The large-scale organization of metabolic networks

@article{Jeong2000TheLO,
  title={The large-scale organization of metabolic networks},
  author={H. Jeong and B. Tombor and R{\'e}ka Albert and Zolt{\'a}n N. Oltvai and A L Barabasi},
  journal={Nature},
  year={2000},
  volume={407},
  pages={651-654}
}
In a cell or microorganism, the processes that generate mass, energy, information transfer and cell-fate specification are seamlessly integrated through a complex network of cellular constituents and reactions. However, despite the key role of these networks in sustaining cellular functions, their large-scale structure is essentially unknown. Here we present a systematic comparative mathematical analysis of the metabolic networks of 43 organisms representing all three domains of life. We show… 
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References

SHOWING 1-10 OF 69 REFERENCES
Robustness in simple biochemical networks
TLDR
It is argued that the key properties of biochemical networks should be robust in order to ensure their proper functioning, and it is shown that this applies in particular to bacterial chemotaxis.
Engineering stability in gene networks by autoregulation
TLDR
Simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli are designed and constructed and the gain of stability produced by negative feedback is shown.
A synthetic oscillatory network of transcriptional regulators
TLDR
This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.
Size and form in efficient transportation networks
TLDR
The theory accounts in a general way for the quarter-power allometric scaling of living organisms and predicts scaling relations applicable to all efficient transportation networks, which is verified from observational data on the river drainage basins.
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
TLDR
The WIT (What Is There) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases.
Error and attack tolerance of complex networks
TLDR
It is found that scale-free networks, which include the World-Wide Web, the Internet, social networks and cells, display an unexpected degree of robustness, the ability of their nodes to communicate being unaffected even by unrealistically high failure rates.
Emergence of scaling in random networks
TLDR
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.
Emergent properties of networks of biological signaling pathways.
TLDR
Biochemical signaling networks were constructed with experimentally obtained constants and analyzed by computational methods to understand their role in complex biological processes and raise the possibility that information for "learned behavior" of biological systems may be stored within intracellular biochemical reactions that comprise signaling pathways.
Noise-based switches and amplifiers for gene expression.
TLDR
A model describing the regulation of gene expression and the effects of noise are developed and it is suggested that an external noise source could be used as a switch and/or amplifier for gene expression.
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
  • J. Edwards, B. Palsson
  • Biology, Engineering
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
TLDR
It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.
...
1
2
3
4
5
...