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本文引用的文献

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Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism.计算重建组织特异性代谢模型：在人类肝脏代谢中的应用。
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Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection.铜绿假单胞菌慢性囊性纤维化肺部感染期间的代谢网络分析。
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Compartmentalization of the Edinburgh Human Metabolic Network.爱丁堡人类代谢网络的分区化。
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Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis.嗜盐古菌 Natronomonas pharaonis 的生长和代谢特征。
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Biofuel production improvement with genome-scale models: The role of cell composition.基于基因组尺度模型的生物燃料生产改进：细胞组成的作用。
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High-throughput DNA sequencing--concepts and limitations.高通量 DNA 测序--概念与局限。
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OptFlux: an open-source software platform for in silico metabolic engineering.OptFlux：用于计算机辅助代谢工程的开源软件平台。
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What is flux balance analysis?通量平衡分析是什么？
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Imaging enzymes at work: metabolic mapping by enzyme histochemistry.在工作中对酶进行成像：通过酶组织化学进行代谢作图。
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A protocol for generating a high-quality genome-scale metabolic reconstruction.生成高质量基因组尺度代谢重建的方案。
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全基因组代谢网络重建与基于约束的建模。

Whole-genome metabolic network reconstruction and constraint-based modeling.

作者信息

Haggart Charles R, Bartell Jennifer A, Saucerman Jeffrey J, Papin Jason A

机构信息

Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.

出版信息

Methods Enzymol. 2011;500:411-33. doi: 10.1016/B978-0-12-385118-5.00021-9.

DOI:10.1016/B978-0-12-385118-5.00021-9
PMID:21943909
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3361743/
Abstract

With the advent of modern high-throughput genomics, there is a significant need for genome-scale analysis techniques that can assist in complex systems analysis. Metabolic genome-scale network reconstructions (GENREs) paired with constraint-based modeling are an efficient method to integrate genomics, transcriptomics, and proteomics to conduct organism-specific analysis. This text explains key steps in the GENRE construction process and several methods of constraint-based modeling that can help elucidate basic life processes and development of disease treatment, bioenergy solutions, and industrial bioproduction applications.

摘要

随着现代高通量基因组学的出现，迫切需要能够辅助复杂系统分析的基因组规模分析技术。代谢基因组规模网络重建（GENREs）与基于约束的建模相结合，是整合基因组学、转录组学和蛋白质组学以进行特定生物体分析的有效方法。本文解释了GENRE构建过程中的关键步骤以及几种基于约束的建模方法，这些方法有助于阐明基本生命过程以及疾病治疗、生物能源解决方案和工业生物生产应用的发展。