Related papers: Modularity "for free" in genome architecture?

We report on parallel observations in two seemingly unrelated areas of dynamical network research. The one is the so-called small world phenomenon and/or the observation of scale freeness in certain types of large (empirical) networks and…

This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…

We introduce a new mechanism of connectivity evolution in networks to account for the emergence of scale-free behavior. The mechanism works on a fixed set of nodes and promotes growth from a minimally connected initial topology by the…

We show how scale-free degree distributions can emerge naturally from growing networks by using random walks for selecting vertices for attachment. This result holds for several variants of the walk algorithm and for a wide range of…

The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…

Despite their diverse origin, networks of large real-world systems reveal a number of common properties including small-world phenomena, scale-free degree distributions and modularity. Recently, network self-similarity as a natural outcome…

Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…

In this work we study a simple evolutionary model of bipartite networks which its evolution is based on the duplication of nodes. Using analytical results along with numerical simulation of the model, we show that the above evolutionary…

Although most networks in nature exhibit complex topology the origins of such complexity remains unclear. We introduce a model of a growing network of interacting agents in which each new agent's membership to the network is determined by…

Many real life networks present an average path length logarithmic with the number of nodes and a degree distribution which follows a power law. Often these networks have also a modular and self-similar structure and, in some cases -…

Several fundamental properties of real complex networks, such as the small-world effect, the scale-free degree distribution, and recently discovered topological fractal structure, have presented the possibility of a unique growth mechanism…

We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…

In the context of growing networks, we introduce a simple dynamical model that unifies the generic features of real networks: scale-free distribution of degree and the small world effect. While the average shortest path length increases…

Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity - the near decomposability of the…

We propose a novel paradigm for modeling real-world scale-free networks, where the integration of new nodes is driven by the combined attractiveness of degree and betweenness centralities, the competition of which (expressed by a parameter…

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition and deletion of edges, as well as the…

We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement…

Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…

We analyze about two hundred naturally occurring networks with distinct dynamical origins to formally test whether the commonly assumed hypothesis of an underlying scale-free structure is generally viable. This has recently been questioned…