Author

Yan Shi

Peking University

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

Same name, identified by ORCID

Biology Disciplines

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Immunology· 2 Bioengineering· 1 Cell Biology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:mouse· 3 Approach:statistical model· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2

Frequent Co-Authors

Jie KangiD· 2 shared Naixu Liu· 2 shared Xiaobo Wang· 2 shared Yongqi Liu· 2 shared Yuanyuan Miao· 2 shared Zhiliang YueiD· 2 shared Alexey SergushicheviD· 1 shared Alwin J. van der HamiD· 1 shared

Activity by Year

2026-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersImmunology

Jie KangORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Programming Biomolecular Interactions with All-Atom Generative Model

Xiangzhe Kong, Junwei Chen, Ziting Zhang, Gaodeng Li, Qingyuan Zhu, L Wei, Mingyu Li, Yan Shi, Weiyang Dai, Zishen Zhang, Wenjuan Tan, Rui Jiao, Xiaolun Wang, Jiqing Zheng, Ziyang Yu, , Jianzhu Ma

This paper introduces AnewOmni, a generative model that designs biomolecules across scales by learning interaction patterns and physical constraints from 5 million complexes.

bioRxiv · Jun 4, 2026 · PreprintBioengineering

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

Isoform-resolved spatial transcriptomics on a lab-made high-density array via a single-chip NGS-TGS workflow

Zhiliang Yue, Min Liu, Yongqi Liu, Dongdong Lu, Menglong Zhang, Yuntong Wang, Yan Shi, Yuanyuan Miao, Suchen Wang, Yifan Jiang, Yue Wang, Jun Zhao, Naixu Liu, Chunyu Lv, Jixian Zhai, Bosheng Li

The paper presents a low-cost lab-made spatial transcriptomics chip that enables isoform-resolved analysis using a dual-platform sequencing workflow, identifying novel splicing events in tomato-pepper grafts and mouse embryos.

bioRxiv · Mar 18, 2026 · PreprintPlant Biology

Super-resolution single-cell spatial atlas of plant de novo regeneration

Xiehai Song, Shaoman Zhang, Zhiliang Yue, Yongqi Liu, Shanshan Chen, Yani Niu, Yan Shi, Hengjia Yang, Li Xu, Naixu Liu, Yuanyuan Miao, Man Lv, J. C. Li, Tong Wang, Meizhi Xu, , Bosheng Li

The paper constructs a super-resolution single-cell spatial atlas of tomato de novo regeneration using multimodal spatial transcriptomics.

bioRxiv · Feb 20, 2026 · PreprintCell Biology

O-GlcNAcylation and low glycolysis underpin Th2 polarization by dendritic cells

Leonard R. Pelgrom, Marjolein Quik, José Javier Fernández, Thiago A. Patente, Graham A. Heieis, Alexey Sergushichev, Jie Kang, Xiaobo Wang, Justine Dontaine, Marie-Sophie Fabre, Frank Otto, Alwin J. van der Ham, Lisa W. Bloemberg, Marion H. König, Béatrice M. F. Winkel, , Bart Everts

This study identifies O-GlcNAcylation and reduced glycolysis as key factors in Th2 polarization by dendritic cells, showing their role in immune synapse regulation and TCR signaling.

bioRxiv · Feb 5, 2026 · PreprintImmunology