About Me

I am a first-year Ph.D. student 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.

Previously, I was fortunate to be supervised by Zhiyuan Yuan at Fudan University, Na Sun at the Whitehead Institute, and Tatsuya Akutsu at Kyoto University. I obtained my M.Sc. from Kyoto University and B.Eng. from University of Electronic Science and Technology of China (UESTC).

Selected Publications

* denotes equal contribution; Yan Cui is highlighted.

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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

Whitehead Institute

Research Intern

Cambridge, USA Feb 2025 – Sep 2025

CartaBio

Remote Research Intern

Remote Mar 2024 – Feb 2025

ISTBI, Fudan University

Research Intern

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

Kyoto, Japan Oct 2022 – Oct 2024

University of Electronic Science and Technology of China

B.Eng. in Automation

Chengdu, China Sep 2018 – Jul 2022