-
3
-
-
0037075690
-
Modeling and simulation: Tools for metabolic engineering
-
A critical review of different modeling approaches with respect to their potential for metabolic engineering.
-
Wiechert W. Modeling and simulation: tools for metabolic engineering. J. Biotechnol. 94:2002;37-63 A critical review of different modeling approaches with respect to their potential for metabolic engineering.
-
(2002)
J. Biotechnol.
, vol.94
, pp. 37-63
-
-
Wiechert, W.1
-
4
-
-
33749133230
-
Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction
-
Reprinted from Biotechnology and Bioengineering, Vol. 41, pp 633-646 (1993)
-
Vallino JJ, Stephanopoulos G: Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. [Reprinted from Biotechnology and Bioengineering, Vol. 41, pp 633-646 (1993).] Biotechnol Bioeng 2000, 67:872-885.
-
(2000)
Biotechnol Bioeng
, vol.67
, pp. 872-885
-
-
Vallino, J.J.1
Stephanopoulos, G.2
-
5
-
-
0032600888
-
Metabolic fluxes and metabolic engineering
-
Stephanopoulos G. Metabolic fluxes and metabolic engineering. Metab. Eng. 1:1999;1-11.
-
(1999)
Metab. Eng.
, vol.1
, pp. 1-11
-
-
Stephanopoulos, G.1
-
6
-
-
0033987329
-
Metabolic network analysis. A powerful tool in metabolic engineering
-
Christensen B., Nielsen J. Metabolic network analysis. A powerful tool in metabolic engineering. Adv. Biochem. Eng. Biotechnol. 66:2000;209-231.
-
(2000)
Adv. Biochem. Eng. Biotechnol.
, vol.66
, pp. 209-231
-
-
Christensen, B.1
Nielsen, J.2
-
7
-
-
0042825675
-
Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry
-
Klapa M.I., Aon J.C., Stephanopoulos G. Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry. Eur. J. Biochem. 270:2003;3525-3542.
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 3525-3542
-
-
Klapa, M.I.1
Aon, J.C.2
Stephanopoulos, G.3
-
9
-
-
0027223982
-
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates
-
Varma A., Boesch B.W., Palsson B.O. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59:1993;2465-2473.
-
(1993)
Appl. Environ. Microbiol.
, vol.59
, pp. 2465-2473
-
-
Varma, A.1
Boesch, B.W.2
Palsson, B.O.3
-
11
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18:2000;326-332.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
12
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
-
Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203:2000;229-248.
-
(2000)
J. Theor. Biol.
, vol.203
, pp. 229-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
13
-
-
0037308505
-
Two approaches for metabolic pathway analysis?
-
Klamt S., Stelling J. Two approaches for metabolic pathway analysis? Trends Biotechnol. 21:2003;64-69.
-
(2003)
Trends Biotechnol
, vol.21
, pp. 64-69
-
-
Klamt, S.1
Stelling, J.2
-
14
-
-
0037406237
-
Development of network-based pathway definitions: The need to analyze real metabolic networks
-
Palsson B.O., Price N.D., Papin J.A. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol. 21:2003;195-198.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 195-198
-
-
Palsson, B.O.1
Price, N.D.2
Papin, J.A.3
-
15
-
-
0036713452
-
Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae
-
Cronwright G.R., Rohwer J.M., Prior B.A. Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 68:2002;4448-4456.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 4448-4456
-
-
Cronwright, G.R.1
Rohwer, J.M.2
Prior, B.A.3
-
16
-
-
0041508906
-
Metabolic control analysis of xylose catabolism in Aspergillus
-
Prathumpai W., Gabelgaard J.B., Wanchanthuek P., Van De Vondervoort P.J., De Groot M.J., McIntyre M., Nielsen J. Metabolic control analysis of xylose catabolism in Aspergillus. Biotechnol. Prog. 19:2003;1136-1141.
-
(2003)
Biotechnol. Prog.
, vol.19
, pp. 1136-1141
-
-
Prathumpai, W.1
Gabelgaard, J.B.2
Wanchanthuek, P.3
Van De Vondervoort, P.J.4
De Groot, M.J.5
McIntyre, M.6
Nielsen, J.7
-
17
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
Edwards J.S., Palsson B.O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA. 97:2000;5528-5533.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
18
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed J.L., Vo T.D., Schilling C.H., Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4:2003;R54.
-
(2003)
Genome Biol.
, vol.4
, pp. 54
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
19
-
-
0033580813
-
Systems properties of the Haemophilus influenzae Rd metabolic genotype
-
Edwards J.S., Palsson B.O. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274:1999;17410-17416.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17410-17416
-
-
Edwards, J.S.1
Palsson, B.O.2
-
20
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
Schilling C.H., Covert M.W., Famili I., Church G.M., Edwards J.S., Palsson B.O. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184:2002;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
-
21
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
The first genome-scale model of a eukaryotic organism, which also demonstrates the reconstruction of the largest stoichiometric model to date.
-
Forster J., Famili I., Fu P., Palsson B.O., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:2003;244-253 The first genome-scale model of a eukaryotic organism, which also demonstrates the reconstruction of the largest stoichiometric model to date.
-
(2003)
Genome Res.
, vol.13
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
23
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
Using pathway analysis, the authors have devised a theoretical method for predicting key aspects of regulation in the metabolic network from network structure alone.
-
Stelling J., Klamt S., Bettenbrock K., Schuster S., Gilles E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature. 420:2002;190-193 Using pathway analysis, the authors have devised a theoretical method for predicting key aspects of regulation in the metabolic network from network structure alone.
-
(2002)
Nature
, vol.420
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
24
-
-
0036286631
-
Energy balance for analysis of complex metabolic networks
-
Incorporation of explicit thermodynamic constraints into FBA reduces the solution space and leads to improved physiological predictions.
-
Beard D.A., Liang S.D., Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 83:2002;79-86 Incorporation of explicit thermodynamic constraints into FBA reduces the solution space and leads to improved physiological predictions.
-
(2002)
Biophys. J.
, vol.83
, pp. 79-86
-
-
Beard, D.A.1
Liang, S.D.2
Qian, H.3
-
25
-
-
0035725112
-
Use of network analysis of metabolic systems in bioengineering
-
Schuster S., Klamt S., Weckwerth W., Moldenhauer F., Pfeiffer T. Use of network analysis of metabolic systems in bioengineering. Bioprocess Biosyst. Eng. 24:2002;363-372.
-
(2002)
Bioprocess Biosyst. Eng.
, vol.24
, pp. 363-372
-
-
Schuster, S.1
Klamt, S.2
Weckwerth, W.3
Moldenhauer, F.4
Pfeiffer, T.5
-
26
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
Edwards J.S., Ibarra R.U., Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19:2001;125-130.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
27
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
Evidence that the E. coli metabolic network has evolved for optimum growth is presented. Experiments show that evolution of a suboptimal network is in the direction of metabolic state determined a priori using in silico analysis.
-
Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 420:2002;186-189 Evidence that the E. coli metabolic network has evolved for optimum growth is presented. Experiments show that evolution of a suboptimal network is in the direction of metabolic state determined a priori using in silico analysis.
-
(2002)
Nature
, vol.420
, pp. 186-189
-
-
Ibarra, R.U.1
Edwards, J.S.2
Palsson, B.O.3
-
28
-
-
0344824417
-
Saccharomyces cerevisiae phenotype can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
-
Famili I, Forster J, Nielsen J, Palsson BO: Saccharomyces cerevisiae phenotype can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA 2003, 100:13134-13139.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13134-13139
-
-
Famili, I.1
Forster, J.2
Nielsen, J.3
Palsson, B.O.4
-
29
-
-
0038293216
-
Optimization-based framework for inferring and testing hypothesized metabolic objective functions
-
Using an optimization approach the authors developed a mathematical framework to test whether experimental flux data are consistent with hypothesized objective function.
-
Burgard A.P., Maranas C.D. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol. Bioeng. 82:2003;670-677 Using an optimization approach the authors developed a mathematical framework to test whether experimental flux data are consistent with hypothesized objective function.
-
(2003)
Biotechnol. Bioeng.
, vol.82
, pp. 670-677
-
-
Burgard, A.P.1
Maranas, C.D.2
-
30
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
Using experimental flux data from E. coli, the authors demonstrate that the metabolic network of genetically modified strains does not necessarily operate in an optimum growth regime.
-
Segre D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA. 99:2002;15112-15117 Using experimental flux data from E. coli, the authors demonstrate that the metabolic network of genetically modified strains does not necessarily operate in an optimum growth regime.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
31
-
-
0042816453
-
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
-
Forster J., Famili I., Palsson B.O., Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 7:2003;193-202.
-
(2003)
OMICS
, vol.7
, pp. 193-202
-
-
Forster, J.1
Famili, I.2
Palsson, B.O.3
Nielsen, J.4
-
32
-
-
0036284760
-
An expanded role for microbial physiology in metabolic engineering and functional genomics: Moving towards systems biology(1)
-
Nielsen J., Olsson L. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology(1). FEM Yeast Res. 2:2002;175-181.
-
(2002)
FEM Yeast Res.
, vol.2
, pp. 175-181
-
-
Nielsen, J.1
Olsson, L.2
-
33
-
-
0035812464
-
Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
-
Burgard A.P., Maranas C.D. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74:2001;364-375.
-
(2001)
Biotechnol. Bioeng.
, vol.74
, pp. 364-375
-
-
Burgard, A.P.1
Maranas, C.D.2
-
34
-
-
0343035686
-
Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
-
Pramanik J., Keasling J.D. Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 56:1997;398-421.
-
(1997)
Biotechnol. Bioeng.
, vol.56
, pp. 398-421
-
-
Pramanik, J.1
Keasling, J.D.2
-
35
-
-
0031015551
-
Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae
-
Nissen T.L., Schulze U., Nielsen J., Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiol. 143:1997;203-218.
-
(1997)
Microbiol.
, vol.143
, pp. 203-218
-
-
Nissen, T.L.1
Schulze, U.2
Nielsen, J.3
Villadsen, J.4
-
36
-
-
0035824029
-
Regulation of gene expression in flux balance models of metabolism
-
Covert M.W., Schilling C.H., Palsson B.O. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213:2001;73-88.
-
(2001)
J. Theor. Biol.
, vol.213
, pp. 73-88
-
-
Covert, M.W.1
Schilling, C.H.2
Palsson, B.O.3
-
37
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
A step towards incorporation of transcriptional regulation into stoichiometric models to obtain improved predictions of phenotypes.
-
Covert M.W., Palsson B.O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277:2002;28058-28064 A step towards incorporation of transcriptional regulation into stoichiometric models to obtain improved predictions of phenotypes.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
38
-
-
0037424661
-
Constraints-based models: Regulation of gene expression reduces the steady-state solution space
-
Covert M.W., Palsson B.O. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221:2003;309-325.
-
(2003)
J. Theor. Biol.
, vol.221
, pp. 309-325
-
-
Covert, M.W.1
Palsson, B.O.2
-
39
-
-
0036708443
-
Dynamic flux balance analysis of diauxic growth in Escherichia coli
-
Mahadevan R., Edwards J.S., Doyle F.J. III Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83:2002;1331-1340.
-
(2002)
Biophys. J.
, vol.83
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.S.2
Doyle III, F.J.3
-
40
-
-
0030571222
-
Pathway analysis, engineering, and physiological considerations for redirecting central metabolism
-
Liao J.C., Hou S.-Y., Chao Y.-P. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52:1996;129-140.
-
(1996)
Biotechnol. Bioeng.
, vol.52
, pp. 129-140
-
-
Liao, J.C.1
Hou, S.-Y.2
Chao, Y.-P.3
-
41
-
-
0037142769
-
Metabolic pathway analysis of a recombinant yeast for rational strain development
-
Carlson R., Fell D., Srienc F. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79:2002;121-134.
-
(2002)
Biotechnol. Bioeng.
, vol.79
, pp. 121-134
-
-
Carlson, R.1
Fell, D.2
Srienc, F.3
-
42
-
-
0036039060
-
Combinatorial complexity of pathway analysis in metabolic networks
-
Klamt S., Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29:2002;233-236.
-
(2002)
Mol. Biol. Rep.
, vol.29
, pp. 233-236
-
-
Klamt, S.1
Stelling, J.2
-
44
-
-
0242267924
-
Reconstruction of the central carbon metabolism of Aspergillus niger
-
David H., Åkesson M., Nielsen J. Reconstruction of the central carbon metabolism of Aspergillus niger. Eur. J. Biochem. 270:2003;4243-4253.
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 4243-4253
-
-
David, H.1
Åkesson, M.2
Nielsen, J.3
-
45
-
-
0242487787
-
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard A.P., Pharkya P., Maranas C.D. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84:2003;647-657.
-
(2003)
Biotechnol. Bioeng.
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
47
-
-
0036469172
-
Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints
-
Phelps T.J., Palumbo A.V., Beliaev A.S. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr. Opin. Biotechnol. 13:2002;20-24.
-
(2002)
Curr. Opin. Biotechnol.
, vol.13
, pp. 20-24
-
-
Phelps, T.J.1
Palumbo, A.V.2
Beliaev, A.S.3
-
48
-
-
0037716676
-
Building with a scaffold: Emerging strategies for high- to low-level cellular modeling
-
Ideker T., Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 21:2003;255-262.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 255-262
-
-
Ideker, T.1
Lauffenburger, D.2
-
50
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
Kuffner R., Zimmer R., Lengauer T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics. 16:2000;825-836.
-
(2000)
Bioinformatics
, vol.16
, pp. 825-836
-
-
Kuffner, R.1
Zimmer, R.2
Lengauer, T.3
-
51
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
A framework for analysis of different level omics data to extract biologically relevant information.
-
Ideker T., Ozier O., Schwikowski B., Siegel A.F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 18:2002;S233-S240 A framework for analysis of different level omics data to extract biologically relevant information.
-
(2002)
Bioinformatics
, vol.18
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
52
-
-
0037200931
-
A functional genomics approach using metabolomics and in silico pathway analysis
-
Forster J., Gombert A.K., Nielsen J. A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioeng. 79:2002;703-712.
-
(2002)
Biotechnol. Bioeng.
, vol.79
, pp. 703-712
-
-
Forster, J.1
Gombert, A.K.2
Nielsen, J.3
|