Related papers: One Hub-One Process: A Tool Based View on Regulato…
We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and,…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
Complex systems often exhibit highly structured network topologies that reflect functional constraints. In this work, we investigate how, under varying combinations of system-wide selection rules and special agents, different classes of…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
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…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained…
The investigation of topological properties of ovarian cancer network (OCN) and the roles of hubs involved in it by digging the network at various levels of organization are important to understand how OCN is organized to understand disease…
A neural network with fixed topology can be regarded as a parametrization of functions, which decides on the correlations between functional variations when parameters are adapted. We propose an analysis, based on a differential geometry…
Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of…
Nature is rife with networks that are functionally optimized to propagate inputs in order to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
Recent work in cognitive neuroscience has focused on analyzing the brain as a network, rather than as a collection of independent regions. Prior studies taking this approach have found that individual differences in the degree of modularity…
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…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
Cognition is supported by neurophysiological processes that occur both in local anatomical neighborhoods and in distributed large-scale circuits. Recent evidence from network control theory suggests that white matter pathways linking…