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Methods: Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
- Christoph Kaleta,
- Luís Filipe de Figueiredo,
- and Stefan Schuster
Genome Res. October 2009 19: 1872-1883; Published in Advance June 18, 2009, doi:10.1101/gr.090639.108
...Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns Christoph Kaleta 1 , 2 , 3 , Luís Filipe de Figueiredo 1 and Stefan Schuster 1 1 Department of Bioinformatics...
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LETTER: Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
- Jochen Förster,
- Iman Famili,
- Patrick Fu,
- Bernhard Ø. Palsson,
- and Jens Nielsen
Genome Res. February 1, 2003 13: 244-253; doi:10.1101/gr.234503
...), and it was demonstrated how such reconstructed metabolic models allow direct correlation between the genomic information and metabolic activity at the flux level. In these reconstructed metabolic networks, which consist of several hundred reactions and several hundred metabolites, it was possible to simulate...
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LETTER: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
- Irina Borodina,
- Preben Krabben,
- and Jens Nielsen
Genome Res. June 2005 15: 820-829; doi:10.1101/gr.3364705
...with the Streptomyces avermitilis genome, we showed that the metabolic genes are highly conserved between these species and therefore the model is suitable for use with other Streptomycetes. Flux balance analysis was applied for studies of the reconstructed metabolic network and to assess its metabolic capabilities...
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Methods: Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States
- Jennifer L. Reed and
- Bernhard Ø. Palsson
Genome Res. September 2004 14: 1797-1805; doi:10.1101/gr.2546004
...programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84 : 647 -657. ↵ Burgard, A.P., Nikolaev, E.V., Schilling, C.H., and Maranas, C.D. 2004 . Flux coupling analysis of -scale metabolic network reconstructions. Genome Res. 14 : 301 -312...
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LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
- Natalie C. Duarte,
- Markus J. Herrgård,
- and Bernhard Ø. Palsson
Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
...assembly is preferred because it allows for the inclusion of disparate data sources, such as annotations, gene expression experiments, enzymatic assays, and physiological data, rather than exclusively genomic data ( Covert et al. 2001 ). Genome-scale metabolic networks have been manually reconstructed...
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Methods: Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling
- Jacob G. Bundy,
- Balázs Papp,
- Rebecca Harmston,
- Roy A. Browne,
- Edward M. Clayson,
- Nicola Burton,
- Richard J. Reece,
- Stephen G. Oliver,
- and Kevin M. Brindle
Genome Res. April 2007 17: 510-519; Published in Advance March 5, 2007, doi:10.1101/gr.5662207
...). For example, in the yeast Saccharomyces cerevisiae , flux balance analysis of the reconstructed metabolic network was shown to predict the qualitative effect of single-gene deletions with a combined accuracy of 81%–89%, with 96%–98% of viable and 68%–80% of lethal deletions correctly identified ( Kuepfer et...
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Method: Control of fluxes in metabolic networks
- Georg Basler,
- Zoran Nikoloski,
- Abdelhalim Larhlimi,
- Albert-László Barabási,
- and Yang-Yu Liu
Genome Res. July 2016 26: 956-968; Published in Advance May 19, 2016, doi:10.1101/gr.202648.115
...tomissing reactions” in the Supplemental Material). Altogether, these robustness tests demonstrate the power of our method in making predictions from incomplete network reconstructions (Monk et al. 2014). A B DEF Figure 2. Clustering of flux coupling profiles. (A, top) Silhouette index over number...
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LETTER: Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
- Markus J. Herrgård,
- Baek-Seok Lee,
- Vasiliy Portnoy,
- and Bernhard Ø. Palsson
Genome Res. May 2006 16: 627-635; Published in Advance April 10, 2006, doi:10.1101/gr.4083206
...regulation of metabolism in the form of the regulated flux-balance analysis (rFBA) approach ( Covert et al. 2001 ). This approach requires first reconstructing the transcriptional regulatory network structure in the form of Boolean rules based on the various available data sources and then integrating...
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LETTER: Metabolic functions of duplicate genes in Saccharomyces cerevisiae
- Lars Kuepfer,
- Uwe Sauer,
- and Lars M. Blank
Genome Res. October 2005 15: 1421-1430; doi:10.1101/gr.3992505
..., the positioning of duplicate genes at key points of the network topology provides circumstantial evidence for differential regulation of the encoded isoenzymes. Genome-scale analysis of the reconciled model with the flux coupling finder ( Burgard et al. 2004 ) revealed between 65 and 67 coupled reaction sets...
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RESOURCE: OptStrain: A computational framework for redesign of microbial production systems
- Priti Pharkya,
- Anthony P. Burgard,
- and Costas D. Maranas
Genome Res. November 2004 14: 2367-2376; doi:10.1101/gr.2872004
...-native functionalities that need to be added into a specific host organism network. Mathematically, this is achieved by first introducing a set of binary variables yj that serve as switches to turn the associated reaction fluxes vj on or off. Note that the binary variable yj assumes a value of 1 if reaction j is active...

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