Related papers: Modularity "for free" in genome architecture?
Modularity is designed to measure the strength of division of a network into clusters (known also as communities). Networks with high modularity have dense connections between the vertices within clusters but sparse connections between…
Recently, one paper in Nature(Papadopoulos, 2012) raised an old debate on the origin of the scale-free property of complex networks, which focuses on whether the scale-free property origins from the optimization or not. Because the…
Natural selection successfully explains how organisms accumulate adaptive change despite that traits acquired over a lifetime are eliminated at the end of each generation. However, in some domains that exhibit cumulative, adaptive change --…
Networks that are organized as a hierarchy of modules have been the subject of much research, mainly focusing on algorithms that can extract this community structure from data. The question of why modular hierarchical organizations are so…
The ever-increasing knowledge of the structure of various real-world networks has uncovered their complex multi-mechanism-governed evolution processes. Therefore, a better understanding of the structure and evolution of these networked…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology 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…
Modular networks, such as critical infrastructures, are often built from distinct, densely connected modules (e.g., cities) that are sparsely interconnected. When such networks are gradually and randomly disrupted under a percolation…
We describe systems using Kauffman and similar networks. They are directed funct ioning networks consisting of finite number of nodes with finite number of discr ete states evaluated in synchronous mode of discrete time. In this paper we…
We study the growth of random networks under a constraint that the diameter, defined as the average shortest path length between all nodes, remains approximately constant. We show that if the graph maintains the form of its degree…
Many real networks have cliques as their constitutional units. Here we present a family of scale-free network model consist of cliques, which is established by a simple recursive algorithm. We investigate the networks both analytically and…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
In a range of scientific coauthorship networks, transitions emerge in degree distributions, correlations between degrees and local clustering coefficients, etc. The existence of those transitions could be regarded as a result of the…
We propose an extended local-world evolving network model including a triad formation step. In the process of network evolution, random fluctuation in the number of new edges is involved. We derive analytical expressions for degree…
Complex networks from such different fields as biology, technology or sociology share similar organization principles. The possibility of a unique growth mechanism promises to uncover universal origins of collective behaviour. In…
The human brain exhibits a complex structure made of scale-free highly connected modules loosely interconnected by weaker links to form a small-world network. These features appear in healthy patients whereas neurological diseases often…
Activity or spin patterns on random scale-free network are studied by mean field analysis and computer simulations. These activity patterns evolve in time according to local majority-rule dynamics which is implemented using (i) parallel or…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…