-
1
-
-
0032189439
-
Calculation of standard transformed formation properties of biochemical reactants and standard apparent reduction potentials of half reactions
-
Alberty, R. A. 1998. Calculation of standard transformed formation properties of biochemical reactants and standard apparent reduction potentials of half reactions. Arch. Biochem. Biophys. 358:25-39.
-
(1998)
Arch. Biochem. Biophys
, vol.358
, pp. 25-39
-
-
Alberty, R.A.1
-
2
-
-
33745433792
-
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
-
Kummel, A., S. Panke, and M. Heinemann. 2006. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2:2006-2034.
-
(2006)
Mol. Syst. Biol
, vol.2
, pp. 2006-2034
-
-
Kummel, A.1
Panke, S.2
Heinemann, M.3
-
4
-
-
85030526212
-
-
Westerhoff, H. V., and International Study Group of Biological Thermodynamics Control and Kinetics. 1994. Biothermokinetics. Intercept, Andover, Hampshire, England.
-
Westerhoff, H. V., and International Study Group of Biological Thermodynamics Control and Kinetics. 1994. Biothermokinetics. Intercept, Andover, Hampshire, England.
-
-
-
-
5
-
-
0031018721
-
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates
-
Nielsen, J. 1997. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates. Biochem. J. 321:133-138.
-
(1997)
Biochem. J
, vol.321
, pp. 133-138
-
-
Nielsen, J.1
-
7
-
-
0025701406
-
Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution
-
Mavrovouniotis, M. L. 1990. Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol. Bioeng. 36:1070-1082.
-
(1990)
Biotechnol. Bioeng
, vol.36
, pp. 1070-1082
-
-
Mavrovouniotis, M.L.1
-
8
-
-
0026353854
-
Estimation of standard Gibbs energy changes of biotransformations
-
Mavrovouniotis, M. L. 1991. Estimation of standard Gibbs energy changes of biotransformations. J. Biol. Chem. 266:14440-14445.
-
(1991)
J. Biol. Chem
, vol.266
, pp. 14440-14445
-
-
Mavrovouniotis, M.L.1
-
9
-
-
0031877180
-
Calculation of standard transformed Gibbs energies and standard transformed enthalpies of biochemical reactants
-
Alberty, R. A. 1998. Calculation of standard transformed Gibbs energies and standard transformed enthalpies of biochemical reactants. Arch. Biochem. Biophys. 353:116-130.
-
(1998)
Arch. Biochem. Biophys
, vol.353
, pp. 116-130
-
-
Alberty, R.A.1
-
10
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4:54.1-54.12.
-
(2003)
Genome Biol
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
11
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
Edwards, J. S., and B. O. Palsson. 2000. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA. 97:5528-5533.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
12
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
Schilling, C. H., M. W. Covert, I. Famili, G. M. Church, J. S. Edwards, and B. O. Palsson. 2002. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184:4582-4593.
-
(2002)
J. Bacteriol
, vol.184
, pp. 4582-4593
-
-
Schilling, C.H.1
Covert, M.W.2
Famili, I.3
Church, G.M.4
Edwards, J.S.5
Palsson, B.O.6
-
13
-
-
9544253891
-
Genome-scale models of microbial cells: Evaluating the consequences of constraints
-
Price, N. D., J. L. Reed, and B. O. Palsson. 2004. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol. 2:886-897.
-
(2004)
Nat. Rev. Microbiol
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
14
-
-
0036286631
-
Energy balance for analysis of complex metabolic networks
-
Beard, D. A., S. C. Liang, and H. Qian. 2002. Energy balance for analysis of complex metabolic networks. Biophys. J. 83:79-86.
-
(2002)
Biophys. J
, vol.83
, pp. 79-86
-
-
Beard, D.A.1
Liang, S.C.2
Qian, H.3
-
15
-
-
0037315604
-
Stoichiometric network theory for nonequilibrium biochemical systems
-
Qian, H., D. A. Beard, and S. D. Liang. 2003. Stoichiometric network theory for nonequilibrium biochemical systems. Eur. J. Biochem. 270:415-421.
-
(2003)
Eur. J. Biochem
, vol.270
, pp. 415-421
-
-
Qian, H.1
Beard, D.A.2
Liang, S.D.3
-
16
-
-
2342627280
-
Thermodynamic constraints for biochemical networks
-
Beard, D. A., E. Babson, E. Curtis, and H. Qian. 2004. Thermodynamic constraints for biochemical networks. J. Theor. Biol. 228:327-333.
-
(2004)
J. Theor. Biol
, vol.228
, pp. 327-333
-
-
Beard, D.A.1
Babson, E.2
Curtis, E.3
Qian, H.4
-
17
-
-
13844289127
-
Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism
-
Beard, D. A., and H. Qian. 2005. Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. Am. J. Physiol. Endocrinol. Metab. 288:E633-E644.
-
(2005)
Am. J. Physiol. Endocrinol. Metab
, vol.288
-
-
Beard, D.A.1
Qian, H.2
-
18
-
-
2042440312
-
Identification of qualitatively feasible metabolic pathways
-
L. Hunter, editor. AAAI Press/MIT Press, Menlo Park, California
-
Mavrovouniotis, M. L. 1993. Identification of qualitatively feasible metabolic pathways. In Artificial Intelligence and Molecular Biology. L. Hunter, editor. AAAI Press/MIT Press, Menlo Park, California.
-
(1993)
Artificial Intelligence and Molecular Biology
-
-
Mavrovouniotis, M.L.1
-
19
-
-
27844495174
-
Identification of localized and distributed bottlenecks in metabolic pathways
-
Mavrovouniotis, M. L. 1993. Identification of localized and distributed bottlenecks in metabolic pathways. Proc. Int. Conf. Intell. Syst. Mol. Biol. 93:273-283.
-
(1993)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.93
, pp. 273-283
-
-
Mavrovouniotis, M.L.1
-
20
-
-
27744527638
-
How reliable are thermodynamic feasibility statements in biochemical pathways?
-
Maskow, T., and U. V. Stockar. 2005. How reliable are thermodynamic feasibility statements in biochemical pathways? Biotechnol. Bioeng. 92:223-230.
-
(2005)
Biotechnol. Bioeng
, vol.92
, pp. 223-230
-
-
Maskow, T.1
Stockar, U.V.2
-
21
-
-
33645752331
-
Genome-scale thermodynamic analysis of Escherichia coli metabolism
-
Henry, C. S., M. D. Jankowski, L. J. Broadbelt, and V. Hatzimanikatis. 2006. Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys. J. 90:1453-1461.
-
(2006)
Biophys. J
, vol.90
, pp. 1453-1461
-
-
Henry, C.S.1
Jankowski, M.D.2
Broadbelt, L.J.3
Hatzimanikatis, V.4
-
22
-
-
85030502288
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
23
-
-
0021383728
-
Equations and calculations for fermentations of butyric-acid bacteria
-
Papoutsakis, E. T. 1984. Equations and calculations for fermentations of butyric-acid bacteria. Biotechnol. Bioeng. 26:174-187.
-
(1984)
Biotechnol. Bioeng
, vol.26
, pp. 174-187
-
-
Papoutsakis, E.T.1
-
24
-
-
0027716622
-
Metabolic capabilities of Escherichia coli.1. Synthesis of biosynthetic precursors and cofactors
-
Varma, A., and B. O. Palsson. 1993. Metabolic capabilities of Escherichia coli.1. Synthesis of biosynthetic precursors and cofactors. J. Theor. Biol. 165:477-502.
-
(1993)
J. Theor. Biol
, vol.165
, pp. 477-502
-
-
Varma, A.1
Palsson, B.O.2
-
25
-
-
0036001069
-
Metabolic modeling of microbes: The flux-balance approach
-
Edwards, J. S., M. Covert, and B. Palsson. 2002. Metabolic modeling of microbes: the flux-balance approach. Environ. Microbiol. 4:133-140.
-
(2002)
Environ. Microbiol
, vol.4
, pp. 133-140
-
-
Edwards, J.S.1
Covert, M.2
Palsson, B.3
-
26
-
-
0021918026
-
Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations
-
Papoutsakis, E. T., and C. L. Meyer. 1985. Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations. Biotechnol. Bioeng. 27:50-66.
-
(1985)
Biotechnol. Bioeng
, vol.27
, pp. 50-66
-
-
Papoutsakis, E.T.1
Meyer, C.L.2
-
27
-
-
3242658291
-
Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae
-
Jin, Y. S., and T. W. Jeffries. 2004. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab. Eng. 6:229-238.
-
(2004)
Metab. Eng
, vol.6
, pp. 229-238
-
-
Jin, Y.S.1
Jeffries, T.W.2
-
28
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
Edwards, J. S., R. U. Ibarra, and B. O. Palsson. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19:125-130.
-
(2001)
Nat. Biotechnol
, vol.19
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
29
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
Varma, A., and B. O. Palsson. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60:3724-3731.
-
(1994)
Appl. Environ. Microbiol
, vol.60
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
30
-
-
0027723421
-
Metabolic capabilities of Escherichia coli. 2. Optimal-growth patterns
-
Varma, A., and B. O. Palsson. 1993. Metabolic capabilities of Escherichia coli. 2. Optimal-growth patterns. J. Theor. Biol. 165:503-522.
-
(1993)
J. Theor. Biol
, vol.165
, pp. 503-522
-
-
Varma, A.1
Palsson, B.O.2
-
31
-
-
0035812464
-
Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
-
Burgard, A. P., and C. D. Maranas. 2001. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74:364-375.
-
(2001)
Biotechnol. Bioeng
, vol.74
, pp. 364-375
-
-
Burgard, A.P.1
Maranas, C.D.2
-
32
-
-
0034519221
-
Robustness analysis of the Escherichia coli metabolic network
-
Edwards, J. S., and B. O. Palsson. 2000. Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16:927-939.
-
(2000)
Biotechnol. Prog
, vol.16
, pp. 927-939
-
-
Edwards, J.S.1
Palsson, B.O.2
-
33
-
-
21244477594
-
K-cone analysis: Determining all candidate values for kinetic parameters on a network scale
-
Famili, I., R. Mahadevan, and B. O. Palsson. 2005. K-cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys. J. 88:1616-1625.
-
(2005)
Biophys. J
, vol.88
, pp. 1616-1625
-
-
Famili, I.1
Mahadevan, R.2
Palsson, B.O.3
-
34
-
-
10044224601
-
Metabolic control analysis under uncertainty: Framework development and case studies
-
Wang, L. Q., I. Birol, and V. Hatzimanikatis. 2004. Metabolic control analysis under uncertainty: framework development and case studies. Biophys. J. 87:3750-3763.
-
(2004)
Biophys. J
, vol.87
, pp. 3750-3763
-
-
Wang, L.Q.1
Birol, I.2
Hatzimanikatis, V.3
-
35
-
-
0021847426
-
Metabolic control and its analysis. Additional relationships between elasticities and control coefficients
-
Fell, D. A., and H. M. Sauro. 1985. Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. Eur. J. Biochem. 148:555-561.
-
(1985)
Eur. J. Biochem
, vol.148
, pp. 555-561
-
-
Fell, D.A.1
Sauro, H.M.2
-
37
-
-
0015989446
-
A linear steady-state treatment of enzymatic chains. General properties, control and effector strength
-
Heinrich, R., and T. A. Rapoport. 1974. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42:89-95.
-
(1974)
Eur. J. Biochem
, vol.42
, pp. 89-95
-
-
Heinrich, R.1
Rapoport, T.A.2
-
39
-
-
8844259501
-
Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry
-
Goldberg, R. N., Y. B. Tewari, and T. N. Bhat. 2004. Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. Bioinformatics. 20:2874-2877.
-
(2004)
Bioinformatics
, vol.20
, pp. 2874-2877
-
-
Goldberg, R.N.1
Tewari, Y.B.2
Bhat, T.N.3
-
41
-
-
0017343370
-
Energy conservation in chemotrophic anaerobic bacteria
-
Thauer, R. K., K. Jungermann, and K. Decker. 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41:100-180.
-
(1977)
Bacteriol. Rev
, vol.41
, pp. 100-180
-
-
Thauer, R.K.1
Jungermann, K.2
Decker, K.3
-
42
-
-
33847773201
-
United States National Bureau of Standards, American Chemical Society and American Institute of Physics
-
American Chemical Society and the American Institute of Physics for the National Bureau of Standards, New York; Washington, DC
-
Wagman, D. D. United States National Bureau of Standards, American Chemical Society and American Institute of Physics. 1982. The NBS Tables of Chemical Thermodynamic Properties: Selected Values for Inorganic and C1 and C2 Organic Substances in SI Units. American Chemical Society and the American Institute of Physics for the National Bureau of Standards, New York; Washington, DC.
-
(1982)
The NBS Tables of Chemical Thermodynamic Properties: Selected Values for Inorganic and C1 and C2 Organic Substances in SI Units
-
-
Wagman, D.D.1
-
43
-
-
0001021650
-
Thermodynamic and transport-properties of carbohydrates and their monophosphates - the pentoses and hexoses
-
Goldberg, R. N., and Y. B. Tewari. 1989. Thermodynamic and transport-properties of carbohydrates and their monophosphates - the pentoses and hexoses. J. Phys. Chem. Ref. Data. 18:809-880.
-
(1989)
J. Phys. Chem. Ref. Data
, vol.18
, pp. 809-880
-
-
Goldberg, R.N.1
Tewari, Y.B.2
-
44
-
-
0002855324
-
Thermochemistry of the reactions between adenosine, adenosine 5′-monophosphate, inosine, and inosine 5′-monophosphate - the conversion of L-histidine to (urocanic acid plus ammonia)
-
Larson, J. W., Y. B. Tewari, and R. N. Goldberg. 1993. Thermochemistry of the reactions between adenosine, adenosine 5′-monophosphate, inosine, and inosine 5′-monophosphate - the conversion of L-histidine to (urocanic acid plus ammonia). J. Chem. Thermodyn. 25:73-90.
-
(1993)
J. Chem. Thermodyn
, vol.25
, pp. 73-90
-
-
Larson, J.W.1
Tewari, Y.B.2
Goldberg, R.N.3
-
45
-
-
0025865784
-
Thermodynamics of the disproportionation of adenosine 5′diphosphate to adenosine 5′-triphosphate and adenosine 5′-monophosphate. 1. Equilibrium-model
-
Goldberg, R. N., and Y. B. Tewari. 1991. Thermodynamics of the disproportionation of adenosine 5′diphosphate to adenosine 5′-triphosphate and adenosine 5′-monophosphate. 1. Equilibrium-model. Biophys. Chem. 40:241-261.
-
(1991)
Biophys. Chem
, vol.40
, pp. 241-261
-
-
Goldberg, R.N.1
Tewari, Y.B.2
-
46
-
-
85030512185
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
48
-
-
0141504947
-
Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout
-
Yang, C., Q. Hua, T. Baba, H. Mori, and K. Shimizu. 2003. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol. Bioeng. 84:129-144.
-
(2003)
Biotechnol. Bioeng
, vol.84
, pp. 129-144
-
-
Yang, C.1
Hua, Q.2
Baba, T.3
Mori, H.4
Shimizu, K.5
-
49
-
-
0025276048
-
Cellular concentrations of enzymes and their substrates
-
Albe, K. R., M. H. Butler, and B. E. Wright. 1990. Cellular concentrations of enzymes and their substrates. J. Theor. Biol. 143:163-195.
-
(1990)
J. Theor. Biol
, vol.143
, pp. 163-195
-
-
Albe, K.R.1
Butler, M.H.2
Wright, B.E.3
-
50
-
-
4644220226
-
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states
-
Reed, J. L., and B. O. Palsson. 2004. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res. 14:1797-1805.
-
(2004)
Genome Res
, vol.14
, pp. 1797-1805
-
-
Reed, J.L.1
Palsson, B.O.2
-
51
-
-
0021337801
-
Dihydroorotase from Escherichia coli - purification and characterization
-
Washabaugh, M. W., and K. D. Collins. 1984. Dihydroorotase from Escherichia coli - purification and characterization. J. Biol. Chem. 259:3293-3298.
-
(1984)
J. Biol. Chem
, vol.259
, pp. 3293-3298
-
-
Washabaugh, M.W.1
Collins, K.D.2
-
52
-
-
0018100973
-
Multi-enzyme complex of glutamine-dependent carbamoyl-phosphate synthetase with aspartate carbamoyltransferase and dihydroorotase from rat ascites-hepatoma cells. Purification, molecular properties and limited proteolysis
-
Mori, M., and M. Tatibana. 1978. Multi-enzyme complex of glutamine-dependent carbamoyl-phosphate synthetase with aspartate carbamoyltransferase and dihydroorotase from rat ascites-hepatoma cells. Purification, molecular properties and limited proteolysis. Eur. J. Biochem. 86:381-388.
-
(1978)
Eur. J. Biochem
, vol.86
, pp. 381-388
-
-
Mori, M.1
Tatibana, M.2
-
53
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan, R., and C. H. Schilling. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5:264-276.
-
(2003)
Metab. Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
54
-
-
0017397091
-
Charges of nicotinamide adenine-nucleotides and adenylate energy-charge as regulatory parameters of metabolism in Escherichia coli
-
Andersen, K. B., and K. V. Meyenburg. 1977. Charges of nicotinamide adenine-nucleotides and adenylate energy-charge as regulatory parameters of metabolism in Escherichia coli. J. Biol. Chem. 252:4151-4156.
-
(1977)
J. Biol. Chem
, vol.252
, pp. 4151-4156
-
-
Andersen, K.B.1
Meyenburg, K.V.2
-
55
-
-
2442707990
-
Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements
-
Peng, L., M. J. Arauzo-Bravo, and K. Shimizu. 2004. Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol. Lett. 235:17-23.
-
(2004)
FEMS Microbiol. Lett
, vol.235
, pp. 17-23
-
-
Peng, L.1
Arauzo-Bravo, M.J.2
Shimizu, K.3
-
56
-
-
0017794395
-
Amino acid biosynthesis and its regulation
-
Umbarger, H. E. 1978. Amino acid biosynthesis and its regulation. Annu. Rev. Biochem. 47:532-606.
-
(1978)
Annu. Rev. Biochem
, vol.47
, pp. 532-606
-
-
Umbarger, H.E.1
|