Publications

Nature Methods · Accepted, 2026

An agentic AI spatial molecular foundation model of the brain

Y. He, H. Sheng, M. Yuan, Y. Zhou, H. Shi, W. X. Wang, Z. Tang, Z. Lin, W. Wang, N. Li, J. Liu* and X. Wang*

Nature, 2025

Brain implantation of tissue-level-soft bioelectronics via embryonic development

Hao Sheng#, Ren Liu#, Qiang Li#, Zuwan Lin#, Yichun He, Thomas 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, and Jia Liu*

• Cover highlight · Nature

bioRxiv, 2025

SpatialAgent: An Autonomous AI Agent for Spatial Biology

Hanchen Wang#*, Yichun He#, Paula Coelho#, Matthew Bucci#, Abbas Nazir, Bob Chen, Linh Trinh, Serena Zhang, Kexin Huang, Vineethkrishna Chandrasekar, Douglas C. Chung, Minsheng Hao, Ana Carolina Leote, Yongju Lee, Bo Li, Tianyu Liu, Jin Liu, Romain Lopez, Lucas Tawaun, Mingyu Ma, Nikita Makarov, Lisa McGinnis, Linna Peng, Stephen Ra, Gabriele Scalia, Avtar Singh, Liming Tao, Masatoshi Uehara, Chenyu Wang, Runmin Wei, Ryan Copping, Orit Rozenblatt-Rosen, Jure Leskovec, Aviv Regev*

bioRxiv, 2025

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*, Jia Liu*

Nature Neuroscience · Accepted

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*

Nature Methods, 2025

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*

ICLR, 2025

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Chenyu Wang#, Masatoshi Uehara#, Yichun He, Amy Wang, Tommaso Biancalani, Avantika Lal, Tommi Jaakkola*, Sergey Levine*, Hanchen Wang*, Aviv Regev*

bioRxiv, 2024

End-to-end multimodal deep learning for real-time decoding of months-long neural activity from the same cells

Yichun He#, Arnau Marin-Llobet#, Hao Sheng, Ren Liu, Jia Liu*

Nature, 2023

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*

• Cover & perspective highlight · Nature whole mouse brain collection
• Harvard Brain Science Initiative · Google Map of the Mouse Brain at Molecular Resolution

Cell, 2023

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*

Nature Methods, 2023

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 Communications, 2023

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*

• Editors’ Highlights · Nature Communications: Biotechnology and Methods; Computational Science

Cell, 2023

Multimodal charting of molecular and functional cell states via in situ electro-seq

Qiang Li#, Zuwan Lin#, Ren Liu#, Xin Tang#, Jiahao Huang, Yichun He, Xin Sui, Weiwen Tian, Hao Shen, Haowen Zhou, Hao Sheng, Hailing Shi, Ling Xiao, Xiao Wang*, Jia Liu*

• Cover highlight · Cell
• Perspective highlight · Nature Methods

Biophysics Reviews, 2022

Soft bioelectronics for cardiac interfaces

Xin Tang#, Yichun He#, Jia Liu*

• Editor’s highlight · AIP Scilight

Nature Communications, 2021

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*

• Harvard SEAS · Mapping RNAs