Related papers: Preferential attachment in the protein network evo…

Complex systems can be characterized by classes of equivalency of their elements defined according to system specific rules. We propose a generalized preferential attachment model to describe the class size distribution. The model…

We study mixing patterns in networks, meaning the propensity for nodes of different kinds to connect to one another. The phenomenon of assortative mixing, whereby nodes prefer to connect to others that are similar to themselves, has been…

The web of relations linking technological innovation can be fairly described in terms of patent citations. The resulting patent citation network provides a picture of the large-scale organization of innovations and its time evolution. Here…

Preferential attachment --- by which new nodes attach to existing nodes with probability proportional to the existing nodes' degree --- has become the standard growth model for scale-free networks, where the asymptotic probability of a node…

To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…

We introduce a mechanism which models the emergence of the universal properties of complex networks, such as scale independence, modularity and self-similarity, and unifies them under a scale-free organization beyond the link. This brings a…

In this paper, we characterise the notion of preferential attachment in networks as action at a distance, and argue that it can only be an emergent phenomenon -- the actual mechanism by which networks grow always being the closing of…

We investigate a class of growing graphs embedded into the $d$-dimensional torus where new vertices arrive according to a Poisson process in time, are randomly placed in space and connect to existing vertices with a probability depending on…

The co-evolution of structure and dynamics, known as adaptivity, is a fundamental property in various systems and drives diverse emergent behaviors. However, the adaptivity in previous works is primarily stemmed from pairwise situations,…

The linear preferential attachment hypothesis has been shown to be quite successful to explain the existence of networks with power-law degree distributions. It is then quite important to determine if this mechanism is the consequence of a…

We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…

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 show that the protein-protein interaction networks can be surprisingly well described by a very simple evolution model of duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the…

We introduce a new type of preferential attachment tree that includes choices in its evolution, like with Achlioptas processes. At each step in the growth of the graph, a new vertex is introduced. Two possible neighbor vertices are selected…

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…

Recently several authors have proposed stochastic evolutionary models for the growth of complex networks that give rise to power-law distributions. These models are based on the notion of preferential attachment leading to the ``rich get…

Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…

The graph of communities is a network emerging above the level of individual nodes in the hierarchical organisation of a complex system. In this graph the nodes correspond to communities (highly interconnected subgraphs, also called modules…

We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…

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…