Related papers: Randomizing genome-scale metabolic networks
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
We describe a new method for the random sampling of connected networks with a specified degree sequence. We consider both the case of simple graphs and that of loopless multigraphs. The constraints of fixed degrees and of connectedness are…
In a social network individuals or nodes connect to other nodes by choosing one of the channels of communication at a time to re-establish the existing social links. Since available data sets are usually restricted to a limited number of…
Routing information through networks is a universal phenomenon in both natural and manmade complex systems. When each node has full knowledge of the global network connectivity, finding short communication paths is merely a matter of…
From the perspective of network analysis, the ubiquitous networks are comprised of regular and irregular components, which makes uncovering the complexity of network structures to be a fundamental challenge. Exploring the regular…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
Within the last fifteen years, network theory has been successfully applied both to natural sciences and to socioeconomic disciplines. In particular, bipartite networks have been recognized to provide a particularly insightful…
Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the…
In network science, a group of nodes connected with each other at higher probability than with those outside the group is referred to as a community. From the perspective that individual communities are associated with functional modules…
Network data have appeared frequently in recent research. For example, in comparing the effects of different types of treatment, network models have been proposed to improve the quality of estimation and hypothesis testing. In this paper,…
Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of…
In certain instances an electric network transforms in natural ways by the addition or removal of an edge. This can have interesting consequences for random walks, in light of the known relationships between electric resistance and random…
Recent progress has clarified many features of the global architecture of biological metabolic networks, which have highly organized and optimized tolerances and tradeoffs (HOT) for functional requirements of flexibility, efficiency,…
The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to…
We study the properties of discrete-time random walks on networks formed by randomly interconnected cliques, namely, random networks of cliques. Our purpose is to derive the parameters that define the network structure -- specifically, the…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…