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We propose a new method for assessing agents influence in network structures, which takes into consideration nodes attributes, individual and group influences of nodes, and the intensity of interactions. This approach helps us to identify…
The large amounts of data continuously generated online offer opportunities to identify and analyse trends in various aspects of society. For instance, data from online social media are frequently used as a means of analysing informal…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
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…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Studying the topology of so-called {\em real networks}, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that…
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…
The large-scale structural ingredients of the brain and neural connectomes have been identified in recent years. These are, similar to the features found in many other real networks: the arrangement of brain regions into modules and the…
A complex system can be represented and analyzed as a network, where nodes represent the units of the network and edges represent connections between those units. For example, a brain network represents neurons as nodes and axons between…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…
A model is proposed for the creation and transmission of scientific knowledge, based on the network of citations among research articles. The model allows to assign to each article a nonnegative value for its creativity, i. e. its creation…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
One of the most interesting scientific challenges nowadays deals with the analysis and the understanding of complex networks' dynamics. A major issue is the definition of new frameworks for the exploration of the dynamics at play in real…
In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…
In many real-world networks, nodes have class labels, attributes, or variables that affect the network's topology. If the topology of the network is known but the labels of the nodes are hidden, we would like to select a small subset of…
Inference of new biological knowledge, e.g., prediction of protein function, from protein-protein interaction (PPI) networks has received attention in the post-genomic era. A popular strategy has been to cluster the network into…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
The observed architecture of ecological and socio-economic networks differs significantly from that of random networks. From a network science standpoint, non-random structural patterns observed in real networks call for an explanation of…