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Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may, however, introduce dynamical possibilities that are not accessible to the original system. We show that large random networks of variables coupled through continuous transfer functions often fail to exhibit the complex dynamics of corresponding Boolean models in the disordered (chaotic) regime, even when each individual function appears to be a good candidate for Boolean idealization. A suitably modified Boolean theory explains the behavior of systems in which information does not propagate faithfully down certain chains of nodes. Model networks incorporating calculated or directly measured transfer functions reported in the literature on transcriptional regulation of genes are described by the modified theory.
Boolean networks are discrete dynamical systems for modeling regulation and signaling in living cells. We investigate a particular class of Boolean functions with inhibiting inputs exerting a veto (forced zero) on the output. We give analytical expre
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a Boltzmann-l
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, d
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
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network m