Related papers: Duplication-divergence model of protein interactio…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
We study the evolution of networks when the creation and decay of links are based on the position of nodes in the network measured by their centrality. We show that the same network dynamics arises under various centrality measures, and…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
The degree distributions of complex networks are usually considered to be power law. However, it is not the case for a large number of them. We thus propose a new model able to build random growing networks with (almost) any wanted degree…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce a hybrid network model composed…
The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link…
We model the evolution of the Internet at the Autonomous System level as a process of competition for users and adaptation of bandwidth capability. We find the exponent of the degree distribution as a simple function of the growth rates of…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Many real world networks, such as social networks, are primarily formed through local interactions between agents. Additionally, in contrast with common network models, social and biological networks exhibit a high degree of clustering.…
We investigate the growth of connectivity in a network. In our model, starting with a set of disjoint nodes, links are added sequentially. Each link connects two nodes, and the connection rate governing this random process is proportional…
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…
Inspired by empirical data on real world complex networks, the last few years have seen an explosion in proposed generative models to understand and explain observed properties of real world networks, including power law degree distribution…
Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…
This Letter introduces a generalization of known duplication-divergence models for growing random graphs. This general duplication-divergence model includes a new coupled divergence asymmetry rate, which allows to obtain the structure of…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Many growing networks possess accelerating statistics where the number of links added with each new node is an increasing function of network size so the total number of links increases faster than linearly with network size. In particular,…