Related papers: Duplication-divergence model of protein interactio…
Network growth as described by the Duplication-Divergence model proposes a simple general idea for the evolution dynamics of natural networks. In particular it is an alternative to the well known Barab\'asi-Albert model when applied to…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
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…
Duplication-divergence models are a popular model for the evolution of gene and protein interaction networks. However, existing duplication-divergence models often neglect realistic features such as loss of interactions. Thus, in this paper…
In recent decades, it has been emphasized that the evolving structure of networks may be shaped by interaction principles that yield sparse graphs with a vertex degree distribution exhibiting an algebraic tail, and other structural traits…
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional…
We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for…
A population of complete subgraphs or cliques in a network evolving via duplication-divergence is considered. We find that a number of cliques of each size scales linearly with the size of the network. We also derive a clique population…
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…
Duplication graphs are graphs that grow by duplication of existing vertices, and are important models of biological networks, including protein-protein interaction networks and gene regulatory networks. Three models of graph growth are…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
We introduce a minimalistic model based on dynamic node deletion and node duplication with heterodimerisation. The model is intended to capture the essential features of the evolution of protein interaction networks. We derive an exact…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary…
We propose a network model with a fixed number of nodes and links with a dynamics which favors links between nodes differing in connectivity. Parameter regimes where the degree distributions follow power-laws, P(k) ~ k^-gamma, high…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
Are biological networks different from other large complex networks? Both large biological and non-biological networks exhibit power-law graphs (number of nodes with degree k, N(k) ~ k-b) yet the exponents, b, fall into different ranges.…