Towards the construction of a virtual yeast.
为推进细胞生命的计算模拟,研究者提出“虚拟酵母”——一种由人工智能驱动的代理,以酿酒酵母为遗传可操作、数据丰富的模式系统,通过整合多模态生物学数据、机制推理与主动实验来模拟真核细胞行为。该系统将细胞复杂性分解为遗传、代谢和结构系统等八个以功能为中心的模块,每个模块由领域专用AI工具实现,并通过基于大语言模型的编排层协调。系统以机制知识、亚细胞结构和动态状态三大数据支柱为基础,在闭环学习流程中整合表征学习与生成建模,自主设计和执行实验。虚拟酵母可作为优化生物合成通路、支持多种细胞过程假设生成与优先级排序以及加速靶点发现的概念与操作平台,为构建虚拟真核细胞和推进合成生物学提供可推广的蓝图。
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完整作者
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
作者机构
- Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China.
- Center for Machine Learning Research, Peking University, Beijing, China.
- AI for Science Institute, Beijing, China.
- National Engineering Laboratory for Big Data Analysis and Applications, Beijing, China.
- Center for Data Science, Peking University, Beijing, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Institute of Research on Cancer and Ageing of Nice (IRCAN), Faculté de Médecine, Nice, France.
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité, Berlin, Germany.
- Center for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Biomedicine, University of Basel, Basel, Switzerland.
- Department of Artificial Intelligence, School of Engineering, Westlake University, Hangzhou, China.
- Biomedical Research Core Facilities, Westlake University, Hangzhou, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, Illkirch, France.
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- South China Hospital, Health Science Center, Guangdong Key Laboratory of Genome Instability and Disease Prevention, Shenzhen University School of Medicine, Shenzhen, China.
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics Driven Cancer Precision Medicine (Chinese Academy of Medical Sciences), Beijing, China.
- International Academy of Phronesis Medicine (Guangdong), Guangzhou, China.
- DP Technology Co. Ltd., Beijing, China.
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, China.
- State Key Laboratory of Medical Proteomics, Beijing, China.
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Center for Life Sciences, College of Future Technology, Peking University, Beijing, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
- Bruker Switzerland AG, Faellanden, Switzerland.
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China.
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center of Biostatistics and Data Science, National Center for Translational Medicine, MoE Key Lab of Artificial Intelligence, AI Institute Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.
- School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
- Generative and Synthetic Genomics, Wellcome Sanger Institute, Cambridge, UK.
- Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- School of Mathematical Sciences, Peking University, Beijing, China.
- State Key Laboratory of Gene Function and Modulation Research, Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Center for Bioinformatics (CBI), Peking University, Beijing, China.
- School of Mathematical Sciences and School of AI, Shanghai Jiao Tong University, Shanghai, China.
- AI Laboratory, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
- Department of Chemistry, Fudan University, Shanghai, China.
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
- Center for Interdisciplinary Studies, Westlake University, Hangzhou, China.
- Wuhan Metware Biotechnology Co. Ltd., Wuhan, China.
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China.
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing, China.
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, China.
- Autolab, Westlake University, Hangzhou, China.
- School of Engineering, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Medical Artificial Intelligence Laboratory, Westlake University, Hangzhou, China.
- Department of Electronic Engineering, Tsinghua University, Beijing, China.
- Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. guotiannan@westlake.edu.cn.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China. guotiannan@westlake.edu.cn.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China. guotiannan@westlake.edu.cn.
技术路线
多模态生物数据与机理知识、亚细胞结构、动态状态三类数据支柱 → 细胞复杂性分解为八个功能模块(遗传、代谢、结构系统),各模块为领域AI工具并由大语言模型调度层协调
最近 5 个完整年度引用趋势
不含 2026 年,仅展示最近 5 个完整年度。

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