TY - JOUR AU - Varma, A. AU - Palsson, B. PY - 1994 DA - 1994// TI - Metabolic flux balancing: basic concepts, scientific and practical use JO - Nature Biotechnology VL - 12 UR - https://doi.org/10.1038/nbt1094-994 DO - 10.1038/nbt1094-994 ID - Varma1994 ER - TY - JOUR AU - Edwards, J. S. AU - Ibarra, R. U. AU - Palsson, B. PY - 2001 DA - 2001// TI - In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data JO - Nature Biotechnology VL - 19 UR - https://doi.org/10.1038/84379 DO - 10.1038/84379 ID - Edwards2001 ER - TY - CHAP AU - Schütz, R. AU - Kuepfer, L. AU - Sauer, U. PY - 2007 DA - 2007// TI - Systematic evaluation of objective functions for predicting intracellular fluxes in E. coli BT - Molecular Systems Biology ID - Schütz2007 ER - TY - JOUR AU - Szyperski, T. PY - 1995 DA - 1995// TI - Biosynthetically directed fractional 13C-labelling of proteinogenic amino acids JO - European Journal of Biochemistry VL - 232 UR - https://doi.org/10.1111/j.1432-1033.1995.tb20829.x DO - 10.1111/j.1432-1033.1995.tb20829.x ID - Szyperski1995 ER - TY - JOUR AU - Dauner, M. AU - Sauer, U. PY - 2000 DA - 2000// TI - GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing JO - Biotechnology Progress VL - 16 UR - https://doi.org/10.1021/bp000058h DO - 10.1021/bp000058h ID - Dauner2000 ER - TY - JOUR AU - Rousu, J. AU - Rantanen, A. AU - Ketola, R. AU - Kokkonen, J. PY - 2005 DA - 2005// TI - Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra JO - Spectroscopy VL - 19 UR - https://doi.org/10.1155/2005/575686 DO - 10.1155/2005/575686 ID - Rousu2005 ER - TY - JOUR AU - Schmidt, K. AU - Carlsen, M. AU - Nielsen, J. AU - Viladsen, J. PY - 1997 DA - 1997// TI - Modeling Isotopomer Distributions in Biochemical Networks Using Isotopomer Mapping Matrices JO - Biotechnology and Bioengineering VL - 55 UR - https://doi.org/3.0.CO;2-H DO - 3.0.CO;2-H ID - Schmidt1997 ER - TY - JOUR AU - Wiechert, W. AU - Petersen, M. ö. l. l. n. e. y. S. AU - de Graaf, A. PY - 2001 DA - 2001// TI - A Universal Framework for 13C Metabolic Flux Analysis JO - Metabolic Engineering VL - 3 UR - https://doi.org/10.1006/mben.2001.0188 DO - 10.1006/mben.2001.0188 ID - Wiechert2001 ER - TY - JOUR AU - Wiechert, W. AU - de Graaf, A. PY - 1997 DA - 1997// TI - Bidirectional Reaction Steps in Metabolic Networks: I. Modeling and simulation of carbon isotope labeling experiments JO - Biotechnology and Bioengineering VL - 55 UR - https://doi.org/3.0.CO;2-P DO - 3.0.CO;2-P ID - Wiechert1997 ER - TY - JOUR AU - Antoniewicz, M. AU - Kelleher, J. AU - Stephanopoulos, G. PY - 2007 DA - 2007// TI - Elementary Metabolite Units (EMU): a novel framework for modeling isotopic distributions JO - Metabolic Engineering VL - 9 UR - https://doi.org/10.1016/j.ymben.2006.09.001 DO - 10.1016/j.ymben.2006.09.001 ID - Antoniewicz2007 ER - TY - JOUR AU - van Winden, W. AU - Heijnen, J. AU - Verheijen, P. PY - 2002 DA - 2002// TI - Cumulative bondomers: a new concept in flux analysis from 2D [13C, 1H] COSY NMR data JO - Biotechnology and Bioengineering VL - 80 UR - https://doi.org/10.1002/bit.10429 DO - 10.1002/bit.10429 ID - van Winden2002 ER - TY - JOUR AU - Nöh, K. AU - Wahl, A. AU - Wiechert, W. PY - 2006 DA - 2006// TI - Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions JO - Metabolic Engineering VL - 8 UR - https://doi.org/10.1016/j.ymben.2006.05.006 DO - 10.1016/j.ymben.2006.05.006 ID - Nöh2006 ER - TY - JOUR AU - Nöh, K. AU - Grönke, K. AU - Luo, B. AU - Takors, R. AU - Oldiges, M. AU - Wiechert, W. PY - 2007 DA - 2007// TI - Metabolic flux analysis at ultra short time scale: Isotopically non-stationary 13C labeling experiments JO - Journal of Biotechnology VL - 129 UR - https://doi.org/10.1016/j.jbiotec.2006.11.015 DO - 10.1016/j.jbiotec.2006.11.015 ID - Nöh2007 ER - TY - JOUR AU - Young, J. AU - Walther, J. AU - M, A. AU - Yoo, H. AU - Stephanopoulos, G. PY - 2007 DA - 2007// TI - An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis JO - Biotechnology and Bioengineering VL - 99 UR - https://doi.org/10.1002/bit.21632 DO - 10.1002/bit.21632 ID - Young2007 ER - TY - JOUR AU - Ghosh, S. AU - Zhu, T. AU - Grossmann, I. AU - Ataai, M. AU - Domach, M. PY - 2005 DA - 2005// TI - Closing the loop between feasible flux scenario identification for construct evaluation and resolution of realized fluxes via NMR JO - Computers and Chemical Engineering VL - 29 UR - https://doi.org/10.1016/j.compchemeng.2004.08.027 DO - 10.1016/j.compchemeng.2004.08.027 ID - Ghosh2005 ER - TY - JOUR AU - Blank, L. AU - Kuepfer, L. AU - Sauer, U. PY - 2005 DA - 2005// TI - Large-scale 13C-flux analysis reveals mechanistic principles metabolic network robustness to null mutations in yeast JO - Genome Biology VL - 6 UR - https://doi.org/10.1186/gb-2005-6-6-r49 DO - 10.1186/gb-2005-6-6-r49 ID - Blank2005 ER - TY - JOUR AU - Blank, L. AU - Lehmbeck, F. AU - Sauer, U. PY - 2005 DA - 2005// TI - Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts JO - FEMS Yeast Research VL - 5 UR - https://doi.org/10.1016/j.femsyr.2004.09.008 DO - 10.1016/j.femsyr.2004.09.008 ID - Blank2005 ER - TY - JOUR AU - Fischer, E. AU - Sauer, U. PY - 2003 DA - 2003// TI - Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS JO - European Journal of Biochemistry VL - 270 UR - https://doi.org/10.1046/j.1432-1033.2003.03448.x DO - 10.1046/j.1432-1033.2003.03448.x ID - Fischer2003 ER - TY - JOUR AU - Szyperski, T. AU - Glaser, R. AU - Hochuli, M. AU - Fiaux, J. AU - Sauer, U. AU - Bailey, J. AU - Wütrich, K. PY - 1999 DA - 1999// TI - Bioreaction Network Topology and Metabolic Flux Ratio Analysis by Biosynthetic Fractional 13C Labeling and Two-Dimensional NMR Spectrometry JO - Metabolic Engineering VL - 1 UR - https://doi.org/10.1006/mben.1999.0116 DO - 10.1006/mben.1999.0116 ID - Szyperski1999 ER - TY - JOUR AU - Fischer, E. AU - Zamboni, N. AU - Sauer, U. PY - 2004 DA - 2004// TI - High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints JO - Analytical Biochemistry VL - 325 UR - https://doi.org/10.1016/j.ab.2003.10.036 DO - 10.1016/j.ab.2003.10.036 ID - Fischer2004 ER - TY - CHAP AU - Rousu, J. AU - Rantanen, A. AU - Maaheimo, H. AU - Pitkänen, E. AU - Saarela, K. AU - Ukkonen, E. PY - 2003 DA - 2003// TI - A method for estimating metabolic fluxes from incomplete isotopomer information BT - Computational Methods in Systems Biology, Proceedings of the First International Workshop, CMSB Volume 2602 of Lecture Notes in Computer Science ID - Rousu2003 ER - TY - JOUR AU - Sauer, U. AU - Hatzimanikatis, V. AU - Bailey, J. AU - Hochuli, M. AU - Szyperski, T. AU - Wüthrich, K. PY - 1997 DA - 1997// TI - Metabolic fluxes in riboflavin-producing Bacillus subtilis JO - Nature Biotechnology VL - 15 UR - https://doi.org/10.1038/nbt0597-448 DO - 10.1038/nbt0597-448 ID - Sauer1997 ER - TY - JOUR AU - Maaheimo, H. AU - Fiaux, J. AU - Cakar, Z. AU - Bailey, J. AU - Sauer, U. AU - Szyperski, T. PY - 2001 DA - 2001// TI - Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labeling of common amino acids JO - European Journal of Biochemistry VL - 268 UR - https://doi.org/10.1046/j.1432-1327.2001.02126.x DO - 10.1046/j.1432-1327.2001.02126.x ID - Maaheimo2001 ER - TY - JOUR AU - Zamboni, N. AU - Sauer, U. PY - 2003 DA - 2003// TI - Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis JO - FEMS Microbiology Letters VL - 226 UR - https://doi.org/10.1016/S0378-1097(03)00614-1 DO - 10.1016/S0378-1097(03)00614-1 ID - Zamboni2003 ER - TY - JOUR AU - Sola, A. AU - Maaheimo, H. AU - Ylönen, K. AU - Ferrer, P. AU - Szyperski, T. PY - 2004 DA - 2004// TI - Amino acid biosynthesis and metabolic flux profiling of Pichia pastoris JO - European Journal of Biochemistry VL - 271 UR - https://doi.org/10.1111/j.1432-1033.2004.04176.x DO - 10.1111/j.1432-1033.2004.04176.x ID - Sola2004 ER - TY - JOUR AU - Sola, A. AU - Jouhten, P. AU - Maaheimo, H. AU - Sanchez-Ferrando, F. AU - Szyperski, T. AU - Ferrer, P. PY - 2007 DA - 2007// TI - Metabolic flux profiling of Pichia pastoris grown on glycerol/methanol mixtures in chemostat cultures at low and high dilution rates JO - Microbiology VL - 153 UR - https://doi.org/10.1099/mic.0.29263-0 DO - 10.1099/mic.0.29263-0 ID - Sola2007 ER - TY - JOUR AU - Rantanen, A. AU - Maaheimo, H. AU - Pitkänen, E. AU - Rousu, J. AU - Ukkonen, E. PY - 2006 DA - 2006// TI - Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation JO - Transactions on Computational Systems Biology VI, Lecture Notes in Bioinformatics VL - 4220 ID - Rantanen2006 ER - TY - JOUR AU - Kleijn, R. AU - Geertman, J. AU - Nfor, B. AU - Ras, C. AU - Schipper, D. AU - Pronk, J. AU - Heijnen, J. AU - van Maris, A. AU - van Winden, W. PY - 2006 DA - 2006// TI - Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR derived 13C-labeling data JO - FEMS Yeast Research VL - 7 UR - https://doi.org/10.1111/j.1567-1364.2006.00180.x DO - 10.1111/j.1567-1364.2006.00180.x ID - Kleijn2006 ER - TY - JOUR AU - Arita, M. PY - 2003 DA - 2003// TI - In Silico Atomic Tracing of Substrate-Product Relationships in Escherichia coli Intermediary Metabolism JO - Genome Research VL - 13 UR - https://doi.org/10.1101/gr.1212003 DO - 10.1101/gr.1212003 ID - Arita2003 ER - TY - CHAP AU - Zamboni, N. AU - Fischer, E. AU - Sauer, U. PY - 2005 DA - 2005// TI - FiatFlux – a software for metabolic flux analysis from 13 C-glucose experiments BT - BMC Bioinformatics ID - Zamboni2005 ER - TY - JOUR AU - Szyperski, T. PY - 1998 DA - 1998// TI - 13 C-NMR, MS and metabolic flux balancing in biotechnology research JO - Quarterly Reviews of Biophysics VL - 31 UR - https://doi.org/10.1017/S0033583598003412 DO - 10.1017/S0033583598003412 ID - Szyperski1998 ER - TY - CHAP AU - Weitzel, M. AU - Wiechert, W. AU - Nöh, K. PY - 2007 DA - 2007// TI - The topology of metabolic isotope labeling networks BT - BMC Bioinformatics ID - Weitzel2007 ER - TY - JOUR AU - van Winden, W. AU - van Dam, J. AU - Ras, C. AU - Kleijn, R. AU - Vinke, J. AU - Gulik, W. AU - Heijnen, J. PY - 2005 DA - 2005// TI - Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of 13C-labeled primary metabolites JO - FEMS Yeast Research VL - 5 UR - https://doi.org/10.1016/j.femsyr.2004.10.007 DO - 10.1016/j.femsyr.2004.10.007 ID - van Winden2005 ER - TY - JOUR AU - Rantanen, A. AU - Mielikäinen, T. AU - Rousu, J. AU - Maaheimo, H. AU - Ukkonen, E. PY - 2006 DA - 2006// TI - Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl069 DO - 10.1093/bioinformatics/btl069 ID - Rantanen2006 ER - TY - JOUR AU - Schmidt, K. AU - Nielsen, J. AU - Villadsen, J. PY - 1999 DA - 1999// TI - Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models JO - Journal of Biotechnology VL - 71 UR - https://doi.org/10.1016/S0168-1656(99)00021-8 DO - 10.1016/S0168-1656(99)00021-8 ID - Schmidt1999 ER - TY - JOUR AU - Rantanen, A. AU - Rousu, J. AU - Ketola, R. AU - Kokkonen, J. AU - Tarkiainen, V. PY - 2002 DA - 2002// TI - Computing Positional Isotopomer Distributions from Tandem Mass Spectrometric Data JO - Metabolic Engineering VL - 4 UR - https://doi.org/10.1006/mben.2002.0232 DO - 10.1006/mben.2002.0232 ID - Rantanen2002 ER - TY - BOOK AU - Aho, A. AU - Hopcroft, J. AU - Ullman, J. PY - 1974 DA - 1974// TI - The Design and Analysis of Computer Algorithms ID - Aho1974 ER - TY - BOOK AU - Appel, A. PY - 1998 DA - 1998// TI - Modern Compiler Implementation in Java ID - Appel1998 ER - TY - JOUR AU - Isermann, N. AU - Wiechert, W. PY - 2003 DA - 2003// TI - Metabolic isotopomer labeling systems. Part II: structural identifibiality analysis JO - Mathematical Biosciences VL - 183 UR - https://doi.org/10.1016/S0025-5564(02)00222-5 DO - 10.1016/S0025-5564(02)00222-5 ID - Isermann2003 ER - TY - JOUR AU - van Winden, W. AU - Heijnen, J. AU - Verheijen, P. AU - Grievink, J. PY - 2001 DA - 2001// TI - A priori analysis of metabolic flux identifiability from 13C-labeling data JO - Biotechnology and Bioengineering VL - 74 UR - https://doi.org/10.1002/bit.1142 DO - 10.1002/bit.1142 ID - van Winden2001 ER - TY - JOUR AU - Covert, M. AU - Schilling, C. AU - Palsson, B. PY - 2001 DA - 2001// TI - Regulation of Gene Expression in Flux Balance Models of Metabolism JO - Journal of Theoretical Biology VL - 213 UR - https://doi.org/10.1006/jtbi.2001.2405 DO - 10.1006/jtbi.2001.2405 ID - Covert2001 ER - TY - CHAP AU - Kümmel, A. AU - Panke, S. AU - Heinemann, M. PY - 2006 DA - 2006// TI - Systematic assignment of thermodynamic constraints in metabolic network models BT - BMC Bioinformatics ID - Kümmel2006 ER - TY - JOUR AU - Henry, C. AU - Broadbelt, L. AU - Hatzimanikatis, V. PY - 2007 DA - 2007// TI - Thermodynamics-Based Metabolic Flux Analysis JO - Biophysical Journal VL - 92 UR - https://doi.org/10.1529/biophysj.106.093138 DO - 10.1529/biophysj.106.093138 ID - Henry2007 ER - TY - CHAP AU - Hoppe, A. AU - Hoffmann, S. AU - Holzhütter, H. PY - 2007 DA - 2007// TI - Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks BT - BMC Systems Biology ID - Hoppe2007 ER - TY - BOOK AU - Schwarz, H. PY - 1989 DA - 1989// TI - Numerical Analysis: A Comprehensive Introduction ID - Schwarz1989 ER - TY - JOUR AU - Klamt, S. AU - Schuster, S. PY - 2002 DA - 2002// TI - Calculating as many fluxes as possible in underdetermined metabolic networks JO - Molecular Biology Reports VL - 29 UR - https://doi.org/10.1023/A:1020394300385 DO - 10.1023/A:1020394300385 ID - Klamt2002 ER - TY - JOUR AU - Bonarius, H. AU - Schmidt, G. AU - Tramper, J. PY - 1997 DA - 1997// TI - Flux analysis of underdetermined metabolic networks: the quest for the missing constraints JO - Trends in Biotechnology VL - 15 UR - https://doi.org/10.1016/S0167-7799(97)01067-6 DO - 10.1016/S0167-7799(97)01067-6 ID - Bonarius1997 ER - TY - JOUR AU - Edwards, J. AU - Covert, M. AU - Palsson, B. PY - 2002 DA - 2002// TI - Metabolic modelling of microbes: the flux-balance approach JO - Environmental Microbiology VL - 4 UR - https://doi.org/10.1046/j.1462-2920.2002.00282.x DO - 10.1046/j.1462-2920.2002.00282.x ID - Edwards2002 ER - TY - JOUR AU - Möllney, M. AU - Wiechert, W. AU - Kownatzki, D. AU - de Graaf, A. PY - 1999 DA - 1999// TI - Bidirectional Reaction Steps in Metabolic Networks IV: Optimal Design of Isotopomer Labeling Experiments JO - Biotechnology and Bioengineering VL - 66 UR - https://doi.org/3.0.CO;2-A DO - 3.0.CO;2-A ID - Möllney1999 ER - TY - JOUR AU - Kleijn, R. AU - van Winden, W. AU - Ras, C. AU - van Gulik, W. AU - Schipper, D. AU - Heijnen, J. PY - 2006 DA - 2006// TI - 13C-Labeled Gluconate Tracing as a Direct and Accurate Method for Determining the Pentose Phosphate Pathway Split Ratio in Penicillium chrysogenum JO - Applied and Environmental Microbiology VL - 72 UR - https://doi.org/10.1128/AEM.02955-05 DO - 10.1128/AEM.02955-05 ID - Kleijn2006 ER - TY - JOUR AU - Araúzo-Bravo, M. AU - Shimizu, K. PY - 2003 DA - 2003// TI - An improved method for statistical analysis of metabolic flux analysis using isotopomer mapping matrices with analytical expressions JO - Journal of Biotechnology VL - 105 UR - https://doi.org/10.1016/S0168-1656(03)00169-X DO - 10.1016/S0168-1656(03)00169-X ID - Araúzo-Bravo2003 ER - TY - JOUR AU - Wiechert, W. AU - Siefke, C. AU - de Graaf, A. AU - Marx, A. PY - 1997 DA - 1997// TI - Bidirectional Reaction Steps in Metabolic Networks: II. Flux Estimation and Statistical Analysis JO - Biotechnology and Bioengineering VL - 55 UR - https://doi.org/3.0.CO;2-I DO - 3.0.CO;2-I ID - Wiechert1997 ER - TY - JOUR AU - Antoniewicz, M. AU - Kelleher, J. AU - Stephanopoulos, G. PY - 2006 DA - 2006// TI - Determination of confidence intervals of metabolic fluxes estimated from stable isotopome measurements JO - Metabolic Engineering VL - 8 UR - https://doi.org/10.1016/j.ymben.2006.01.004 DO - 10.1016/j.ymben.2006.01.004 ID - Antoniewicz2006 ER - TY - JOUR AU - Wiebe, M. AU - Rintala, E. AU - Tamminen, A. AU - Simolin, H. AU - Salusjärvi, L. AU - Toivari, M. AU - Kokkonen, J. AU - Kiuru, J. AU - Ketola, R. AU - Jouhten, P. AU - Huuskonen, A. AU - Maaheimo, H. AU - Ruohonen, L. AU - Penttilä, M. PY - 2008 DA - 2008// TI - Central carbon metabolism of Saccharomyces cerevisiae in anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions JO - FEMS Yeast Research VL - 8 UR - https://doi.org/10.1111/j.1567-1364.2007.00234.x DO - 10.1111/j.1567-1364.2007.00234.x ID - Wiebe2008 ER - TY - JOUR AU - Fiaux, J. AU - Cakar, P. AU - Sonderegger, M. AU - Wüthrich, K. AU - Szyperski, T. AU - Sauer, U. PY - 2003 DA - 2003// TI - Metabolic-Flux Profiling of the Yeasts Saccharomyces cerevisiae and Pichia stipitis JO - Eukaryotic Cell VL - 2 UR - https://doi.org/10.1128/EC.2.1.170-180.2003 DO - 10.1128/EC.2.1.170-180.2003 ID - Fiaux2003 ER -