MACAW：一种半自动检测基因组尺度代谢模型误差的方法

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-03-28 DOI:10.1186/s13059-025-03533-6

Devlin C. Moyer, Justin Reimertz, Daniel Segrè, Juan I. Fuxman Bass

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引用次数: 0

摘要

基因组尺度代谢模型（GSMMs）用于预测代谢通量，其应用范围从鉴定新的药物靶点到工程微生物代谢。错误或缺失的反应，分散在密集互连的网络中，是这些应用的限制因素。我们提出了代谢准确性检查和分析工作流（MACAW），这是一套算法，有助于识别和可视化连接通路水平上的错误，而不是单个反应。我们展示了MACAW如何在人为整理和自动生成的人类、酵母和细菌的gsmm中突出不同严重程度的不准确性，并有助于确定在未来模型构建工作中需要解决的系统问题。

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MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models

Genome-scale metabolic models (GSMMs) are used to predict metabolic fluxes, with applications ranging from identifying novel drug targets to engineering microbial metabolism. Erroneous or missing reactions, scattered throughout densely interconnected networks, are a limiting factor in these applications. We present Metabolic Accuracy Check and Analysis Workflow (MACAW), a suite of algorithms that helps to identify and visualize errors at the level of connected pathways, rather than individual reactions. We show how MACAW highlights inaccuracies of varying severity in manually curated and automatically generated GSMMs for humans, yeast, and bacteria and helps to identify systematic issues to be addressed in future model construction efforts.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.