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Weighted networks capture the structure of complex systems where interaction strength is meaningful. This information is essential to a large number of processes, such as threshold dynamics, where link weights reflect the amount of…
In the study of biological networks, one of the major challenges is to understand the relationships between network structure and dynamics. In this paper, we model in vitro cortical neuronal cultures as stochastic dynamical systems and…
The ongoing need for effective epidemic modeling has driven advancements in capturing the complex dynamics of infectious diseases. Traditional models, such as Susceptible-Infected-Recovered, and graph-based approaches often fail to account…
To any inhibition-dominated threshold-linear network (TLN) we can associate a directed graph that captures the pattern of strong and weak inhibition between neurons. Robust motifs are graphs for which the structure of fixed points in the…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Network theory provides a rich toolbox consisting of methods, measures, and models for studying the structure and dynamics of complex systems found in nature, society, or technology. Recently, it has been pointed out that many real-world…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
This article describes the application of recently introduced complex networks concepts and methods to the characterization and analysis of cortical bone structure. Three-dimensional reconstructions of the system of channels underlying bone…
The use of graph centrality measures applied to biological networks, such as protein interaction networks, underpins much research into identifying key players within biological processes. This approach however is restricted to dyadic…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
We study the evolution of a random weighted network with complex nonlinear dynamics at each node, whose activity may cease as a result of interactions with other nodes. Starting from a knowledge of the micro-level behaviour at each node, we…
We introduce a new framework for the analysis of the dynamics of networks, based on randomly reinforced urn (RRU) processes, in which the weight of the edges is determined by a reinforcement mechanism. We rigorously explain the empirical…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…
Network measures that reflect the most salient properties of complex large-scale networks are in high demand in the network research community. In this paper we adapt a combinatorial measure of negative curvature (also called hyperbolicity)…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…