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Issue 2, 2011
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Reverse engineering of metabolic networks, a critical assessment

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Abstract

Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.

Graphical abstract: Reverse engineering of metabolic networks, a critical assessment

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Publication details

The article was received on 06 Jul 2010, accepted on 11 Oct 2010 and first published on 10 Nov 2010


Article type: Paper
DOI: 10.1039/C0MB00083C
Citation: Mol. BioSyst., 2011,7, 511-520
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    Reverse engineering of metabolic networks, a critical assessment

    D. M. Hendrickx, M. M. W. B. Hendriks, P. H. C. Eilers, A. K. Smilde and H. C. J. Hoefsloot, Mol. BioSyst., 2011, 7, 511
    DOI: 10.1039/C0MB00083C

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