Author
Fudan University
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
Qi Zou, Zhikang Wang, Sijie Li, Senlin Lin, Chuangyi Han, Yan Cui, Shengxi Li, Lin Wang, Daoliang Zhang, Wei Zhang, Binzhi Qian, Rui Gao, Zhiyuan Yuan
GeneSPOT is a gene-centric framework that characterizes spatial gene relationships and their reorganization across biological conditions and time.
bioRxiv · Sep 29, 2026 · PreprintBioinformatics
Pengfei Guo, Yan Cui, Jincan He, Abraham J. Waldman, Jiaxin Zhu, Yufan Chen, Zhi Huang, Jingtian Zhou, Jennifer E. Phillips‐Cremins, Yanxiang Deng
This paper introduces Spatial Hi-C-RNA, a spatial multi-omics technology that co-maps chromatin conformation and transcriptome in tissue, revealing spatially coherent domains and new insights into gene regulation.
Cell · Aug 25, 2026Peer-reviewedGenomics
Caitlin A Morris, William C Bastian, YAN CUI, Zoya Kurago, Eugene F. Douglass
AnchorR improves spatial alignment between H&E images and CosMx data by combining expert-defined landmarks, reducing landmark error from 121.5 m to 14.6 m.
bioRxiv · Aug 11, 2026 · PreprintBioinformatics
Zhikang Wang, Qi Zou, Senlin Lin, Sijie Li, Yan Cui, Daoliang Zhang, Chuangyi Han, Yida Li, Jianmin Li, Yi Chen Zhao, Rui Gao, Jiangning Song, Zhiyuan Yuan
NicheTrans translates single-omics data into spatial multi-omics insights by integrating spatial and multi-modal information, outperforming existing methods in disease and tissue analysis.
Nature Methods · Jul 9, 2026Peer-reviewedBioinformatics
Zhuo Li, Weiran Wu, Chuangyi Han, Yan Cui, Tian Lu, Rongqin Ke, Jian Ye Sun, Zhiyuan Yuan
SOFisher improves spatial omics experiment design by using reinforcement learning to guide FOV selection, outperforming conventional methods in capturing relevant biological features.
Nature Communications · May 25, 2026Peer-reviewedBioinformatics
Yunjie Gu, Zihan Wu, Rui Yan, Zhikang Wang, Yuan Li, Senlin Lin, Yan Cui, Haoran Lai, Xin Luo, Shaohua Kevin Zhou, Zhiyuan Yuan, Jianhua Yao
H2O predicts spatial transcriptomics and proteomics from H&E images using a contrastive learning framework, outperforming existing models and recovering biologically relevant cell-cell communication.
bioRxiv · Apr 24, 2026 · PreprintBioinformatics
Senlin Lin, Zhikang Wang, Yan Cui, Qi Zou, Chuangyi Han, Rui Yan, Zhidong Yang, Wei Zhang, Rui Gao, Jiangning Song, Michael Q. Zhang, Hanchuan Peng, Jintai Yu, Jianfeng Feng, Yi Zhao, Zhiyuan Yuan
SpatialZ generates dense 3D cell atlases from planar spatial transcriptomics data by reconstructing virtual slices, validated with real 3D data and enabling new spatial analyses.
Nature Methods · Dec 31, 2025Peer-reviewedBioinformatics
Jorge Rodríguez-Celma, Robert T. Green, James M. Connorton, Inga Kruse, Yan Cui, Hong Qing Ling, Janneke Balk
This study shows BTSL1 and BTSL2 regulate iron uptake in roots, controlling the transcriptional response to iron deficiency by targeting FIT for degradation.
bioRxiv · Dec 8, 2017 · PreprintPlant Biology