Zuwan Lin

Zuwan Lin, PhD

Postdoctoral Researcher

Harvard University

About Me

Currently I am a postdoctoral researcher in the School of Engineering and Applied Sciences at Harvard University, working with Prof. Na Li. Prior to this, I was co-advised by Prof. Jia Liu at Harvard University and Prof. Xiao Wang at Broad Institute of MIT and Harvard, and earned my Ph.D. in physical chemistry from Harvard University in 2024. I have also worked closely with Prof. Richard T. Lee, Prof. Juan Alvarez, and Prof. Jie Ding. I earned my B.S. in chemical biology from Tsinghua University in 2018.


My research decodes how cells orchestrate functional tissues by integrating three technological frontiers: bioelectronics, spatial transcriptomics, and agentic AI. First, I pioneered cyborg engineering which embeds tissue-like stretchable nanoelectronics into developing cardiac, neural, and pancreatic organoids or into living animals to capture continuous single-cell electrical activity over months. Second, I developed in situ electro-seq, which pairs millisecond-scale electrical recordings with 3D spatial transcriptomics from the same cells, revealing how molecular programs drive cellular function. Third, I create autonomous AI agents powered by multimodal large language models: SpikeAgent automates neural spike sorting with interpretable decision-making, STAgent conducts spatial transcriptomic analysis while integrating scientific literature, and BehaveAgent performs universal behavior analysis from raw video. These agents transform weeks of expert analysis into minutes of automated discovery. By integrating chronic bioelectronic sensing, multimodal molecular profiling, and intelligent automation, my research aims to revolutionize how we study development, disease, and regeneration across biological scales.

Research Interests

Agentic AI
Bioelectronics
Spatial Omics
Cyborg Engineering
Neural Interfaces

Publications

* Denotes equal contribution, # Denotes corresponding author

AI Agent for biology & control

1-1
Spike sorting AI agent
Zuwan Lin*, Arnau Marin-Llobet*, Jongmin Baek, Yichun He, Jaeyong Lee, Wenbo Wang, Xinhe Zhang, Ariel J. Lee, Ningyue Liang, Jin Du, Jie Ding, Na Li, Jia Liu#
bioRxiv, 2025
1-2
Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo
Zuwan Lin*, Wenbo Wang*, Arnau Marin-Llobet, Qiang Li, Samuel D. Pollock, Xin Sui, Almir Aljovic, Jaeyong Lee, Jongmin Baek, Ningyue Liang, Xinhe Zhang, Connie Kangni Wang, Jiahao Huang, Mai Liu, Zihan Gao, Hao Sheng, Jin Du, Stephen J. Lee, Brandon Wang, Yichun He, Jie Ding, Xiao Wang, Juan R. Alvarez-Dominguez#, Jia Liu#
bioRxiv, 2025
1-3
An autonomous AI agent for universal behavior analysis
Almir Aljovic*#, Zuwan Lin*#, Wenbo Wang, Xinhe Zhang, Arnau Marin-Llobet, Ningyue Liang, Bradley Canales, Jaeyong Lee, Jongmin Baek, Ren Liu, Catherine Li, Na Li, Jia Liu#
bioRxiv, 2025
1-4
Explainable multi-task learning for multi-modality biological data analysis
Xin Tang*, Jiawei Zhang*, Yichun He*, Xinhe Zhang, Zuwan Lin, Sebastian Partarrieu, Emma Bou Hanna, Zhaolin Ren, Hao Shen, Yuhong Yang, Xiao Wang, Na Li, Jie Ding#, Jia Liu#
Nature Communications, 2023
1-5
An AI-cyborg system for adaptive intelligent modulation of organoid maturation
Ren Liu*, Zhaolin Ren*, Xinhe Zhang*, Qiang Li, Wenbo Wang, Zuwan Lin, Richard T. Lee, Jie Ding, Na Li#, Jia Liu#
bioRxiv, 2024

Multimodal systems biology

2-1
Multimodal charting of molecular and functional cell states via in situ electro-sequencing
Qiang Li*, Zuwan Lin*, Ren Liu*, Xin Tang*, Jiahao Huang, Yichun He, Xin Sui, Weiwen Tian, Haowen Zhou, Hao Sheng, Hailing Shi, Ling Xiao, Xiao Wang#, Jia Liu#
Cell, 2023
2-2
Tissue-embedded stretchable nanoelectronics reveal endothelial cell–mediated electrical maturation of human 3D cardiac microtissues
Zuwan Lin*, Jessica C. Garbern*, Ren Liu*, Qiang Li, Estela Mancheño Juncosa, Hannah LT. Elwell, Morgan Sokol, Junya Aoyama, Undine-Sophie Deumer, Emma Hsiao, Hao Sheng, Richard T. Lee#, Jia Liu#
Science Advances, 2023
2-3
In situ graphene-seq: spatial transcriptomics and chronic electrophysiology characterization of tissue microenvironments
Jaeyong Lee*, Wenbo Wang*, Qiang Li, Zuwan Lin, Ren Liu, Zefang Tang, Junya Aoyama, Richard T. Lee, Xiao Wang, Jia Liu#
bioRxiv, 2025
2-4
Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation
Giridhar M. Anand*, Heitor C. Megale, Sean H. Murphy, Theresa Weis, Zuwan Lin, Yichun He, Xiao Wang, Jia Liu, Sharad Ramanathan#
Cell, 2023

Bioelectronics for cyborg engineering

3-1
Cyborg organoids integrated with stretchable nanoelectronics can be functionally mapped during development
Zuwan Lin*, Wenbo Wang*, Ren Liu*, Qiang Li*, Jaeyong Lee, Charles Hirschler, Jia Liu#
Nature Protocols, 2025
3-2
Stretchable mesh nanoelectronics for 3D single-cell chronic electrophysiology from developing brain organoids
Paul Le Floch*, Qiang Li*, Zuwan Lin*, Siyuan Zhao, Ren Liu, Kazi Tasnim, Han Jiang, Jia Liu#
Advanced Materials, 2022,
3-3
Cyborg islets: implanted flexible electronics reveal principles of human islet electrical maturation
Qiang Li*, Ren Liu*, Zuwan Lin*, Xinhe Zhang*, Israeli Galicia Silva, Samuel D. Pollock, Juan R. Alvarez-Dominguez#, Jia Liu#
bioRxiv, 2024
3-4
Cyborg organoids: implantation of nanoelectronics via organogenesis for tissue-wide electrophysiology
Qiang Li*, Kewang Nan*, Paul Le Floch*, Zuwan Lin, Hao Sheng, Thomas S. Blum, Jia Liu#
Nano Letters, 2019

Neural interfaces & in vivo bioelectronics

4-2
Brain implantation of tissue-level-soft bioelectronics via embryonic development
Hao Sheng*, Ren Liu*, Qiang Li*, Zuwan Lin*, Yichun He, Thomas S. Blum, Hao Zhao, Xin Tang, Wenbo Wang, Lishuai Jin, Zheliang Wang, Emma Hsiao, Paul Le Floch, Hao Shen, Ariel J. Lee, Rachael Alice Jonas-Closs, James Briggs, Siyi Liu, Daniel Solomon, Xiao Wang, Nanshu Lu, Jia Liu#
Nature, 2025
4-2
Tracking neural activity from the same cells during the entire adult life of mice
Siyuan Zhao*, Xin Tang*, Weiwen Tian*, Sebastian Partarrieu*, Ren Liu, Hao Shen, Jaeyong Lee, Shiqi Guo, Zuwan Lin, Jia Liu#
Nature Neuroscience, 2023

Spatial biology & high-resolution tissue mapping

5-1
Spatial atlas of the mouse central nervous system at molecular resolution
Hailing Shi*, Yichun He*, Yiming Zhou*, Jiahao Huang, Kamal Maher, Brandon Wang, Zefang Tang, Shuchen Luo, Peng Tan, Morgan Wu, Zuwan Lin, Jingyi Ren, Yaman Thapa, Xin Tang, Ken Y. Chan, Benjamin E. Deverman, Hao Shen, Albert Liu, Jia Liu#, Xiao Wang#
Nature, 2023
5-2
ClusterMap for multi-scale clustering analysis of spatial gene expression
Yichun He*, Xin Tang*, Jiahao Huang, Jingyi Ren, Haowen Zhou, Kevin Chen, Albert Liu, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Johain Ounadjela, Emanuelle I. Grody, Jian Shu, Jia Liu#, Xiao Wang#
Nature Communications, 2021
5-3
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape
Jingyi Ren*, Haowen Zhou*, Hu Zeng*, Connie Kangni Wang, Jiahao Huang, Xiaojie Qiu, Xin Sui, Qiang Li, Xunwei Wu, Zuwan Lin, Jennifer A. Lo, Kamal Maher, Yichun He, Xin Tang, Judson Lam, Hongyu Chen, Brian Li, David E. Fisher, Jia Liu, Xiao Wang#
Nature Methods, 2023,
5-4
Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks
Xin Sui*, Jennifer A. Lo*, Shuchen Luo, Yichun He, Zefang Tang, Zuwan Lin, Yiming Zhou, Wendy Xueyi Wang, Jia Liu, Xiao Wang#
bioRxiv, 2024

Invited Talks

2025 - "AI agent for neuroscience and neuroengineering" - Enigma Seminar, Stanford
2025 - "Spike sorting AI agent" - Spike Sorting Seminar, UCSF
2025 - "Spike sorting AI agent" - Spike Sorting Seminar, Flatiron Institute
2024 - "In situ charting of single-cell transcriptional changes at the brain-electrode interface" - Stanley Center Program Meeting, Broad Institute of MIT and Harvard
2023 - "Multimodal charting of molecular and functional cell states via in situ electro-sequencing" - 97th New England Complex Fluids (NECF) Meeting, Harvard University
2023 - "Harnessing AI in multimodal cell state analysis through In situ electro-seq" - Cell Circuits and Epigenomics Seminar, Broad Institute of MIT and Harvard

Teaching Experience

Neuroengineering - BE 131, Harvard University, 2024 & 2023
Foundations and Frontiers of Modern Chemistry - PHYSCI 11, Harvard University, 2019
Foundational Chemistry and Biology - LPS A, Harvard University, 2019