-
1
-
-
0028055202
-
Characterization of the osmotic-stress response in Saccharomyces cerevisiae: osmotic stress and glucose repression regulate glycerol-3-phosphate dehydrogenase independently
-
Albertyn, J., Hohmann, S., and Prior, B.A. (1994) Characterization of the osmotic-stress response in Saccharomyces cerevisiae: osmotic stress and glucose repression regulate glycerol-3-phosphate dehydrogenase independently. Curr Genet 25: 12-18.
-
(1994)
Curr Genet
, vol.25
, pp. 12-18
-
-
Albertyn, J.1
Hohmann, S.2
Prior, B.A.3
-
2
-
-
18844392599
-
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
-
Alper, H., Jin, Y.S., Moxley, J.F., and Stephanopoulos, G. (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 7: 155-164.
-
(2005)
Metab Eng
, vol.7
, pp. 155-164
-
-
Alper, H.1
Jin, Y.S.2
Moxley, J.F.3
Stephanopoulos, G.4
-
3
-
-
70449592325
-
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
-
Asadollahi, M.A., Maury, J., Patil, K.R., Schalk, M., Clark, A., and Nielsen, J. (2009) Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 11: 328-334.
-
(2009)
Metab Eng
, vol.11
, pp. 328-334
-
-
Asadollahi, M.A.1
Maury, J.2
Patil, K.R.3
Schalk, M.4
Clark, A.5
Nielsen, J.6
-
4
-
-
34247627985
-
Cell size at S phase initiation: an emergent property of the G1/S network
-
Barberis, M., Klipp, E., Vanoni, M., and Alberghina, L. (2007) Cell size at S phase initiation: an emergent property of the G1/S network. PLoS Comput Biol 3: 649-666.
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 649-666
-
-
Barberis, M.1
Klipp, E.2
Vanoni, M.3
Alberghina, L.4
-
5
-
-
0036286631
-
Energy balance for analysis of complex metabolic networks
-
Beard, D.A., Liang, S.D., and Qian, H. (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.D.2
Qian, H.3
-
6
-
-
2342627280
-
Thermodynamic constraints for biochemical networks
-
Beard, D.A., Babson, E., Curtis, E., and Qian, H. (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
-
7
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
-
Becker, S.A., Feist, A.M., Mo, M.L., Hannum, G., Palsson, B.O., and Herrgard, M.J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2: 727-738.
-
(2007)
Nat Protoc
, vol.2
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
8
-
-
84860402396
-
-
Methods and organisms for the growth-coupled production of succinate. Patent: 20070111294 (USA).
-
Burgard, A.P., and Van Dien, S.J. (2007) Methods and organisms for the growth-coupled production of succinate. Patent: 20070111294 (USA).
-
(2007)
-
-
Burgard, A.P.1
Van Dien, S.J.2
-
9
-
-
84860390925
-
-
Methods and organisms for the growth-coupled production of 3-hydroxypropionic acid. Patent: 20080199926 (USA).
-
Burgard, A.P., and Van Dien, S.J. (2008a) Methods and organisms for the growth-coupled production of 3-hydroxypropionic acid. Patent: 20080199926 (USA).
-
(2008)
-
-
Burgard, A.P.1
Van Dien, S.J.2
-
10
-
-
84860402395
-
-
Methods and organisms for the growth-coupled production of 1,4-butanediol. Patent: 20090047719 (USA).
-
Burgard, A.P., and Van Dien, S.J. (2008b) Methods and organisms for the growth-coupled production of 1, 4-butanediol. Patent: 20090047719 (USA).
-
(2008)
-
-
Burgard, A.P.1
Van Dien, S.J.2
-
11
-
-
0242487787
-
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard, A.P., Pharkya, P., and Maranas, C.D. (2003) Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647-657.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
12
-
-
84860403902
-
-
Methods and organisms for the growth-coupled production of 1,4-butanediol. Patent: WO/2009/023493.
-
Burgard, A.P., Van Dien, S.J., and Burk, M.J. (2009) Methods and organisms for the growth-coupled production of 1, 4-butanediol. Patent: WO/2009/023493.
-
(2009)
-
-
Burgard, A.P.1
Van Dien, S.J.2
Burk, M.J.3
-
13
-
-
0037025146
-
Dynamic modeling of central carbon metabolism of Echerichia coli
-
Chassagnole, C., Rizzi, N.N., Schmid, J.W., Mauch, K., and Reuss, M. (2002) Dynamic modeling of central carbon metabolism of Echerichia coli. Biotechnol Bioeng 79: 53-73.
-
(2002)
Biotechnol Bioeng
, vol.79
, pp. 53-73
-
-
Chassagnole, C.1
Rizzi, N.N.2
Schmid, J.W.3
Mauch, K.4
Reuss, M.5
-
14
-
-
0033985570
-
Kinetic analysis of a molecular model of the budding yeast cell cycle
-
Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B., and Tyson, J.J. (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11: 369-391.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 369-391
-
-
Chen, K.C.1
Csikasz-Nagy, A.2
Gyorffy, B.3
Val, J.4
Novak, B.5
Tyson, J.J.6
-
15
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
Chen, K.C., Calzone, L., Csikasz-Nagy, A., Cross, F.R., Novak, B., and Tyson, J.J. (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15: 3841-3862.
-
(2004)
Mol Biol Cell
, vol.15
, pp. 3841-3862
-
-
Chen, K.C.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.R.4
Novak, B.5
Tyson, J.J.6
-
16
-
-
0029118323
-
Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature
-
Curto, R., Sorribas, A., and Cascante, M. (1995) Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature. Math Biosci 130: 25-50.
-
(1995)
Math Biosci
, vol.130
, pp. 25-50
-
-
Curto, R.1
Sorribas, A.2
Cascante, M.3
-
17
-
-
77954291914
-
BioMet Toolbox: genome-wide analysis of metabolism
-
Cvijovic, M., Olivares-Hernandez, R., Agren, R., Dahr, N., Vongsangnak, W., Nookaew, I., etal. (2010) BioMet Toolbox: genome-wide analysis of metabolism. Nucleic Acids Res 38: 144-149.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 144-149
-
-
Cvijovic, M.1
Olivares-Hernandez, R.2
Agren, R.3
Dahr, N.4
Vongsangnak, W.5
Nookaew, I.6
-
18
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities
-
Edwards, J.S., and Palsson, B.O. (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
-
19
-
-
0036001069
-
Metabolic modelling of microbes: the flux-balance approach
-
Edwards, J.S., Covert, M., and Palsson, B. (2002) Metabolic modelling 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
-
20
-
-
58549108388
-
Reconstruction of biochemical networks in microbial organisms
-
Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., and Palsson, B.Ø. (2009) Reconstruction of biochemical networks in microbial organisms. Nat Rev Microbiol 7: 129-143.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.5
-
21
-
-
25144505718
-
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
-
Fong, S.S., Burgard, A.P., Herring, C.D., Knight, E.M., Blattner, F.R., Maranas, C.D., and Palsson, B.O. (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91: 643-648.
-
(2005)
Biotechnol Bioeng
, vol.91
, pp. 643-648
-
-
Fong, S.S.1
Burgard, A.P.2
Herring, C.D.3
Knight, E.M.4
Blattner, F.R.5
Maranas, C.D.6
Palsson, B.O.7
-
22
-
-
67650660144
-
Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production
-
Fowler, Z.L., Gikandi, W.W., and Koffas, M.A. (2009) Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production. Appl Environ Microbiol 75: 5831-5839.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5831-5839
-
-
Fowler, Z.L.1
Gikandi, W.W.2
Koffas, M.A.3
-
23
-
-
0027103941
-
Genetics and intermediary metabolism
-
Fraenkel, D.C. (1992) Genetics and intermediary metabolism. Annu Rev Genet 26: 159-177.
-
(1992)
Annu Rev Genet
, vol.26
, pp. 159-177
-
-
Fraenkel, D.C.1
-
24
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
Hatzimanikatis, V., Li, C., Ionita, J.A., Henry, C.S., Jankowski, M.D., and Broadbelt, L.J. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21: 1603-1609.
-
(2005)
Bioinformatics
, vol.21
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.J.6
-
25
-
-
33645752331
-
Genome-scale thermodynamic analysis of Escherichia coli metabolism
-
Henry, C.S., Jankowski, M.D., Broadbelt, L.J., and Hatzimanikatis, V. (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
-
26
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
Henry, C.S., Broadbelt, L.J., and Hatzimanikatis, V. (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92: 1792-1805.
-
(2007)
Biophys J
, vol.92
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
27
-
-
0036229317
-
Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis
-
Hoefnagel, M.H., Starrenburg, M.J., Martens, D.E., Hugenholtz, J., Kleerebezem, M., Van, S., II, etal. (2002) Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis. Microbiology 148: 1003-1013.
-
(2002)
Microbiology
, vol.148
, pp. 1003-1013
-
-
Hoefnagel, M.H.1
Starrenburg, M.J.2
Martens, D.E.3
Hugenholtz, J.4
Kleerebezem, M.5
Van II, S.6
-
28
-
-
0036282743
-
Osmotic stress signaling and osmoadaptation in yeasts
-
Hohmann, S. (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66: 300-372.
-
(2002)
Microbiol Mol Biol Rev
, vol.66
, pp. 300-372
-
-
Hohmann, S.1
-
29
-
-
35748951912
-
Yeast osmoregulation
-
Hohmann, S., Krantz, M., and Nordlander, B. (2007) Yeast osmoregulation. Methods Enzymol 428: 29-45.
-
(2007)
Methods Enzymol
, vol.428
, pp. 29-45
-
-
Hohmann, S.1
Krantz, M.2
Nordlander, B.3
-
30
-
-
51049107514
-
Group contribution method for thermodynamic analysis of complex metabolic networks
-
Jankowski, M.D., Henry, C.S., Broadbelt, L.J., and Hatzimanikatis, V. (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95: 1487-1499.
-
(2008)
Biophys J
, vol.95
, pp. 1487-1499
-
-
Jankowski, M.D.1
Henry, C.S.2
Broadbelt, L.J.3
Hatzimanikatis, V.4
-
31
-
-
33747856186
-
Metatool 5.0: fast and flexible elementary modes analysis
-
von Kamp, A., and Schuster, S. (2006) Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22: 1930-1931.
-
(2006)
Bioinformatics
, vol.22
, pp. 1930-1931
-
-
von Kamp, A.1
Schuster, S.2
-
32
-
-
33644524741
-
Cell-signalling dynamics in time and space
-
Kholodenko, B.N. (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 7: 165-176.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 165-176
-
-
Kholodenko, B.N.1
-
33
-
-
0037316342
-
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
Klamt, S., Stelling, J., Ginkel, M., and Gilles, E.D. (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269.
-
(2003)
Bioinformatics
, vol.19
, pp. 261-269
-
-
Klamt, S.1
Stelling, J.2
Ginkel, M.3
Gilles, E.D.4
-
34
-
-
36949000057
-
Modelling dynamic processes in yeast
-
Klipp, E. (2007) Modelling dynamic processes in yeast. Yeast 24: 943-959.
-
(2007)
Yeast
, vol.24
, pp. 943-959
-
-
Klipp, E.1
-
35
-
-
23444449142
-
Integrative model of the response of yeast to osmotic shock
-
Klipp, E., Nordlander, B., Kruger, R., Gennemark, P., and Hohmann, S. (2005) Integrative model of the response of yeast to osmotic shock. Nat Biotechnol 23: 975-982.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 975-982
-
-
Klipp, E.1
Nordlander, B.2
Kruger, R.3
Gennemark, P.4
Hohmann, S.5
-
36
-
-
34147189103
-
Systems biology standards - the community speaks
-
Klipp, E., Liebermeister, W., Helbig, A., Kowald, A., and Schaber, J. (2007) Systems biology standards - the community speaks. Nat Biotechnol 25: 390-391.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 390-391
-
-
Klipp, E.1
Liebermeister, W.2
Helbig, A.3
Kowald, A.4
Schaber, J.5
-
37
-
-
0038514074
-
Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression
-
Koffas, M.A., Jung, G.Y., and Stephanopoulos, G. (2003) Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metab Eng 5: 32-41.
-
(2003)
Metab Eng
, vol.5
, pp. 32-41
-
-
Koffas, M.A.1
Jung, G.Y.2
Stephanopoulos, G.3
-
38
-
-
33745433792
-
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
-
Kümmel, A., Panke, S., and Heinemann, M. (2006) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2: 2006-0034.
-
(2006)
Mol Syst Biol
, vol.2
, pp. 2006-0034
-
-
Kümmel, A.1
Panke, S.2
Heinemann, M.3
-
39
-
-
0030571222
-
Pathway analysis, engineering, and physiological considerations for redirecting central metabolism
-
Liao, J.C., Hou, S.Y., and Chao, Y.P. (1996) Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol Bioeng 52: 129-140.
-
(1996)
Biotechnol Bioeng
, vol.52
, pp. 129-140
-
-
Liao, J.C.1
Hou, S.Y.2
Chao, Y.P.3
-
40
-
-
27744527638
-
How reliable are thermodynamic feasibility statements of biochemical pathways?
-
Maskow, T., and von Stockar, U. (2005) How reliable are thermodynamic feasibility statements of biochemical pathways? Biotechnol Bioeng 92: 223-230.
-
(2005)
Biotechnol Bioeng
, vol.92
, pp. 223-230
-
-
Maskow, T.1
von Stockar, U.2
-
41
-
-
0027901886
-
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 1: 275-283.
-
(1993)
Proc Int Conf Intell Syst Mol Biol
, vol.1
, pp. 275-283
-
-
Mavrovouniotis, M.L.1
-
42
-
-
73849090293
-
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
-
Milne, C.B., Kim, P.J., Eddy, J.A., and Price, N.D. (2009) Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J 4: 1653-1670.
-
(2009)
Biotechnol J
, vol.4
, pp. 1653-1670
-
-
Milne, C.B.1
Kim, P.J.2
Eddy, J.A.3
Price, N.D.4
-
43
-
-
0040559975
-
Disruption of phacA, an Aspergillus nidulans gene encoding a novel cytochrome P450 monooxygenase catalyzing phenylacetate 2-hydroxylation, results in penicillin overproduction
-
Mingot, J.M., Penalva, M.A., and Fernandez-Canon, J.M. (1999) Disruption of phacA, an Aspergillus nidulans gene encoding a novel cytochrome P450 monooxygenase catalyzing phenylacetate 2-hydroxylation, results in penicillin overproduction. J Biol Chem 274: 14545-14550.
-
(1999)
J Biol Chem
, vol.274
, pp. 14545-14550
-
-
Mingot, J.M.1
Penalva, M.A.2
Fernandez-Canon, J.M.3
-
44
-
-
0036668632
-
Dealing with osmostress through MAP kinase activation
-
de Nadal, E., Alepuz, P.M., and Posas, F. (2002) Dealing with osmostress through MAP kinase activation. EMBO Rep 3: 735-740.
-
(2002)
EMBO Rep
, vol.3
, pp. 735-740
-
-
de Nadal, E.1
Alepuz, P.M.2
Posas, F.3
-
46
-
-
38349164135
-
Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae
-
Nielsen, J., and Jewett, M.C. (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 8: 122-131.
-
(2008)
FEMS Yeast Res
, vol.8
, pp. 122-131
-
-
Nielsen, J.1
Jewett, M.C.2
-
47
-
-
0030787863
-
Modeling the control of DNA replication in fission yeast
-
Novak, B., and Tyson, J.J. (1997) Modeling the control of DNA replication in fission yeast. Proc Natl Acad Sci USA 94: 9147-9152.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 9147-9152
-
-
Novak, B.1
Tyson, J.J.2
-
48
-
-
0032485826
-
Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions
-
Novak, B., Csikasz-Nagy, A., Gyorffy, B., Chen, K., and Tyson, J.J. (1998) Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions. Biophys Chem 72: 185-200.
-
(1998)
Biophys Chem
, vol.72
, pp. 185-200
-
-
Novak, B.1
Csikasz-Nagy, A.2
Gyorffy, B.3
Chen, K.4
Tyson, J.J.5
-
49
-
-
0035579883
-
Mathematical model of the cell division cycle of fission yeast
-
Novak, B., Pataki, Z., Ciliberto, A., and Tyson, J.J. (2001) Mathematical model of the cell division cycle of fission yeast. Chaos 11: 277-286.
-
(2001)
Chaos
, vol.11
, pp. 277-286
-
-
Novak, B.1
Pataki, Z.2
Ciliberto, A.3
Tyson, J.J.4
-
50
-
-
74849102606
-
Industrial systems biology
-
Otero, J.M., and Nielsen, J. (2010) Industrial systems biology. Biotechnol Bioeng 105: 439-460.
-
(2010)
Biotechnol Bioeng
, vol.105
, pp. 439-460
-
-
Otero, J.M.1
Nielsen, J.2
-
51
-
-
0345869627
-
Overproduction of trehalose: heterologous expression of Escherichia coli trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in Corynebacterium glutamicum
-
Padilla, L., Kramer, R., Stephanopoulos, G., and Agosin, E. (2004) Overproduction of trehalose: heterologous expression of Escherichia coli trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in Corynebacterium glutamicum. Appl Environ Microbiol 70: 370-376.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 370-376
-
-
Padilla, L.1
Kramer, R.2
Stephanopoulos, G.3
Agosin, E.4
-
52
-
-
0035989610
-
In silico biology through 'omics'
-
Palsson, B. (2002) In silico biology through 'omics'. Nat Biotechnol 20: 649-650.
-
(2002)
Nat Biotechnol
, vol.20
, pp. 649-650
-
-
Palsson, B.1
-
53
-
-
13444278821
-
Reconstruction of cellular signalling networks and analysis of their properties
-
Papin, J.A., Hunter, T., Palsson, B.O., and Subramaniam, S. (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6: 99-111.
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 99-111
-
-
Papin, J.A.1
Hunter, T.2
Palsson, B.O.3
Subramaniam, S.4
-
54
-
-
1242283921
-
Use of genome-scale microbial models for metabolic engineering
-
Patil, K.R., Akesson, M., and Nielsen, J. (2004) Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 15: 64-69.
-
(2004)
Curr Opin Biotechnol
, vol.15
, pp. 64-69
-
-
Patil, K.R.1
Akesson, M.2
Nielsen, J.3
-
55
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
Patil, K.R., Rocha, I., Forster, J., and Nielsen, J. (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6: 308.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 308
-
-
Patil, K.R.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
56
-
-
0347762731
-
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock
-
Pharkya, P., Burgard, A.P., and Maranas, C.D. (2003) Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol Bioeng 84: 887-899.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 887-899
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
57
-
-
8744224466
-
OptStrain: a computational framework for redesign of microbial production systems
-
Pharkya, P., Burgard, A.P., and Maranas, C.D. (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14: 2367-2376.
-
(2004)
Genome Res
, vol.14
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
58
-
-
0008056562
-
Thermodynamics of metabolic pathways for penicillin production: analysis of thermodynamic feasibility and free energy changes during fed-batch cultivation
-
Pissarra, P.D., and Nielsen, J. (1997) Thermodynamics of metabolic pathways for penicillin production: analysis of thermodynamic feasibility and free energy changes during fed-batch cultivation. Biotechnol Prog 13: 156-165.
-
(1997)
Biotechnol Prog
, vol.13
, pp. 156-165
-
-
Pissarra, P.D.1
Nielsen, J.2
-
59
-
-
0036840340
-
Extreme pathways and Kirchhoff's second law
-
Price, N.D., Famili, I., Beard, D.A., and Palsson, B.O. (2002) Extreme pathways and Kirchhoff's second law. Biophys J 83: 2879-2882.
-
(2002)
Biophys J
, vol.83
, pp. 2879-2882
-
-
Price, N.D.1
Famili, I.2
Beard, D.A.3
Palsson, B.O.4
-
60
-
-
0037385718
-
Genome-scale microbial in silico models: the constraints-based approach
-
Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B.O. (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21: 162-169.
-
(2003)
Trends Biotechnol
, vol.21
, pp. 162-169
-
-
Price, N.D.1
Papin, J.A.2
Schilling, C.H.3
Palsson, B.O.4
-
61
-
-
0343907200
-
In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model
-
Rizzi, M., Baltes, M., Theobald, U., and Reuss, M. (1997) In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol Bioeng 55: 592-608.
-
(1997)
Biotechnol Bioeng
, vol.55
, pp. 592-608
-
-
Rizzi, M.1
Baltes, M.2
Theobald, U.3
Reuss, M.4
-
62
-
-
0014649230
-
Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions
-
Savageau, M.A. (1969a) Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 25: 365-369.
-
(1969)
J Theor Biol
, vol.25
, pp. 365-369
-
-
Savageau, M.A.1
-
63
-
-
0014658880
-
Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation
-
Savageau, M.A. (1969b) Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol 25: 370-379.
-
(1969)
J Theor Biol
, vol.25
, pp. 370-379
-
-
Savageau, M.A.1
-
64
-
-
0014733809
-
Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation
-
Savageau, M.A. (1970) Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation. J Theor Biol 26: 215-226.
-
(1970)
J Theor Biol
, vol.26
, pp. 215-226
-
-
Savageau, M.A.1
-
65
-
-
0034615788
-
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
-
Schilling, C.H., and Palsson, B.O. (2000) Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 203: 249-283.
-
(2000)
J Theor Biol
, vol.203
, pp. 249-283
-
-
Schilling, C.H.1
Palsson, B.O.2
-
66
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic functions from a pathway-oriented perspective
-
Schilling, C.H., Letscher, D., and Palsson, B.O. (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic functions from a pathway-oriented perspective. J Theor Biol 203: 229-284.
-
(2000)
J Theor Biol
, vol.203
, pp. 229-284
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
67
-
-
0033080396
-
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
-
Schuster, S., Dandekar, T., and Fell, D.A. (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biothechnol 17: 53-60.
-
(1999)
Trends Biothechnol
, vol.17
, pp. 53-60
-
-
Schuster, S.1
Dandekar, T.2
Fell, D.A.3
-
68
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
Segre, D., Vitkup, D., and Church, G.M. (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99: 15112-15117.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
69
-
-
0034447725
-
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
-
Schilling, C.H., Edwards, J.S., Letscher, D., and Palsson, B.O. (2000) Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng 71: 286-306.
-
(2000)
Biotechnol Bioeng
, vol.71
, pp. 286-306
-
-
Schilling, C.H.1
Edwards, J.S.2
Letscher, D.3
Palsson, B.O.4
-
70
-
-
19644386033
-
Regulatory on/off minimization of metabolic flux changes after genetic perturbations
-
Shlomi, T., Berkman, O., and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102: 7695-7700.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7695-7700
-
-
Shlomi, T.1
Berkman, O.2
Ruppin, E.3
-
71
-
-
0029147559
-
Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior
-
Sorribas, A., Curto, R., and Cascante, M. (1995) Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior. Math Biosci 130: 71-84.
-
(1995)
Math Biosci
, vol.130
, pp. 71-84
-
-
Sorribas, A.1
Curto, R.2
Cascante, M.3
-
72
-
-
0037133330
-
Optimizing bioconversion pathways through systems analysis and metabolic engineering
-
Stafford, D.E., Yanagimachi, K.S., Lessard, P.A., Rijhwani, S.K., Sinskey, A.J., and Stephanopoulos, G. (2002) Optimizing bioconversion pathways through systems analysis and metabolic engineering. Proc Natl Acad Sci USA 99: 1801-1806.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1801-1806
-
-
Stafford, D.E.1
Yanagimachi, K.S.2
Lessard, P.A.3
Rijhwani, S.K.4
Sinskey, A.J.5
Stephanopoulos, G.6
-
73
-
-
0035989624
-
Metabolic engineering by genome shuffling
-
Stephanopoulos, G. (2002) Metabolic engineering by genome shuffling. Nat Biotechnol 20: 666-668.
-
(2002)
Nat Biotechnol
, vol.20
, pp. 666-668
-
-
Stephanopoulos, G.1
-
74
-
-
0032077442
-
The danger of metabolic pathways with turbo design
-
Teusink, B., Walsh, M.C., van Dam, K., and Westerhoff, H.V. (1998) The danger of metabolic pathways with turbo design. Trends Biochem Sci 23: 162-169.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 162-169
-
-
Teusink, B.1
Walsh, M.C.2
van Dam, K.3
Westerhoff, H.V.4
-
75
-
-
0033857139
-
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
-
Teusink, B., Passarge, J., Reijenga, C.A., Esgalhado, E., van der Weijden, C.C., Schepper, M., etal. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313-5329.
-
(2000)
Eur J Biochem
, vol.267
, pp. 5313-5329
-
-
Teusink, B.1
Passarge, J.2
Reijenga, C.A.3
Esgalhado, E.4
van der Weijden, C.C.5
Schepper, M.6
-
76
-
-
45749137679
-
Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses
-
Trinh, C.T., Unrean, P., and Srienc, F. (2008) Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol 74: 3634-3643.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 3634-3643
-
-
Trinh, C.T.1
Unrean, P.2
Srienc, F.3
-
77
-
-
58149154663
-
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
-
Trinh, C.T., Wlaschin, A., and Srienc, F. (2009) Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 81: 813-826.
-
(2009)
Appl Microbiol Biotechnol
, vol.81
, pp. 813-826
-
-
Trinh, C.T.1
Wlaschin, A.2
Srienc, F.3
-
78
-
-
77952888809
-
Toward design-based engineering of industrial microbes
-
Tyo, K.E., Kocharin, K., and Nielsen, J. (2010) Toward design-based engineering of industrial microbes. Curr Opin Microbiol 13: 255-262.
-
(2010)
Curr Opin Microbiol
, vol.13
, pp. 255-262
-
-
Tyo, K.E.1
Kocharin, K.2
Nielsen, J.3
-
79
-
-
0033928677
-
Response of Saccharomyces cerevisiae to severe osmotic stress: evidence for a novel activation mechanism of the HOG MAP kinase pathway
-
Van Wuytswinkel, O., Reiser, V., Siderius, M., Kelders, M.C., Ammerer, G., Ruis, H., and Mager, W.H. (2000) Response of Saccharomyces cerevisiae to severe osmotic stress: evidence for a novel activation mechanism of the HOG MAP kinase pathway. Mol Microbiol 37: 382-397.
-
(2000)
Mol Microbiol
, vol.37
, pp. 382-397
-
-
Van Wuytswinkel, O.1
Reiser, V.2
Siderius, M.3
Kelders, M.C.4
Ammerer, G.5
Ruis, H.6
Mager, W.H.7
-
80
-
-
10044224601
-
Metabolic control analysis under uncertainty: framework development and case studies
-
Wang, L., Birol, I., and Hatzimanikatis, V. (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.1
Birol, I.2
Hatzimanikatis, V.3
|