Related papers: Duplication-divergence model of protein interactio…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
We investigate a network model based on an infinite regular square lattice embedded in the Euclidean plane where the node connection probability is given by the geometrical distance of nodes. We show that the degree distribution in the…
We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement…
The evolution of complex networks is governed by both growing rules and internal properties. Most evolving network models (e.g. preferential attachment) emphasize on the growing strategy, while neglecting the characteristics of individual…
Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition and deletion of edges, as well as the…
Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…
The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the…
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows…
We introduce a growing network model---the copying model---in which a new node attaches to a randomly selected target node and, in addition, independently to each of the neighbors of the target with copying probability $p$. When…
Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole…
The study of epidemic spreading on populations of networked individuals has seen recently a great deal of significant progresses. A common point of all past studies is, however, that there is only one peak of infected density in each single…
We present a link rewiring mechanism to produce surrogates of a network where both the degree distribution and the rich--club connectivity are preserved. We consider three real networks, the AS--Internet, the protein interaction and the…
Evolving network models under a dynamic growth rule which comprises the addition and deletion of nodes are investigated. By adding a node with a probability $P_a$ or deleting a node with the probability $P_d=1-P_a$ at each time step, where…
The in-degree and out-degree distributions of a growing network model are determined. The in-degree is the number of incoming links to a given node (and vice versa for out-degree. The network is built by (i) creation of new nodes which each…
We study the evolution of a random weighted network with complex nonlinear dynamics at each node, whose activity may cease as a result of interactions with other nodes. Starting from a knowledge of the micro-level behaviour at each node, we…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
The scale free structure p(k)~k^{-gamma} of protein-protein interaction networks can be reproduced by a static physical model in simulation. We inspect the model theoretically, and find the key reason for the model to generate apparent…
In many complex systems, the dynamic processes that take place on a network and the changes in the network topology are intertwined. Here, we propose a model of coevolutionary dynamics of information spreading which is accompanied with link…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…