Reference : Robust flux balance analysis of multi- scale biochemical reaction networks

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	To cite this reference:	http://hdl.handle.net/10993/17460

Title :	Robust flux balance analysis of multi- scale biochemical reaction networks
Language :	English
Author, co-author :	Sun, Y []
	Fleming, Ronan MT [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Thiele, Ines [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Saunders, MA []
Publication date :	2013
Journal title :	BMC Bioinformatics
Publisher :	BioMed Central
Volume :	1
Issue/season :	14
Pages :	240
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
e-ISSN :	1471-2105
Abstract :	[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.
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Systems Biochemistry (Fleming Group)
Permalink :	http://hdl.handle.net/10993/17460
DOI :	10.1186/1471-2105-14-240

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