Reconstruction of biochemical networks in microorganisms
TLDR
The process that is currently used to achieve comprehensive network reconstructions is described and how these reconstructions are curated and validated is discussed to aid the growing number of researchers who are carrying out reconstructions for particular target organisms.Abstract:
Systems analysis of metabolic and growth functions in microbial organisms is rapidly developing and maturing. Such studies are enabled by reconstruction, at the genomic scale, of the biochemical reaction networks that underlie cellular processes. The network reconstruction process is organism specific and is based on an annotated genome sequence, high-throughput network-wide data sets and bibliomic data on the detailed properties of individual network components. Here we describe the process that is currently used to achieve comprehensive network reconstructions and discuss how these reconstructions are curated and validated. This Review should aid the growing number of researchers who are carrying out reconstructions for particular target organisms.read more
Citations
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What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
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How antibiotics kill bacteria: from targets to networks
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A protocol for generating a high-quality genome-scale metabolic reconstruction.
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Applications of genome-scale metabolic reconstructions
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Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
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