Related papers: Duplication-divergence model of protein interactio…

Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…

We introduce a community network model which exhibits scale-free property and study the evolutionary Prisoner's Dilemma game (PDG) on this network model. It is found that the frequency of cooperators decreases with the increment of the…

We consider models for growing networks incorporating two effects not previously considered: (i) different species of nodes, with each species having different properties (such as different attachment probabilities to other node species);…

Different types of interactions coexist and coevolve to shape the structure and function of a multiplex network. We propose here a general class of growth models in which the various layers of a multiplex network coevolve through a set of…

In this note we make some specific observations on the distribution of the degree of a given vertex in certain model of randomly growing networks. The rule for network growth is the following. Starting with an initial graph of minimum…

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…

We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…

Conventional studies of network growth models mainly look at the steady state degree distribution of the graph. Often long time behavior is considered, hence the initial condition is ignored. In this contribution, the time evolution of the…

The study of human interactions is of central importance for understanding the behavior of individuals, groups and societies. Here, we observe the formation and evolution of networks by monitoring the addition of all new links and we…

When real networks are considered, coupled networks with connectivity and feedback-dependency links are not rare but more general. Here we develop a mathematical framework and study numerically and analytically percolation of interacting…

Mechanistic network models specify the mechanisms by which networks grow and change, allowing researchers to investigate complex systems using both simulation and analytical techniques. Unfortunately, it is difficult to write likelihoods…

Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as degree distributions or clustering…

Many complex networks from the World-Wide-Web to biological networks are growing taking into account the heterogeneous features of the nodes. The feature of a node might be a discrete quantity such as a classification of a URL document as…

High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…

We present a simple model of network growth and solve it by writing down the dynamic equations for its macroscopic characteristics like the degree distribution and degree correlations. This allows us to study carefully the percolation…

We introduce a new family of models for growing networks. In these networks new edges are attached preferentially to vertices with higher number of connections, and new vertices are created by already existing ones, inheriting part of their…

We consider a preferential attachment model that incorporates an anomaly. Our goal is to understand the evolution of the network before and after the occurrence of the anomaly by studying the influence of the anomaly on the structural…

Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…

We address the problem of link reciprocity, the non-random presence of two mutual links between pairs of vertices. We propose a new measure of reciprocity that allows the ordering of networks according to their actual degree of correlation…

Nodes in a complex networked system often engage in more than one type of interactions among them; they form a multiplex network with multiple types of links. In real-world complex systems, a node's degree for one type of links and that for…