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The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological networks, discussing their scale-free and hierarchical features. We illustrate the major network characteristics using examples from the metabolic network of the bacterium Escherichia coli. We also discuss the principles of network utilization, acknowledging that the interactions in a real network have unequal strengths. We study the interplay between topology and reaction fluxes provided by flux-balance analysis. We find that the cellular utilization of the metabolic network is both globally and locally highly inhomogeneous, dominated by hot-spots, representing connected high-flux pathways.
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory funct
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses (FBA) have
Metabolic networks are known to be scale free but the evolutionary origin of this structural property is not clearly understood. One way of studying the dynamical process is to compare the metabolic networks of species that have arisen at different p
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this b
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization