Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks.

@article{Huss2007CurrencyAC,
  title={Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks.},
  author={Mikael Huss and Petter Holme},
  journal={IET systems biology},
  year={2007},
  volume={1 5},
  pages={
          280-5
        }
}
  • M. Huss, P. Holme
  • Published 31 March 2006
  • Computer Science
  • IET systems biology
The large-scale shape and function of metabolic networks are intriguing topics of systems biology. [] Key Result The networks are found to be more modular than random networks but far from perfectly divisible into modules. We argue that cross-modular edges are the key for the robustness of metabolism.

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References

SHOWING 1-10 OF 41 REFERENCES
Functional cartography of complex metabolic networks
TLDR
A methodology is proposed that can find functional modules in complex networks, and classify nodes into universal roles according to their pattern of intra- and inter-module connections, which yields a ‘cartographic representation’ of complex networks.
The small world inside large metabolic networks
  • Andreas Wagner, D. Fell
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 2001
TLDR
A graph theoretical analysis of the E. coli metabolic network is found that this network is a small–world graph, a type of graph distinct from both regular and random networks and observed in a variety of seemingly unrelated areas, such as friendship networks in sociology, the structure of electrical power grids, and the nervous system of Caenorhabditis elegans.
Subnetwork hierarchies of biochemical pathways
TLDR
A method to decompose biochemical networks into subnetworks based on the global geometry of the network is presented and is applied to 43 organisms from the WIT database.
The large-scale organization of metabolic networks
TLDR
This analysis of metabolic networks of 43 organisms representing all three domains of life shows that, despite significant variation in their individual constituents and pathways, these metabolic networks have the same topological scaling properties and show striking similarities to the inherent organization of complex non-biological systems.
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
TLDR
A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented and the applicability is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae, which gives rise to 19 subnetworks.
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
TLDR
A new decomposition method is proposed, which uses a distance definition derived from the path length between two reactions, based on combined properties of the global network structure and local reaction connectivity rather than, primarily, on the connection degree of metabolites.
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
TLDR
The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network.
Complex networks theory for analyzing metabolic networks
TLDR
This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.
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.
...
...