Journal ArticleDOI
Network Motifs: Simple Building Blocks of Complex Networks
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TLDR
Network motifs, patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks, are defined and may define universal classes of networks.Abstract:
Complex networks are studied across many fields of science. To uncover their structural design principles, we defined “network motifs,” patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. Thisread more
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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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The Structure and Function of Complex Networks
TL;DR: Developments in this field are reviewed, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.
Journal ArticleDOI
Modularity and community structure in networks
TL;DR: In this article, the modularity of a network is expressed in terms of the eigenvectors of a characteristic matrix for the network, which is then used for community detection.
Journal ArticleDOI
Complex brain networks: graph theoretical analysis of structural and functional systems
Edward T. Bullmore,Olaf Sporns +1 more
TL;DR: This article reviews studies investigating complex brain networks in diverse experimental modalities and provides an accessible introduction to the basic principles of graph theory and highlights the technical challenges and key questions to be addressed by future developments in this rapidly moving field.
Journal ArticleDOI
Complex networks: Structure and dynamics
TL;DR: The major concepts and results recently achieved in the study of the structure and dynamics of complex networks are reviewed, and the relevant applications of these ideas in many different disciplines are summarized, ranging from nonlinear science to biology, from statistical mechanics to medicine and engineering.
References
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Book
Social Network Analysis
TL;DR: In this article, the development of social network analysis, tracing its origins in classical sociology and its more recent formulation in social scientific and mathematical work, is described and discussed. But it is argued that the analysis of social networks is not a purely static process.