Mengsha Tong

Dr. Tong earned her Ph.D. in Biology from Tsinghua University from September 2016 to June 2019. Since August 2025, she has been a Tenured Associate Professor at the School of Life Sciences, Xiamen University. Dr. Tong currently serves as a member of the Systems Biology Committee of the Chinese Bioinformatics Society (since 2025), a council member of the Fujian Bioinformatics Society (since 2021), and a member of the Youth Working Committee of the Xiamen Society for Immunology (since 2026). Dr. Tong has developed a series of innovative algorithms for cancer proteomics and spatial omics data to advance precision medicine: (1) She developed the TiRank algorithm for identifying clinically relevant spatial niches. TiRank demonstrated high accuracy in identifying drug-sensitive cells and clinically relevant spatial niches across multiple cancer types, and the newly discovered spatial niches were validated by spatial proteomics (Genome Medicine, 2026, last corresponding author); (2) She developed IDEPA, an individualized differential protein analysis algorithm based on tumor proteomics, which effectively improves the accuracy and sensitivity of differential protein identification in tumors (Briefings in Bioinformatics, 2022, co-corresponding author); (3) She developed PhosMap, an interactive data analysis platform for exploring the phosphoproteome, providing an important technical foundation for interpreting complex phosphoproteomics data and revealing kinase regulatory networks in tumors. This work was honored with the “π-HuB Rising Star Award” at the Global Summit of the Human Proteome Navigation (π-HuB) International Science Program and the 12th Chinese Proteomics Conference.

Selected publications:
1. Yuxiang Lin#, Zening Huang#, Ziyan Lin#, Yating Lin#, Ling Luo, Jinsheng Song, Youxin Gao, Junjie Lin, Xinyu Li, Chenyu Liang, Lei Zhang, Xinkang Wang, Xushi Zhang, Yufan Liao, Yuqin Sun*, Rongshan Yu*, Qiyue Chen*, and Mengsha Tong*. TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery. Genome Medicine.2026 Feb 13;18(1):23.
2. Jiajing Xie#, Yuhang Song#, Hailong Zheng, Shijie Luo, Ying Chen, Chen Zhang, Rongshan Yu*, Mengsha Tong*. PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation. Briefings in Bioinformatics, 2024 Sep 23; 25(6):bbae497.
3. Mengsha Tong#*, Yuxiang Lin#, Wenxian Yang, Jinsheng Song, Zheyang Zhang, Jiajing Xie, Jingyi Tian, Shijie Luo, Chenyu Liang, Jialiang Huang*, Rongshan Yu*. Prioritizing prognostic-associated. subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer. Briefings in Bioinformatics, 2023 May 19;24(3):bbad078.
4. Jiajing Xie#, Ying Chen#, Shijie Luo#, Wenxian Yang, Yuxiang Lin, Liansheng Wang, Xin Ding* Mengsha Tong*, Rongshan Yu*. BPformer: Tracing Unknown Tumor Origins with a Biological Pathway-based Transformer Model. Cell reports Methods, 2024 Jun 17;4(6):100797.
5. Yachen Liu , Yalan Lin, Yuxiang Lin, Yujuan,Wu, Zheyang Zhang, Nuoqi Lin, Xianlong Wang, Mengsha Tong*, Rongshan Yu*. Application of individualized differential expression analysis in human cancer proteome. Briefings in Bioinformatics, 2022 Apr 2;bbac096.