Publications

2026

1. Nature Catalysis

   A geometric foundation model for enzyme retrieval with evolutionary insights

   Y. Liu, C. Hua, M. Xu, T. Zeng, J. Rao, Z. Zhang, J. K. Weng, C. W. Coley, and S. Zheng

   Nature Catalysis , 2026

   A structure-aware enzyme retrieval model that connects geometric protein representations with evolutionary signals for enzyme discovery.

   enzyme foundation models enzyme retrieval evolutionary insights biocatalysis

   Code
2. Cancer Cell

   OpenIO: An open framework for AI-native immunotherapy

   Y. Wu, H. Xiao, N. Jiang, W. Hua, J. Ma, J. Ge, Y. Liu, Z. Zhang, J. X. Chen, R. Jin, Y. Wang, J. Zhou, J. Fan, Z. Zheng, L. Bai, H. Ye, Q. Liu, G. Guo, Z. Zhang, S. Sun, T. Guo, S. Zheng, and Q. Gao

   Cancer Cell , Jul 2026

   An open framework for AI-native immunotherapy that supports coordinated modeling, discovery, and translational workflows.

   AI-native immunotherapy drug discovery biomedical agents translational oncology
3. arXiv

   Tactile: Giving Computer-Using Agents Hands and Feet

   Y. Liu, Z. Zhong, and Z. Shi

   arXiv , Jul 2026

   A framework for giving computer-using agents grounded interaction capabilities across desktop and browser environments.

   computer-using agents embodied interaction UI automation AI agents

   arXiv Code

2025

1. bioRxiv

   Origene: A self-evolving virtual disease biologist automating therapeutic target discovery

   Z. Zhang, Z. Qiu, Y. Wu, S. Li, D. Wang, Y. Liu, Z. Zhou, Y. Hu, Y. Chen, D. An, Y. Wang, Y. Li, Z. Zhong, C. Ou, Z. Wang, F. Tang, J. X. Chen, R. Ma, J. Li, X. Wang, W. Lu, H. Xue, W. Zhang, Z. Wei, R. Ma, Z. Shi, K. Wang, Q. Liu, B. Dong, Y. He, T. Liu, J. Gu, S. Song, Q. Feng, J. Zhang, B. Zhang, L. Tian, L. Bai, Q. Gao, S. Sun, and S. Zheng

   bioRxiv , 2025

   A self-evolving virtual disease biologist for automating therapeutic target discovery and hypothesis generation.

   autonomous discovery therapeutic targets disease biology scientific agents

   Code

2024

1. arXiv

   EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics

   C. Hua, Y. Liu, D. Zhang, O. Zhang, S. Luan, K. K. Yang, G. Wolf, D. Precup, and S. Zheng

   arXiv , 2024

   A flow-matching approach for generating reaction-specific catalytic pockets with co-evolutionary dynamics.

   enzyme design flow matching catalytic pockets co-evolutionary dynamics

   arXiv Code
2. arXiv

   Reaction-conditioned de novo enzyme design with genzyme

   C. Hua, J. Lu, Y. Liu, O. Zhang, J. Tang, R. Ying, W. Jin, G. Wolf, D. Precup, and S. Zheng

   arXiv , 2024

   A reaction-conditioned approach to de novo enzyme design for connecting molecular transformations with protein generation.

   de novo enzyme design reaction conditioning protein generation molecular transformations

   arXiv Code