Reference : Robust flux balance analysis of multi- scale biochemical reaction networks
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/17460
Robust flux balance analysis of multi- scale biochemical reaction networks
English
Sun, Y []
Fleming, Ronan MT mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Thiele, Ines mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Saunders, MA []
2013
BMC Bioinformatics
BioMed Central
1
14
240
Yes (verified by ORBilu)
International
1471-2105
[en] Background:Biological processes such as metabolism, signaling, and macromolecular synthesis can be modeled as large networks of biochemical reactions. Large and comprehensive networks, like integrated networks that represent metabolism and macromolecular synthesis, are inherently multiscale because reaction rates can vary over many orders of magnitude. They require special methods for accurate analysis because naive use of standard optimization systems can produce inaccurate or erroneously infeasible results.
Results: We describe techniques enabling off-the-shelf optimization software to compute accurate solutions to the poorly scaled optimization problems arising from flux balance analysis of multiscale biochemical reaction networks. We implement lifting techniques for flux balance analysis within the openCOBRA toolbox and demonstrate our techniques using the first integrated reconstruction of metabolism and macromolecular synthesis for E. coli.
Conclusion:Our techniques enable accurate flux balance analysis of multiscale networks using off-the-shelf optimization software. Although we describe lifting techniques in the context of flux balance analysis, our methods can be used to handle a variety of optimization problems arising from analysis of multiscale network reconstructions.
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Systems Biochemistry (Fleming Group)
http://hdl.handle.net/10993/17460
10.1186/1471-2105-14-240

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