About Me

I am a Ph.D. candidate in Bioengineering at the University of Pennsylvania, co-supervised by Zhi Huang and Yanxiang Deng. My research focuses on Computational Biology, and AI Agents for Scientific Discovery.

If you work in biology and want to push further into spatial omics or computational analysis, or you come from a computational / AI agents background and are looking to collaborate on biological questions — or if you would just like to say hi — please drop me an email.

Selected Publications

* denotes equal contribution; Yan Cui is highlighted.

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Spatial Hi-C-RNA simultaneously maps genome architecture and gene expression from the same tissue

Pengfei Guo*, Yan Cui*, Jincan He, Abraham J. Waldman, Jiaxin Zhu, Yufan Chen, Zhi Huang, Jingtian Zhou, Jennifer E. Phillips-Cremins, and Yanxiang Deng

Cell, 2026

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SOFisher: reinforcement learning-guided experiment designs for spatial omics

Zhuo Li*, Weiran Wu*, Chuangyi Han*, Yan Cui*, and Zhiyuan Yuan

Nature Communications, 2026

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Linking spatial biology and clinical histology via Haiku

Yan Cui*, Jacob S. Leiby*, Wenhui Lei, Dokyoon Kim, Yanxiang Deng, Aaron T. Mayer, Zhenqin Wu, Alexandro E. Trevino, and Zhi Huang

arXiv:2605.00925, 2026

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Prioritizing perturbation-responsive gene patterns using interpretable deep learning

Yan Cui and Zhiyuan Yuan

Nature Communications, 16(1):6095, 2025

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Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases

Senlin Lin*, Zhikang Wang*, Yan Cui*, Qi Zou, Chuangyi Han, Rui Yan, Zhidong Yang, Wei Zhang, Rui Gao, Jiangning Song, et al.

Nature Methods, 2024

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Haruka resolves perturbation response heterogeneity in spatial cell niches

Yan Cui, Jasmine Blandin, Kipp Weiskopf, and Na Sun

bioRxiv, 2025

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Other Publications

Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues

Pengfei Guo, Yufan Chen, Liran Mao, Angelysia Cardilla, Chin Nien Lee, Yan Cui, Dengge Jin, Yucong Hua, Xiaowei Xu, and Yanxiang Deng

Nature Communications, 16(1):5945, 2025

Reusability report: Exploring the transferability of self-supervised learning models from single-cell to spatial transcriptomics

Chuangyi Han, Senlin Lin, Zhikang Wang, Yan Cui, Qi Zou, and Zhiyuan Yuan

Nature Machine Intelligence, 2025

Complete spatially resolved gene expression is not necessary for identifying spatial domains

Senlin Lin, Yan Cui, Fangyuan Zhao, Zhidong Yang, Jiangning Song, Jianhua Yao, Yu Zhao, Bin-Zhi Qian, Yi Zhao, and Zhiyuan Yuan

Cell Genomics, 4(6), 2024

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Zhiyuan Yuan, Fangyuan Zhao, Senlin Lin, Yu Zhao, Jianhua Yao, Yan Cui, Xiao-Yong Zhang, and Yi Zhao

Nature Methods, 21(4):712-722, 2024

Experience

Arc Institute

Research Intern, Zhou Lab · Advisor: Jingtian Zhou

Palo Alto, USA Jun 2026 – Aug 2026

Whitehead Institute

Research Intern · Advisor: Na Sun

Cambridge, USA Feb 2025 – Sep 2025

CartaBio

Remote Research Intern

Remote Mar 2024 – Feb 2025

ISTBI, Fudan University

Research Intern · Advisor: Zhiyuan Yuan

Shanghai, China Oct 2023 – Feb 2025

Education

University of Pennsylvania

Ph.D. in Bioengineering

Philadelphia, USA Sep 2025 – Present

Kyoto University

M.Sc. in Intelligence Science and Technology · Advisor: Tatsuya Akutsu

Kyoto, Japan Oct 2022 – Oct 2024

University of Electronic Science and Technology of China

B.Eng. in Automation

Chengdu, China Sep 2018 – Jul 2022