Optimization based automated curation of metabolic reconstructions

Background: Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them. Results: In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. This connectivity restoration ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas
• Keywords: BMCBI 2007, Escherichia Coli, Eukaryotic Metabolic Reconstructions, Metabolites