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 organizationread more
Citations
More filters
Journal ArticleDOI
Complex stock trading network among investors
Zhi-Qiang Jiang,Wei-Xing Zhou +1 more
TL;DR: Li et al. as discussed by the authors provided an empirical investigation aimed at uncovering the statistical properties of intricate stock trading networks based on the order flow data of a highly liquid stock (Shenzhen Development Bank) listed on Shenzhen Stock Exchange during the whole year of 2003.
Journal ArticleDOI
Detecting Communities Based on Network Topology
TL;DR: This work defined community based on three properties, and proposed a simple and novel framework to detect communities based on network topology, and analyzed 16 different types of networks.
Journal ArticleDOI
A scale-free systems theory of motivation and addiction.
TL;DR: Conceptualizing addiction as pathological alteration of scale-free motivational-behavioral repertoires unifies neurobiological, neurocomputational and behavioral research while addressing addiction vulnerability in adolescence and psychiatric illness.
Journal ArticleDOI
A Multiobjective Evolutionary-Simplex Hybrid Approach for the Optimization of Differential Equation Models of Gene Networks
TL;DR: The proposed GA is shown to perform better than NSGA-II and SPEA-2 on standard benchmarks, as well as for the optimization of a genetic model for flowering time control in rice, and tradeoffs between accuracy in gene activity levels versus in the plant traits that they influence suggest that data mining the Pareto front may be useful in bioinformatics.
Journal ArticleDOI
How advancement in biological network analysis methods empowers proteomics.
TL;DR: This review considers briefly current trends in proteomics technologies and argues that holistic analysis based on biological networks provides a suitable background on which more robust models and interpretations can be built upon; and introduces some recently developed approaches.
References
More filters
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Community structure in social and biological networks
Michelle Girvan,Mark Newman +1 more
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.