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RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations

Joonhoon Kim12 and Jennifer L Reed12*

Author Affiliations

1 Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA

2 DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA

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Genome Biology 2012, 13:R78  doi:10.1186/gb-2012-13-9-r78

Published: 26 September 2012

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Additional File 1:

Supplementary Materials and methods.

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Additional File 2:

Supplementary Figure S1. Sensitivity analysis of parameters using E. coli knockout strains (Δpgi, Δppc, and Δtpi) before and after adaptive evolution.

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Additional File 3:

Supplementary Table S1. Comparison of predicted and experimentally measured values of growth, substrate uptake, and product secretion rates for four E. coli mutants before adaptive evolution.

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Additional File 4:

Supplementary Table S2. Comparison of predicted and experimentally measured values of growth, substrate uptake, and product secretion rates for four E. coli mutants after adaptive evolution.

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Additional File 5:

Supplementary Figure S2. Sensitivity analysis of data used to generate reference flux distributions.

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Additional File 6:

Supplementary Figure S3. Sensitivity analysis of metabolic network models.

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Additional File 7:

Supplementary Table S3. Growth rate predictions for 22 single knockout E. coli mutants.

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Additional File 8:

Supplementary Table S4. Growth phenotype predictions for 1,260 single knockout E. coli mutants.

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Additional File 9:

Supplementary Table S5. RELATCH prediction errors (SSE) for E. coli, S. cerevisiae, and B. subtilis knockout mutants shown in Figure 4.

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Additional File 10:

Supplementary Figure S4. Comparison of metabolic flux predictions using RELATCH and MOMA for knockout mutants of S. cerevisiae and B. subtilis.

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Additional File 11:

Supplementary Figure S5. Comparison of MFA estimated fluxes and predictions by RELATCH for E. coli strains grown on galactose.

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Additional File 12:

Implementation of RELATCH. RELATCH is implemented using the COBRA Toolbox for MATLAB.

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