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We present a model, in which some nodes (called interconnecting nodes) in two networks merge and play the roles in both the networks. The model analytic and simulation discussions show a monotonically increasing dependence of…
Understanding functional associations among genes discovered in sequencing projects is a key issue in post-genomic biology. However, reliable interpretation of the protein interaction data has been difficult. In this work, we show that if…
Networks are useful for describing systems of interacting objects, where the nodes represent the objects and the edges represent the interactions between them. The applications include chemical and metabolic systems, food webs as well as…
Recently, the structural controllability theory has been introduced to analyze the Protein-Protein Interaction (PPI) network. The indispensable nodes, which their removal increase the number of driver nodes to control the network, are found…
Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Entrainment by a pacemaker, representing an element with a higher frequency, is numerically investigated for several classes of random networks which consist of identical phase oscillators. We find that the entrainment frequency window of a…
A rank-dependent deactivation mechanism is introduced to network evolution. The growth dynamics of the network is based on a finite memory of individuals, which is implemented by deactivating one site at each time step. The model shows…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices…
In this note we describe the theory of functional asynchronous networks and one of the main results, the Modularization of Dynamics Theorem, which for a large class of functional asynchronous networks gives a factorization of dynamics in…
The Saccharomyces cerevisiae protein-protein interaction map, as well as many natural and man-made networks, shares the scale-free topology. The preferential attachment model was suggested as a generic network evolution model that yields…
Our daily social and political life is more and more impacted by social networks. The functioning of our living bodies is deeply dependent on biological regulation networks such as neural, genetic, and protein networks. And the physical…
We model membrane proteins as anisotropic objects characterized by symmetric-traceless tensors and determine the coupling between these order-parameters and membrane curvature. We consider the interactions between transmembrane proteins…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
We analyze the interplay of synchronization and structure evolution in an evolving network of phase oscillators. An initially random network is adaptively rewired according to the dynamical coherence of the oscillators, in order to enhance…
This work proposes action networks as a semantically well-founded framework for reasoning about actions and change under uncertainty. Action networks add two primitives to probabilistic causal networks: controllable variables and persistent…
The enormous diversity of life forms thriving in drastically different environmental milieus involves a complex interplay among constituent proteins interacting with each other. However, the organizational principles characterizing the…
The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the…