Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.

ABSTRACT: Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict the effects of genetic changes and to design strains with desired metabolic properties. The major bottleneck in modeling genome-scale metabolic systems is the establishment and manual curation of reliable stoichiometric models. Initial reconstructions are typically refined through comparisons to experimental growth data from gene knockouts or nutrient environments. Existing methods iteratively correct one erroneous model prediction at a time, resulting in accumulating network changes that are often not globally optimal. We present GlobalFit, a bi-level optimization method that finds a globally optimal network, by identifying the minimal set of network changes needed to correctly pr

SUBMITTER: Hartleb D 

PROVIDER: S-EPMC4970803 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature