Author

Xinyi Liu

Shanghai Jiao Tong University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Biology Disciplines

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Bioinformatics· 3 Immunology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 3 Approach:deep learning· 2 Approach:experimental assay· 2 Assay:protein structure· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Chengwei Wu· 3 shared Jinyin ZhaiD· 3 shared Wenming QiniD· 3 shared Zhen ZhengiD· 3 shared Jian ZhangiD· 2 shared Jie ZhongiD· 2 shared Mingyu Li· 2 shared Qiancheng SheniD· 2 shared

Activity by Year

2025-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Chengwei Wu

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Author profile →

5 papers

Recent·Most cited

Cross-state representation learning enables prospective discovery of dynamic protein allosteric sites

Qiuhan Ren, Liying Wu, Jinyin Zha, Mingyu Li, Wanting Feng, Haijiao Zhang, He Yang, Rui Li, Xinyi Liu, Jixiao He, Wanyao Zhou, Yuchengze Song, Chengwei Wu, Qiancheng Shen, Xi Cheng, , Jian Zhang

This paper introduces a deep learning framework for identifying dynamic protein allosteric sites across different conformational states, achieving improved performance over existing methods.

bioRxiv · Nov 10, 2026 · PreprintBioinformatics

Hierarchical Immune Suppressive Functions of Regulatory T Cells Built on Mechanical Force

Xinyi Liu, Cao Huang, Xiaobo Wang, Jie Kang, Chunlin Zou, Yanni Xu, Longyan Wu, Yan Shi

This study identifies a hierarchical mechanical force-based model of Treg suppression, showing that stable adhesion is required for localized cytokine delivery to dendritic cells.

bioRxiv · May 21, 2026 · PreprintImmunology

Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability

Xiuxiao Tang, Ranran Dai, Qi Li, Zhida Zhang, Hongmei Li, Lizi Lu, Hancheng Lin, Danling Ji, Wei Dan, Yuqi He, Xinyi Liu, Tao Yang, Wakam Chang, Yang Mao, Shisheng Sun, Junjun Ding

The paper shows that nuclear N-glycans modify INM proteins, regulate H3K9me3, and maintain genomic stability by interacting with SETDB1.

Nature Cell Biology · Apr 28, 2026Peer-reviewedMolecular Biology

Large-scale quantum computing framework enhances drug discovery in multiple stages

Kai Wen, Jinyin Zha, Shaobo Chen, Jie Zhong, Lixin Yuan, Cui Yunxia, Xinchao Shi, Wenming Qin, Xiaobing Lan, Yonghui Liu, Xiuyan Yang, Hui Qin, Mingyu Li, Putuo Guo, Qingjie Xiao, , Jian Zhang

This paper presents a quantum computing framework for drug discovery that improves stability and performance in multiple stages, identifying novel druggable sites and compounds.

bioRxiv · Feb 11, 2026 · PreprintBioinformatics

Sampling Function-Related Metastable States of Proteins With DASH

Jinyin Zha, Zhen Zheng, Jie Zhong, W.K. Wang, Qiancheng Shen, Qiao Li, Mingyu Kenneth Li, Chengwei Wu, Qingjie Xiao, Qiuhan Ren, Nuan Li, Hao Zhang, Xinyi Liu, Li Feng, Wenming Qin, Jian Zhang

DASH samples function-related metastable states of proteins, revealing new folding states and allosteric sites, verified by experiments and crystal structures.

bioRxiv · Dec 25, 2025 · PreprintBioinformatics