Publications
Peer-reviewed articles and preprints curated from Google Scholar, arXiv, ORCID, and DOI metadata.
SlideChat is a multimodal generative artificial intelligence assistant for whole-slide computational pathology across cancer types
Ying Chen, Chenglong Ma, Qiongqiong Li, Fang Yan, Yirong Chen, Tianbin Li, Jin Ye, Ming Hu, Yuxiang Lin, Yanjun Li, Guoan Wang, Huihui Xu, Hui Dong, Xiang Wang, Xiaoxiao Xu, Yanyan Zhou, Xia Zhu, Sen Yang, Xiyue Wang, Lu Zhang, Yu Qiao, Rongshan Yu, Junjun He, Yuanfeng Ji
Nature Cancer 2026
A multimodal generative AI assistant for whole-slide computational pathology across cancer types.
HyperST: Hierarchical Hyperbolic Learning for Spatial Transcriptomics Prediction
Chen Zhang, Yilu An, Ying Chen, Hao Li, Xitong Ling, Lihao Liu, Junjun He, Yuxiang Lin, Zihui Wang, Rongshan Yu
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), Spotlight 2026
A CVPR 2026 Spotlight paper on hierarchical hyperbolic learning for spatial transcriptomics prediction.
ST-Align: Multi-Scale Image-Gene Foundation Modeling for Spatial Transcriptomics via Spot-Niche Alignment
Yuxiang Lin, Ling Luo, Ying Chen, Xushi Zhang, Zihui Wang, Rongshan Yu
ICLR 2026 Workshop on Foundation Models for Science 2026
A multi-scale image-gene foundation modeling method for spatial transcriptomics via spot-niche alignment.
TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery
Yuxiang Lin, Zening Huang, Ziyan Lin, Yating Lin, Jinsheng Song, Ling Luo, Jiayao Chi, Yeyang Zheng, Youxin Gao, Junjie Lin, Xinyu Li, Chenyu Liang, Lei Zhang, Xinkang Wang, Yuqin Sun, Rongshan Yu, Qiyue Chen, Mengsha Tong
Genome Medicine 2026
A computational framework for prioritizing clinically relevant phenotypic niches in the tumor microenvironment.
SurvMamba: State Space Model with Multi-Grained Multi-Modal Interaction for Survival Prediction
Ying Chen, Jiajing Xie, Yuxiang Lin, Yuhang Song, Chen Zhang, Wenxian Yang, Rongshan Yu
2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2025
A state-space-model survival prediction framework with multi-grained multi-modal interaction.
BioMTAN: A Biological Knowledge-guided Multi-task Attention Network for Co-enhanced Cancer Diagnosis and Prognosis
Ying Chen, Jiajing Xie, Yuxiang Lin, Yuhang Song, Wenxian Yang, Rongshan Yu
IEEE Journal of Biomedical and Health Informatics 2025
A biological knowledge-guided multi-task attention network for jointly improving cancer diagnosis and prognosis modeling.
Accurate Cell Abundance Quantification using Multi-positive and Unlabeled Self-learning
Yating Lin, Xiaoqi Chen, Yuxiang Lin, Xu Xiao, Zhibin Huang, Wenxian Yang, Rongshan Yu, Jiahuai Han
bioRxiv 2024
A preprint developing a self-learning strategy for accurate cell abundance quantification under multi-positive and unlabeled settings.
Ccl2-Induced Regulatory T Cells Balance Inflammation Through Macrophage Polarization During Liver Reconstitution
Rui Wang, Qing Liang, Qian Zhang, Shuchao Zhao, Yuxiang Lin, Bing Liu, Yinjiang Ma, Xiaoya Mai, Quanze Fu, Xiaorui Bao, Nan Wang, Binglin Chen, Peng Yan, Yongsheng Zhu, Kejia Wang
Advanced Science 2024
A study of inflammatory balance during liver reconstitution through regulatory T cells and macrophage polarization.
Tracing unknown tumor origins with a biological-pathway-based transformer model
Jiajing Xie, Ying Chen, Shijie Luo, Wenxian Yang, Yuxiang Lin, Liansheng Wang, Xin Ding, Mengsha Tong, Rongshan Yu
Cell Reports Methods 2024
A biological-pathway-based transformer model for identifying unknown tumor origins from molecular profiles.
PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics
Mengsha Tong, Zan Liu, Jiaao Li, Xin Wei, Wenhao Shi, Chenyu Liang, Chunyu Yu, Rongting Huang, Yuxiang Lin, Xinkang Wang, Shun Wang, Yi Wang, Jialiang Huang, Yini Wang, Tingting Li, Jun Qin, Dongdong Zhan, Zhi-Liang Ji
Computers in Biology and Medicine 2024
An ensemble bioinformatic platform for interactive analysis of quantitative phosphoproteomics data.
SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer
Mengsha Tong, Shijie Luo, Lin Gu, Xinkang Wang, Zheyang Zhang, Chenyu Liang, Huaqiang Huang, Yuxiang Lin, Jialiang Huang
Computers in Biology and Medicine 2024
A cellular similarity detection method applied to diagnosis and prognosis modeling in liver cancer.
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, Jialiang Huang, Rongshan Yu
Briefings in Bioinformatics 2023
scRank prioritizes prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer.
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, Mengsha Tong, Rongshan Yu
Briefings in Bioinformatics 2022
An application of individualized differential expression analysis to human cancer proteome data.