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A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the…
Ecological networks exhibit non-random structural patterns, such as modularity and nestedness, which indicate ecosystem stability, species diversity, and connectance. Such structure-stability relationships are well known. However, another…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…
We propose a modeling framework for growing multiplexes where a node can belong to different networks. We define new measures for multiplexes and we identify a number of relevant ingredients for modeling their evolution such as the coupling…
Trophic coherence, a measure of the extent to which the nodes of a directed network are organised in levels, has recently been shown to be closely related to many structural and dynamical aspects of complex systems, including graph…
To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between…
Contagion processes, representing the spread of infectious diseases, information, or social behaviors, are often schematized as taking place on networks, which encode for instance the interactions between individuals. The impact of the…
Links in a practical network may have different functions, which makes the original network a combination of some functional subnetworks. Here, by a model of coupled oscillators, we investigate how such functional subnetworks are evolved…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from differ- ent domains may vary quite significantly. Since there is an interplay be- tween network architecture…
Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…
Understanding how network structure constrains and enables information processing is a central problem in the statistical mechanics of interacting systems. Here we study random networks across the structural percolation transition and…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
The connectivity of a network contains information about the relationships between nodes, which can denote interactions, associations, or dependencies. We show that this information can be analyzed by measuring the uncertainty (and…
Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth's surface; however, in modern contagions long-range edges -- for example, due to…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…