Related papers: Lethality and centrality in protein networks
Recent genomic analyses on the cellular metabolic network show that reaction flux across enzymes are diverse and exhibit power-law behavior in its distribution. While one may guess that the reactions with larger fluxes are more likely to be…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
Structure entails function and thus a structural description of the brain will help to understand its function and may provide insights into many properties of brain systems, from their robustness and recovery from damage, to their dynamics…
We find that the fractal scaling in a class of scale-free networks originates from the underlying tree structure called skeleton, a special type of spanning tree based on the edge betweenness centrality. The fractal skeleton has the…
Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated…
Connectivity correlations play an important role in the structure of scale-free networks. While several empirical studies exist, there is no general theoretical analysis that can explain the largely varying behavior of real networks. Here,…
In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement…
A dynamical system approaching the first-order transition can exhibit a specific type of critical behavior known as self-organized bistability (SOB). It lies in the fact that the system can permanently switch between the coexisting states…
Recently, it was found by Schneider et al. [Proc. Natl. Acad. Sci. USA, 108, 3838 (2011)], using simulations, that scale-free networks with "onion structure" are very robust against targeted high degree attacks. The onion structure is a…
With the advent of high-throughput wet lab technologies the amount of protein interaction data available publicly has increased substantially, in turn spurring a plethora of computational methods for in silico knowledge discovery from this…
A large number of complex networks, both natural and artificial, share the presence of highly heterogeneous, scale-free degree distributions. A few mechanisms for the emergence of such patterns have been suggested, optimization not being…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
We model the robustness against random failure or intentional attack of networks with arbitrary large-scale structure. We construct a block-based model which incorporates --- in a general fashion --- both connectivity and interdependence…
Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et…
A complete understanding of real networks requires us to understand the consequences of the uneven interaction strengths between a system's components. Here we use the minimum spanning tree (MST) to explore the effect of weight assignment…
Food webs -- networks of predators and prey -- have long been known to exhibit "intervality": species can generally be ordered along a single axis in such a way that the prey of any given predator tend to lie on unbroken compact intervals.…
Many real networks such as the World Wide Web, financial, biological, citation and social networks have a power-law degree distribution. Networks with this feature are also called scale-free. Several models for producing scale-free networks…
In this paper, we compared cancerous and normal cell according to their protein-protein interaction network. Cancer is one of the complicated diseases and experimental investigations have been showed that protein interactions have an…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…