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机器学习助力微生物细胞工厂:综述

Machine Learning Empowering Microbial Cell Factory: A Comprehensive Review.

作者信息

Kong Dechun, Qian Jinyi, Gao Cong, Wang Yuetong, Shi Tianqiong, Ye Chao

机构信息

School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, People's Republic of China.

Ministry of Education Key Laboratory of NSLSCS, Nanjing Normal University, Nanjing, 210023, People's Republic of China.

出版信息

Appl Biochem Biotechnol. 2025 May 21. doi: 10.1007/s12010-025-05260-x.

DOI:10.1007/s12010-025-05260-x
PMID:40397295
Abstract

The wide application of machine learning has provided more possibilities for biological manufacturing, and the combination of machine learning and synthetic biology technology has ignited even more brilliant sparks, which has created an unpredictable value for the upgrading of microbial cell factories. The review delves into the synergies between machine learning and synthetic biology to create research worth investigating in biotechnology. We explore relevant databases, toolboxes, and machine learning-derived models. Furthermore, we examine specific applications of this combined approach in chemical production, human health, and environmental remediation. By elucidating these successful integrations, this review aims to provide valuable guidance for future research at the intersection of biomanufacturing and artificial intelligence.

摘要

机器学习的广泛应用为生物制造提供了更多可能性,机器学习与合成生物学技术的结合更是点燃了更为璀璨的火花,为微生物细胞工厂的升级创造了不可估量的价值。本综述深入探讨了机器学习与合成生物学之间的协同作用,以开创值得在生物技术领域研究的课题。我们探索了相关数据库、工具箱以及源自机器学习的模型。此外,我们考察了这种组合方法在化学生产、人类健康和环境修复方面的具体应用。通过阐明这些成功的整合案例,本综述旨在为生物制造与人工智能交叉领域的未来研究提供有价值的指导。

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本文引用的文献

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Cell factory design with advanced metabolic modelling empowered by artificial intelligence.人工智能赋能的先进代谢建模细胞工厂设计。
Metab Eng. 2024 Sep;85:61-72. doi: 10.1016/j.ymben.2024.07.003. Epub 2024 Jul 20.
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Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based k data.基于机器学习的 k 数据构建嗜热毁丝霉酶约束代谢网络模型
Microb Cell Fact. 2024 May 15;23(1):138. doi: 10.1186/s12934-024-02415-z.
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Optimisation of surfactin yield in using data-efficient active learning and high-throughput mass spectrometry.
利用数据高效主动学习和高通量质谱法优化表面活性素产量。
Comput Struct Biotechnol J. 2024 Feb 15;23:1226-1233. doi: 10.1016/j.csbj.2024.02.012. eCollection 2024 Dec.
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Machine Learning-Guided Optimization of -Coumaric Acid Production in Yeast.机器学习指导酵母中-香豆酸生产的优化。
ACS Synth Biol. 2024 Apr 19;13(4):1312-1322. doi: 10.1021/acssynbio.4c00035. Epub 2024 Mar 28.
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Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches.通过机器学习从组学数据预测代谢通量:从知识驱动方法向数据驱动方法的转变。
Comput Struct Biotechnol J. 2023 Oct 5;21:4960-4973. doi: 10.1016/j.csbj.2023.10.002. eCollection 2023.
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Deep flanking sequence engineering for efficient promoter design using DeepSEED.使用 DeepSEED 进行高效启动子设计的深侧翼序列工程。
Nat Commun. 2023 Oct 9;14(1):6309. doi: 10.1038/s41467-023-41899-y.
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A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets.使用机器迁移学习和小而高质量数据集进行可推广的 Cas9/sgRNA 预测模型。
Nat Commun. 2023 Sep 7;14(1):5514. doi: 10.1038/s41467-023-41143-7.
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J Proteome Res. 2023 Jul 7;22(7):2186-2198. doi: 10.1021/acs.jproteome.2c00394. Epub 2023 Jun 14.
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: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning.通过深度学习预测CRISPR介导的表观基因组编辑的sgRNA活性
Comput Struct Biotechnol J. 2022 Nov 19;21:202-211. doi: 10.1016/j.csbj.2022.11.034. eCollection 2023.
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