Lin; Jialiang Huang (Comput. Biol. Medicine, 2024)

PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics. - Mengsha Tong; Zan Liu; Jiaao Li; Xin Wei; Wenhao Shi; Chenyu Liang 004; Chunyu Yu; Rongting Huang; Yuxiang Lin; Xinkang Wang; Shun Wang; Yi Wang; et al. (Comput. Biol. Medicine, 2024)

ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics. - Yuxiang Lin; Ling Luo; Ying Chen; Xushi Zhang; Zihui Wang; Wenxian Yang; Mengsha Tong; Rongshan Yu (CoRR, 2024)