Related papers: Preferential attachment in the protein network evo…
Complex networks in different areas exhibit degree distributions with heavy upper tail. A preferential attachment mechanism in a growth process produces a graph with this feature. We herein investigate a variant of the simple preferential…
In this paper, we first discuss the origin of preferential attachment. Then we establish the generalized preferential attachment which has two new properties; first, it encapsulates both the topological and weight aspects of a network,…
We analyze the growth models for complex networks including preferential attachment (A.-L. Barabasi and R. Albert, Science 286, 509 (1999)) and fitness model (Caldarelli et al., Phys. Rev. Lett. 89, 258702 (2002)) and demonstrate that,…
Protein-protein interactions can be properly modeled as scale-free complex networks, while the lethality of proteins has been correlated with the node degrees, therefore defining a lethality-centrality rule. In this work we revisit this…
Preferential attachment is a central paradigm in the theory of complex networks. In this contribution we consider various generalizations of preferential attachment including for example node removal and edge rewiring. We demonstrate that…
We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
It has previously been shown that the network of connected minima on a potential energy landscape is scale-free, and that this reflects a power-law distribution for the areas of the basins of attraction surrounding the minima. Here, we set…
Identifying the generating mechanism of a network is challenging as, more often than not, only snapshots are available, but not the full evolution. One candidate for the generating mechanism is preferential attachment which, in its simplest…
Popularity is attractive -- this is the formula underlying preferential attachment, a popular explanation for the emergence of scaling in growing networks. If new connections are made preferentially to more popular nodes, then the resulting…
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…
Network models with preferential attachment, where new nodes are injected into the network and form links with existing nodes proportional to their current connectivity, have been well studied for some time. Extensions have been introduced…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
Core-periphery is a key feature of large-scale networks underlying a wide range of social, biological, and transportation phenomena. Despite its prevalence in empirical data, it is unclear whether this property is a consequence of more…
In principle, the rules of links formation of a network model can be considered as a kind of link prediction algorithm. By revisiting the preferential attachment mechanism for generating a scale-free network, here we propose a class of…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
Preferential attachment is the most popular explanation for the emergence of scaling behavior in the World Wide Web, but this explanation has been challenged by the global information hypothesis, the existence of linear preference and the…
We study the interplay between evolutionary game and network structure and show how the dynamics of the game affect the growth pattern of the network and how the evolution of the network influence the cooperative behavior in the game.…
Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour…
The characterization of the "most connected" nodes in static or slowly evolving complex networks has helped in understanding and predicting the behavior of social, biological, and technological networked systems, including their robustness…