Recent small-world studies of the global structure of metabolic networks have been based on the shortest-path distance. In this paper, we propose new distance measures that are based on the structure of feasible metabolic pathways between metabolites. We argue that these distances capture the complexity of the underlying biochemical processes more accurately than the shortest-path distance. To ...

Mycoplasma pneumoniae is a human pathogen recently proposed as a genome-reduced model for bacterial systems biology. Here, we study the response of its metabolic network to different forms of structural stress, including removal of individual and pairs of reactions and knockout of genes and clusters of co-expressed genes. Our results reveal a network architecture as robust as that of other mode...

We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of random networks, including Erdős-Rényi random graphs and synthetic small world networks of the same connectivity, both the metabolic network and models for the chemical reaction networks of planeta...

Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. Using EFMs, a metabolic network can be transformed into its macroscopic counterpart, in which the internal metabolites have been eliminated and only external metabolites remain. In EFMs-based metabolic flux analysis (MFA) experimentally determined external fluxes are used...

Recent work has demonstrated that genetic programming is capable of automatically creating complex networks (such as analog electrical circuits and controllers) whose behavior is modeled by continuous-time differential equations (both linear and nonlinear) and whose behavior matches prespecified output values. The concentrations of substances participating in networks of chemical reactions are ...

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer prog...

One of the long-expected goals of genome-scale metabolic modeling is to evaluate the influence of the perturbed enzymes to the flux distribution. Both ordinary differential equation (ODE) models and the constraint-based models, like Flux balance analysis (FBA), lack of the room of performing metabolic control analysis (MCA) for large-scale networks. In this study, we developed a Hyper-Cube Shri...

Genome-scale metabolic network reconstructions represent biochemical, genetic, and genomic (BiGG) knowledge bases for a target organism (Reed et al, 2006). Thus, they correspond to two-dimensional genome annotations: that is, they contain all nodes and links that comprise a biochemical reaction network defined by the genome (Palsson, 2004). These reconstructions allow the conversion of biologic...

Reconstruction of genome-scale metabolic networks is now possible using multiple different data types. Constraint-based modeling is an approach to interrogate capabilities of reconstructed networks by constraining possible cellular behavior through the imposition of physicochemical laws. As a result, a steady-state flux space is defined that contains all possible functional states of the networ...