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We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…
We derive a general statistical model of interactions, starting from probabilistic principles and elementary requirements. Prevailing interaction models in biomedical researches diverge both mathematically and practically. In particular,…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
The largest eigenvalue of the adjacency matrix of the networks is a key quantity determining several important dynamical processes on complex networks. Based on this fact, we present a quantitative, objective characterization of the…
Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and…
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…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
Gene essentiality refers to the degree to which a gene is necessary for the survival and reproductive efficacy of a living organism. Although the essentiality of non-coding genes has been documented, there are still aspects of non-coding…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into…
Cycle is the simplest structure that brings redundant paths in network connectivity and feedback effects in network dynamics. Focusing on cycle structure, this paper defines a new matrix, named cycle number matrix, to represent cycle…
Network Medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
The architecture of the network of protein-protein physical interactions in Saccharomyces cerevisiae is exposed through the combination of two complementary theoretical network measures, betweenness centrality and `Q-modularity'. The yeast…
Combinations of random and preferential growth for both on-growing and stationary networks are studied and a hierarchical topology is observed. Thus for real world scale-free networks which do not exhibit hierarchical features preferential…
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…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…