Related papers: Network Structure and Dynamics, and Emergence of R…
Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…
This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction…
Designing plausible network models typically requires scholars to form a priori intuitions on the key drivers of network formation. Oftentimes, these intuitions are supported by the statistical estimation of a selection of network evolution…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
Natural selection and random drift are competing phenomena for explaining the evolution of populations. Combining a highly fit mutant with a population structure that improves the odds that the mutant spreads through the whole population…
In this paper we investigate networks whose evolution is governed by the interaction of a random assembly process and an optimization process. In the first process, new nodes are added one at a time and form connections to randomly selected…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
We investigate a model of evolving random network, introduced by us previously {[}{\it Phys. Rev. Lett.} {\bf 83}, 5587 (1999){]} . The model is a generalization of the Bak-Sneppen model of biological evolution, with the modification that…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We introduce a method that can be used to evolve the topology of a network in a way that preserves both the network's spectral as well as local structure. This method is quite versatile in the sense that it can be used to evolve a network's…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…