Related papers: Lethality and centrality in protein networks
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
The use of graph centrality measures applied to biological networks, such as protein interaction networks, underpins much research into identifying key players within biological processes. This approach however is restricted to dyadic…
While the emergence of a power law degree distribution in complex networks is intriguing, the degree exponent is not universal. Here we show that the betweenness centrality displays a power-law distribution with an exponent \eta which is…
We apply random matrix theory to complex networks. We show that nearest neighbor spacing distribution of the eigenvalues of the adjacency matrices of various model networks, namely scale-free, small-world and random networks follow…
Notable recent works have focused on the multi-layer properties of coevolving diseases. We point out that very similar systems play an important role in population ecology. Specifically we study a meta food-web model that was recently…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidences for hierarchical organization in many real networks have also been reported. Here, we present a new hierarchical model…
We study the influence of global, local and community-level risk perception on the extinction probability of a disease in several models of social networks. In particular, we study the infection progression as a…
The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle…
The scale-free (SF) structure that commonly appears in many complex networks is one of the hot topics related to social, biological, and information sciences. The self-organized generation mechanisms are expected to be useful for efficient…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic…
We study the contact process in the regime of small infection rates on finite scale-free networks with stationary dynamics based on simultaneous updating of all connections of a vertex. We allow the update rates of individual vertices to…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
We investigate the properties of the spanning trees of various real-world and model networks. The spanning tree representing the communication kernel of the original network is determined by maximizing total weight of edges, whose weights…
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…