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Many networks describing complex systems are directed: the interactions between elements are not symmetric. Recent work has shown that these networks can display properties such as trophic coherence or non-normality, which in turn affect…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Robust coordination and organization in large ensembles of nonlinear oscillatory units play a vital role in a wide range of natural and engineered system. The control of self-organizing network-coupled systems has recently seen significant…
Many empirical networks display an inherent tendency to cluster, i.e. to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs,…
This paper considers the problem of inferring the structure of a network from indirect observations. Each observation (a "trace") is the unordered set of nodes which are activated along a path through the network. Since a trace does not…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
Much of social network analysis is - implicitly or explicitly - predicated on the assumption that individuals tend to be more similar to their friends than to strangers. Thus, an observed social network provides a noisy signal about the…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
A fundamental premise of statistical physics is that the particles in a physical system are interchangeable, and hence the state of each specific component is representative of the system as a whole. This assumption breaks down for complex…
The specific connectivity of a neuronal network is reflected in the dynamics of the signals recorded on its nodes. The analysis of how the activity in one node predicts the behaviour of another gives the directionality in their…
Real-world networks typically exhibit several aspects, or layers, of interactions among their nodes. By permuting the role of the nodes and the layers, we establish a new criterion to construct the dual of a network. This approach allows to…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Synchronization is ubiquitous in nature, which is mathematically described by coupled oscillators. Synchronization strongly depends on the interaction network, and the network plays a crucial role in controlling the dynamics. To understand…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
The evolution of networks of coupled chaotic maps with delayed interactions can be studied in the usual way by analyzing the evolution of the state of elements at each iteration time (the "Simulator" point of view), or it can be analyzed…
Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative -- or correlated -- activity in neural populations, and in the…
Many systems of interacting elements can be conceptualized as networks, where network nodes represent the elements and network ties represent interactions between the elements. In systems where the underlying network evolves in time, it is…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
The robust distributed state estimation for a class of continuous-time linear time-invariant systems is achieved by a novel kernel-based distributed observer, which, for the first time, ensures fixed-time convergence properties. The…