Reverse engineering of metabolic networks, a critical assessment |
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Authors: | Hendrickx Diana M Hendriks Margriet M W B Eilers Paul H C Smilde Age K Hoefsloot Huub C J |
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Institution: | Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands. D.M.Hendrickx@uva.nl |
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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. |
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