Related papers: Metabolic networks are almost nonfractal: A compre…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Biological networks, such as cellular metabolic pathways or networks of corticocortical connections in the brain, are intricately organized, yet remarkably robust toward structural damage. Whereas many studies have investigated specific…
The self-similarity of complex networks is typically investigated through computational algorithms the primary task of which is to cover the structure with a minimal number of boxes. Here we introduce a box-covering algorithm that not only…
Over the past three decades, describing the reality surrounding us using the language of complex networks has become very useful and therefore popular. One of the most important features, especially of real networks, is their complexity,…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Controlling complex networks is of paramount importance in science and engineering. Despite the recent development of structural-controllability theory, we continue to lack a framework to control undirected complex networks, especially…
Covering a network with the minimum possible number of boxes can reveal interesting features for the network structure, especially in terms of self-similar or fractal characteristics. Considerable attention has been recently devoted to this…
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
In this article, we present a novel box-covering algorithm for analyzing the fractal properties of complex networks. Unlike traditional algorithms that impose a predetermined box size, our approach assigns nodes to boxes identified by their…
In this paper we define a new class of weighted complex networks sharing several properties with fractal sets, and whose topology can be completely analytically characterized in terms of the involved parameters and of the fractal dimension.…
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…
This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…
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…
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…
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…
Complex networks have recently attracted much attention in diverse areas of science and technology. Many networks such as the WWW and biological networks are known to display spatial heterogeneity which can be characterized by their fractal…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Research on fractal networks is a dynamically growing field of network science. A central issue is to analyze fractality with the so-called box-covering method. As this problem is known to be NP-hard, a plethora of approximating algorithms…
Theoretical frameworks to estimate the tolerance of metabolic networks to various failures are important to evaluate the robustness of biological complex systems in systems biology. In this paper, we focus on a measure for robustness in…