Steady-state 13C fluxomics using openflux

Methods in Molecular Biology

Volumn 1191, Issue , 2014, Pages 209-224

  Quek, Lake Ee ^a   Nielsen, Lars K ^a  

^a NONE

Author keywords

13C tracer; MATLAB; Metabolic flux; Modeling; Nonlinear optimization; OpenFLUX; Steady state

Indexed keywords

CARBON 13; CARBON;

ARTICLE; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLIC FLUX ANALYSIS; NONLINEAR SYSTEM; PRIORITY JOURNAL; STEADY STATE; BIOLOGICAL MODEL; COMPUTER PROGRAM; METABOLISM; PHYSIOLOGY; PROCEDURES; REGRESSION ANALYSIS;

CARBON ISOTOPES; LEAST-SQUARES ANALYSIS; METABOLIC FLUX ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SOFTWARE;

EID: 84921847669     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1170-7_13     Document Type: Article

References (10)

1. Wittmann C (2007) Fluxome analysis using GC-MS. Microb Cell Fact 6:6
2. Quek LE, Wittmann C, Nielsen LK, Kromer JO (2009) OpenFLUX: effi cient modelling software for 13 C-based metabolic fl ux analysis. Microb Cell Fact 8:25
3. Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 9:68–86
4. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007) A genomescale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121
5. Wittmann C (2002) Metabolic fl ux analysis using mass spectrometry. Adv Biochem Eng Biotechnol 74:39–64
6. Zupke C, Stephanopoulos G (1995) Intracellular fl ux analysis in hybridomas using mass balances and in vitro 13 C nmr. Biotechnol Bioeng 45:292–303
7. Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Accurate assessment of amino acid mass isotopomer distributions for metabolic fl ux analysis. Anal Chem 79:7554–7559
8. Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraintbased genome-scale metabolic models. Metab Eng 5:264–276
9. Zupke C, Stephanopoulos G (1994) Modeling of isotope distributions and intracellular fl uxes in metabolic networks using atom mapping matrixes. Biotechnol Prog 10:489–498
10. Antoniewicz MR, Kelleher JK, Stephanopoulos G (2006) Determination of confi dence intervals of metabolic fl uxes estimated from stable isotope measurements. Metab Eng 8:324–337