Publications

^*: equal contribution

Journal Articles and Manuscripts

• Weizhe Wang^*, Zimu Yu^*, Endi Yang, Ziyu Shi, Shize Yu, Jian Hu, Yunxin Xu, and Haipeng Gong. From single-sequence structure prediction to protein fitness landscape through a composable, epistasis-aware mutation atlas. bioRxiv preprint, 2026. Under review at Nature Biotechnology. Preprint · Code · Server

• Kaichen Xu^*, Zimu Yu^*, Zhongkun Qu^*, Kainan Liu, Yunxin Xu, Hao Wu, and Xiaobo Sun. RADAR enables marker-free fine-grained discovery of anomalous cells in multi-sample and multimodal single-cell omics. Manuscript, 2026. Under review at Bioinformatics. Code

• Wei Wang^*, Shize Yu^*, Yunhao Shen, Zimu Yu, Ziyu Shi, Gengjiang Liu, Da Shen, Donghan Li, Yajun Zhang, Yunxin Xu, Haipeng Gong, and Shuyi Zhang. Deciphering the cellular sequence–metabolite synthetic landscape enables predictive design by MetaAI. Manuscript, 2026. Under review at Nature Microbiology. Code

Conference Papers

• Kaichen Xu^*, Yihang Du, Mianpeng Liu, Zimu Yu, and Xiaobo Sun^*. Causality-Induced Positional Encoding for Transformer-Based Representation Learning of Non-Sequential Features. In Proceedings of the 39th Conference on Neural Information Processing Systems (NeurIPS), 2025. Paper · Code