相关论文: Modularity "for free" in genome architecture?

We propose a growing network model that consists of two tunable mechanisms: growth by merging modules which are represented as complete graphs and a fitness-driven preferential attachment. Our model exhibits the three prominent statistical…

Scale-free networks are abundant in nature and society, describing such diverse systems as the world wide web, the web of human sexual contacts, or the chemical network of a cell. All models used to generate a scale-free topology are…

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…

The functional consequences of local and global dynamics can be very different in natural systems. Many such systems have a network description that exhibits strong local clustering as well as high communication efficiency, often termed as…

We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…

Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…

We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…

In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…

A large computer program is typically divided into many hundreds or even thousands of smaller units, whose logical connections define a network in a natural way. This network reflects the internal structure of the program, and defines the…

Various real-life networks of current interest are simultaneously scale-free and modular. Here we study analytically the average distance in a class of deterministically growing scale-free modular networks. By virtue of the recursive…

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…

Several networks occurring in real life have modular structures that are arranged in an hierarchical fashion. In this paper, we have proposed a model for such networks, using a stochastic generation method. Using this model we show that,…

Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…

In this paper we introduce a model of spatial network growth in which nodes are placed at randomly selected locations on a unit square in $\mathbb{R}^2$, forming new connections to old nodes subject to the constraint that edges do not…

What is the underlying mechanism leading to power-law degree distributions of many natural and artificial networks is still at issue. We consider that scale-free networks emerges from self-organizing process, and such a evolving model is…

A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…

Scale-free networks are ubiquitous in social, biological and technological networked systems. Dynamic Scale-free networks and their synchronizations are important to understand and predict the behavior of social, biological and…

Hierarchical organization -- the recursive composition of sub-modules -- is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations…

A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…

The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…