Stability as a natural selection mechanism on interacting networks

Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism based on global stability has been proposed recently [J I Perotti, O V Billoni, F A Tamarit, D R Chialvo, S A Cannas, Phys. Rev. Lett. 103, 108701 (2009)]. This mechanism is incorporated into a model of a growing network of interacting agents in which each new agent's membership in the network is determined by the agent's effect on the network's global stability. We show that, out of this stability constraint, several topological properties observed in biological networks emerge in a self organized manner. The influence of the stability selection mechanism on the dynamics associated to the resulting network is analyzed as well.Comment: 10 pages, 9 figure

Structural patterns in complex networks through spectral analysis

The study of some structural properties of networks is introduced from a graph spectral perspective. First, subgraph centrality of nodes is defined and used to classify essential proteins in a proteomic map. This index is then used to produce a method that allows the identification of superhomogeneous networks. At the same time this method classify non-homogeneous network into three universal classes of structure. We give examples of these classes from networks in different real-world scenarios. Finally, a communicability function is studied and showed as an alternative for defining communities in complex networks. Using this approach a community is unambiguously defined and an algorithm for its identification is proposed and exemplified in a real-world network

Locating influential nodes via dynamics-sensitive centrality

With great theoretical and practical significance, locating influential nodes of complex networks is a promising issues. In this paper, we propose a dynamics-sensitive (DS) centrality that integrates topological features and dynamical properties. The DS centrality can be directly applied in locating influential spreaders. According to the empirical results on four real networks for both susceptible-infected-recovered (SIR) and susceptible-infected (SI) spreading models, the DS centrality is much more accurate than degree, $k$-shell index and eigenvector centrality.Comment: 6 pages, 1 table and 2 figure

Detecting rich-club ordering in complex networks

Uncovering the hidden regularities and organizational principles of networks arising in physical systems ranging from the molecular level to the scale of large communication infrastructures is the key issue for the understanding of their fabric and dynamical properties [1-5]. The ``rich-club'' phenomenon refers to the tendency of nodes with high centrality, the dominant elements of the system, to form tightly interconnected communities and it is one of the crucial properties accounting for the formation of dominant communities in both computer and social sciences [4-8]. Here we provide the analytical expression and the correct null models which allow for a quantitative discussion of the rich-club phenomenon. The presented analysis enables the measurement of the rich-club ordering and its relation with the function and dynamics of networks in examples drawn from the biological, social and technological domains.Comment: 1 table, 3 figure

Modular organisation of interaction networks based on asymptotic dynamics

This paper investigates questions related to the modularity in discrete models of biological interaction networks. We develop a theoretical framework based on the analysis of their asymptotic dynamics. More precisely, we exhibit formal conditions under which agents of interaction networks can be grouped into modules. As a main result, we show that the usual decomposition in strongly connected components fulfils the conditions of being a modular organisation. Furthermore, we point out that our framework enables a finer analysis providing a decomposition in elementary modules

Michaelis-Menten Dynamics in Complex Heterogeneous Networks

Biological networks have been recently found to exhibit many topological properties of the so-called complex networks. It has been reported that they are, in general, both highly skewed and directed. In this paper, we report on the dynamics of a Michaelis-Menten like model when the topological features of the underlying network resemble those of real biological networks. Specifically, instead of using a random graph topology, we deal with a complex heterogeneous network characterized by a power-law degree distribution coupled to a continuous dynamics for each network's component. The dynamics of the model is very rich and stationary, periodic and chaotic states are observed upon variation of the model's parameters. We characterize these states numerically and report on several quantities such as the system's phase diagram and size distributions of clusters of stationary, periodic and chaotic nodes. The results are discussed in view of recent debate about the ubiquity of complex networks in nature and on the basis of several biological processes that can be well described by the dynamics studied.Comment: Paper enlarged and modified, including the title. Some problems with the pdf were detected in the past. If they persist, please ask for the pdf by e-mailing yamir(at_no_spam)unizar.es. Version to appear in Physica

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Structural constraints in complex networks

We present a link rewiring mechanism to produce surrogates of a network where both the degree distribution and the rich--club connectivity are preserved. We consider three real networks, the AS--Internet, the protein interaction and the scientific collaboration. We show that for a given degree distribution, the rich--club connectivity is sensitive to the degree--degree correlation, and on the other hand the degree--degree correlation is constrained by the rich--club connectivity. In particular, in the case of the Internet, the assortative coefficient is always negative and a minor change in its value can reverse the network's rich--club structure completely; while fixing the degree distribution and the rich--club connectivity restricts the assortative coefficient to such a narrow range, that a reasonable model of the Internet can be produced by considering mainly the degree distribution and the rich--club connectivity. We also comment on the suitability of using the maximal random network as a null model to assess the rich--club connectivity in real networks.Comment: To appear in New Journal of Physics (www.njp.org