Authors
Liujia Qian, Zizhuo Zhou, Peijie Zhou, Zhen Dong, Xudong Zhang, Zhenwu Dai, Zhangyang Gao, Siqi Sun, Kevin R Roy, Shuaiyao Wang, Nicola Zamboni, Charles Boone, Michael Costanzo, Jianzhe Li, Gianni Liti, Jia-Xing Yue, Markus Ralser, Evan Williams, Mattia Zampieri, Heng Jiang, Tailin Wu, Yalin Wang, Feiran Li, Joseph Schacherer, Rui Sun, Zhaoxing Li, Yaming Deng, Yi Chen, Zhiping Xie, Huiqiang Lou, Xiaowen Wang, Linhai Xie, Han Wen, Liangyi Chen, Kai Lei, George Rosenberger, Xue Cai, Yingrui Wang, Qi Xiao, Huaizong Shen, Gaowen Liu, Lei Ma, Brenda Andrews, Hui Lu, Kiryl Piatkevich, Yi Zhu, Lei Bai, Yizhi Cai, Yuping Chen, Weinan E, Ge Gao, Fuchu He, Luonan Chen, Stan Z Li, Hongwu Ma, Liang Qiao, Lars M Steinmetz, Leihan Tang, Tang Tang, Xiaofan Zhang, Jing Yang, Yifan Yang, Kaicheng Yu, Jianyang Zeng, Yefeng Zheng, Bowen Zhou, Tiannan Guo
Published in
Nature. Volume 655. Issue 8121. Pages 59-70. Epub Jul 01, 2026.
Abstract
To advance the computational simulation of cellular life, we propose a virtual yeast, an artificial intelligence (AI)-driven agent that models eukaryotic cellular behaviours by integrating multimodal biological data, mechanistic reasoning and active experimentation using Saccharomyces cerevisiae as a genetically tractable and data-rich model system. Cellular complexity is decomposed into eight function-centred modules, spanning genetic, metabolic and structural systems, each realized as a domain-specific AI tool coordinated through a large language model-based orchestration layer. Built on three data pillars, namely, mechanistic knowledge, subcellular architecture and dynamic states, the system integrates representation learning and generative modelling within a closed-loop learning pipeline that autonomously designs and executes experiments. The virtual yeast serves as both a conceptual and an operational platform to optimize biosynthetic pathways, support the generation and prioritization of hypotheses across diverse cellular processes, and accelerate target discovery. By coupling biological realism with autonomous AI reasoning, the virtual yeast establishes a generalizable blueprint for constructing virtual eukaryotic cells and advancing synthetic biology.
PMID:
42387167
Bibliographic data and abstract were imported from PubMed on 02 Jul 2026.
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