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Open AccessJournal ArticleDOI

Hierarchical Organization of Modularity in Metabolic Networks

TLDR
It is shown that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law.
Abstract
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions The identified network architecture may be generic to system-level cellular organization

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Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network

TL;DR: The genomic clustering of miRNAs is closely related to the coordinated regulation in the gene regulatory network and the diverse pattern of regulatory coordination suggests distinct roles of the homo-clustered and the hetero-Clustered mi RNAs in biological processes.
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Detecting community structure in complex networks using simulated annealing with k-means algorithms

TL;DR: The simulated annealing strategy is used to maximize the modularity of a network, associating with a dissimilarity-index-based and with a diffusion-distance-based k-means iterative procedure, which outperform most existing methods as regards the optimal modularity found.
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Biochemical integration of blood redox state in captive zebra finches (Taeniopygia guttata)

TL;DR: Analysis of patterns of functional integration among different molecular components of the blood redox system in zebra finches suggests strong and significant integration between the oxidative state of red blood cells and plasma.
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Emergence of Soft Communities from Geometric Preferential Attachment

TL;DR: This work shows how latent network geometry coupled with preferential attachment of nodes to this geometry fills this gap in growing networks, and calls this mechanism geometric preferential attachment (GPA), and validates it against the Internet.
Journal ArticleDOI

Modular organization of the mammalian Golgi apparatus

TL;DR: The Golgi apparatus is essential for post-translational modifications and sorting of proteins in the secretory pathway and further performs a broad range of specialized functions by combining basic morphological modules of cisternae into higher ordered structures.
References
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Journal ArticleDOI

Collective dynamics of small-world networks

TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
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Emergence of Scaling in Random Networks

TL;DR: A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
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Statistical mechanics of complex networks

TL;DR: In this paper, a simple model based on the power-law degree distribution of real networks was proposed, which was able to reproduce the power law degree distribution in real networks and to capture the evolution of networks, not just their static topology.
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Cluster analysis and display of genome-wide expression patterns

TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
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Community structure in social and biological networks

TL;DR: This article proposes a method for detecting communities, built around the idea of using centrality indices to find community boundaries, and tests it on computer-generated and real-world graphs whose community structure is already known and finds that the method detects this known structure with high sensitivity and reliability.
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