Nemenman et al., 2007a

From Ilya Nemenman: Theoretical Biophysics @ Emory
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I Nemenman, GS Escola, WS Hlavacek, PJ Unkefer, CJ Unkefer, ME Wall. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann. N.Y. Acad. Sci. 1115:102-115, 2007. Arxiv. PDF.

We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high- throughput metabolite profiling data. For this, we generate synthetic metabolic profiles for benchmarking purposes based on a well-established model for red blood cell metabolism. A variety of data sets is generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and temporal dynamics. These data sets are made available online. We apply ARACNE, a mainstream transcriptional networks reverse engineering algorithm, to these data sets and observe performance comparable to that obtained in the transcriptional domain, for which the algorithm was originally designed.
The data sets generated in the course of this work for benchmarking purposes are available at the RBC Metabolic Network page.