Single-cell omics analysis with genome-scale metabolic modeling

IF 7.1 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Current opinion in biotechnology Pub Date : 2024-02-15 DOI:10.1016/j.copbio.2024.103078
Yu Chen , Johan Gustafsson , Jingyu Yang , Jens Nielsen , Eduard J Kerkhoven
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Abstract

Single-cell technologies have been widely used in biological studies and generated a plethora of single-cell data to be interpreted. Due to the inclusion of the priori metabolic network knowledge as well as gene–protein–reaction associations, genome-scale metabolic models (GEMs) have been a powerful tool to integrate and thereby interpret various omics data mostly from bulk samples. Here, we first review two common ways to leverage bulk omics data with GEMs and then discuss advances on integrative analysis of single-cell omics data with GEMs. We end by presenting our views on current challenges and perspectives in this field.

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利用基因组尺度代谢模型进行单细胞全微观分析
单细胞技术已广泛应用于生物学研究,并产生了大量有待解读的单细胞数据。由于包含了先验代谢网络知识以及基因-蛋白质反应关联,基因组尺度代谢模型(GEMs)已成为整合并解释各种omics数据(主要来自大样本)的有力工具。在此,我们首先回顾了利用 GEMs 利用大容量全息数据的两种常见方法,然后讨论了利用 GEMs 综合分析单细胞全息数据的进展。最后,我们将就这一领域当前面临的挑战和前景发表自己的看法。
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来源期刊
Current opinion in biotechnology
Current opinion in biotechnology 工程技术-生化研究方法
CiteScore
16.20
自引率
2.60%
发文量
226
审稿时长
4-8 weeks
期刊介绍: Current Opinion in Biotechnology (COBIOT) is renowned for publishing authoritative, comprehensive, and systematic reviews. By offering clear and readable syntheses of current advances in biotechnology, COBIOT assists specialists in staying updated on the latest developments in the field. Expert authors annotate the most noteworthy papers from the vast array of information available today, providing readers with valuable insights and saving them time. As part of the Current Opinion and Research (CO+RE) suite of journals, COBIOT is accompanied by the open-access primary research journal, Current Research in Biotechnology (CRBIOT). Leveraging the editorial excellence, high impact, and global reach of the Current Opinion legacy, CO+RE journals ensure they are widely read resources integral to scientists' workflows. COBIOT is organized into themed sections, each reviewed once a year. These themes cover various areas of biotechnology, including analytical biotechnology, plant biotechnology, food biotechnology, energy biotechnology, environmental biotechnology, systems biology, nanobiotechnology, tissue, cell, and pathway engineering, chemical biotechnology, and pharmaceutical biotechnology.
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