Related papers: Lethality and centrality in protein networks
In many networks such as transportation or communication networks, distance is certainly a relevant parameter. In addition, real-world examples suggest that when long-range links are existing, they usually connect to hubs-the well connected…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
Protein-protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological…
Very often, when studying topological or dynamical properties of random scale-free networks, it is tacitly assumed that degree-degree correlations are not present. However, simple constraints, such as the absence of multiple edges and…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness…
Co-evolution exhibited by a network system, involving the intricate interplay between the dynamics of the network itself and the subsystems connected by it, is a key concept for understanding the self-organized, flexible nature of…
We show that not only preferential attachment but also preferential depletion leads to scale-free networks. The resulting degree distribution exponents is typically less than two (5/3) as opposed to the case of the growth models studied…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
We show that the connectivity distributions $P(k,t)$ of scale-free growing networks ($t$ is the network size) have the generic scale -- the cut-off at $k_{cut} \sim t^\beta$. The scaling exponent $\beta$ is related to the exponent $\gamma$…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
We study the detailed mechanism of the failure of scale-free networks under intentional attacks. Although it is generally accepted that such networks are very sensitive to targeted attacks, we show that for a particular type of structure…
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
Signaling pathways and networks determine the ability to communicate in systems ranging from living cells to human society. We investigate how the network structure constrains communication in social-, man-made and biological networks. We…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Thanks to recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila…
The concept of nestedness, in particular for ecological and economical networks, has been introduced as a structural characteristic of real interacting systems. We suggest that the nestedness is in fact another way to express a mesoscale…
We confront a network model of human aging and mortality in which nodes represent health attributes that interact within a scale-free network topology, with observational data that uses both clinical and laboratory (pre-clinical) health…
We examine some characteristic properties of reaction-diffusion processes of the A+A->0 type on scale-free networks. Due to the inhomogeneity of the structure of the substrate, as compared to usual lattices, we focus on the characteristics…