Related papers: Metabolic networks are almost nonfractal: A compre…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
Recently, self-similarity of complex networks have attracted much attention. Fractal dimension of complex network is an open issue. Hub repulsion plays an important role in fractal topologies. This paper models the repulsion among the nodes…
Real networks are complex dynamical systems, evolving over time with the addition and deletion of nodes and links. Currently, there exists no principled mathematical theory for their dynamics -- a grand-challenge open problem. Here, we show…
The topological information of a network can be retrieved equivalently from its complement consisting of the same nodes but complementary edges. Hence the partition of a network into certain substructures based on given criteria should be…
We develop a geometric framework to study the structure and function of complex networks. We assume that hyperbolic geometry underlies these networks, and we show that with this assumption, heterogeneous degree distributions and strong…
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…
A plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where…
This work studies the limitations of uniquely identifying the structure (i.e., topology) of a networked linear system from partial measurements of its nodal dynamics. In general, many networks can be consistent with these measurements; this…
This article describes the application of recently introduced complex networks concepts and methods to the characterization and analysis of cortical bone structure. Three-dimensional reconstructions of the system of channels underlying bone…
Numerical analysis of data from international trade and ecological networks has shown that the non-linear fitness-complexity metric is the best candidate to rank nodes by importance in bipartite networks that exhibit a nested structure.…
We introduce the concept of boundaries of a complex network as the set of nodes at distance larger than the mean distance from a given node in the network. We study the statistical properties of the boundaries nodes of complex networks. We…
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…
Many real-world complex networks contain a significant amount of structural redundancy, in which multiple vertices play identical topological roles. Such redundancy arises naturally from the simple growth processes which form and shape many…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…
Fractal scale-free networks are empirically known to exhibit disassortative degree mixing. It is, however, not obvious whether a negative degree correlation between nearest neighbor nodes makes a scale-free network fractal. Here we examine…
It is suggested that the degree distribution for networks of the cell-metabolism for simple organisms reflects an ubiquitous randomness. This implies that natural selection has exerted no or very little pressure on the network degree…