-
1
-
-
0346434985
-
-
4th ed., Garland Science (Taylor & Francis Group), New York
-
B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed., Garland Science (Taylor & Francis Group), New York, 2002.
-
(2002)
Molecular Biology of the Cell
-
-
Alberts, B.1
Johnson, A.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walter, P.6
-
2
-
-
0036007687
-
Metabolomics-The link between genotype and phenotype
-
O. Fiehn, Metabolomics-The link between genotype and phenotype. Plant Mol. Biol. 78, 155- 171 (2002).
-
(2002)
Plant Mol. Biol.
, vol.78
, pp. 155-171
-
-
Fiehn, O.1
-
3
-
-
1942470073
-
Metabolomics by numbers: Acquiring and understanding global metabolite data
-
R. Goodacre, S. Vaidyanathan, W. B. Dunn, G. G. Harrigan, and D. B. Kell, Metabolomics by numbers: Acquiring and understanding global metabolite data. Trends in Biotechnology. 22, 245-252 (2004).
-
(2004)
Trends in Biotechnology
, vol.22
, pp. 245-252
-
-
Goodacre, R.1
Vaidyanathan, S.2
Dunn, W.B.3
Harrigan, G.G.4
Kell, D.B.5
-
4
-
-
0345270397
-
Plant metabolomics: Large-scale phytochemistry in the functional genomics era
-
L. W. Sumner, P. Mendes, and R. Dixon, Plant metabolomics: Large-scale phytochemistry in the functional genomics era. Phytochemistry 62, 817-836 (2003).
-
(2003)
Phytochemistry
, vol.62
, pp. 817-836
-
-
Sumner, L.W.1
Mendes, P.2
Dixon, R.3
-
5
-
-
2942676743
-
Metabolomics and systems biology: Making sense of the soup
-
D. B. Kell, Metabolomics and systems biology: Making sense of the soup. Curr. Opin. Microbiol. 7(3), 296-307 (2004).
-
(2004)
Curr. Opin. Microbiol.
, vol.7
, Issue.3
, pp. 296-307
-
-
Kell, D.B.1
-
6
-
-
4444277707
-
Metabolite profiling: From diagnostics to systems biology
-
A. R. Fernie, R. N. Trethewey, A. J. Krotzky, and L. Willmitzer, Metabolite profiling: From diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 5, 1-7 (2004).
-
(2004)
Nat. Rev. Mol. Cell Biol.
, vol.5
, pp. 1-7
-
-
Fernie, A.R.1
Trethewey, R.N.2
Krotzky, A.J.3
Willmitzer, L.4
-
7
-
-
0004243729
-
-
H. Kitano, ed. MIT Press Cambridge
-
H. Kitano, ed., Foundations of Systems Biology, MIT Press, Cambridge, 2001.
-
(2001)
Foundations of Systems Biology
-
-
-
8
-
-
0037079054
-
Computational systems biology
-
H. Kitano, Computational systems biology. Nature 420, 206-210 (2002).
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
9
-
-
5044227742
-
The evolution of molecular biology into systems biology
-
H. V. Westerhoff and B. Ø. Palsson, The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249-1252 (2002).
-
(2002)
Nat. Biotechnol
, vol.22
, pp. 1249-1252
-
-
Westerhoff, H.V.1
Palsson, B.Ø.2
-
10
-
-
0037716676
-
Building with a scaffold: Emerging strategies for high- to lowlevel cellular modeling
-
T. Ideker and D. Lauffenburger, Building with a scaffold: Emerging strategies for high- to lowlevel cellular modeling. Trends Biotechnol. 21(6), 255-262 (2003).
-
(2003)
Trends Biotechnol
, vol.21
, Issue.6
, pp. 255-262
-
-
Ideker, T.1
Lauffenburger, D.2
-
11
-
-
4344670936
-
Bow ties, metabolism and disease
-
M. Csete and J. Doyle, Bow ties, metabolism and disease. Trends Biotechnol. 22(9), 446-450 (2004).
-
(2004)
Trends Biotechnol
, vol.22
, Issue.9
, pp. 446-450
-
-
Csete, M.1
Doyle, J.2
-
13
-
-
0002275384
-
The dynamics of feedback control circuits in biochemical pathways
-
J. J. Tyson and H. G. Othmer, The dynamics of feedback control circuits in biochemical pathways. Progr. Theor. Biol. 5, 1-62 (1978).
-
(1978)
Progr. Theor. Biol.
, vol.5
, pp. 1-62
-
-
Tyson, J.J.1
Othmer, H.G.2
-
14
-
-
0023497923
-
A theoretical approach to the evolution and structural design of enzymatic networks; linear enzymatic chains, branched pathways and glycolysis of erythrocytes
-
R. Heinrich, H.-G. Holzhütter, and S. Schuster, A theoretical approach to the evolution and structural design of enzymatic networks; linear enzymatic chains, branched pathways and glycolysis of erythrocytes. Bull. Math. Biol. 49(5), 539-595 (1987).
-
(1987)
Bull. Math. Biol.
, vol.49
, Issue.5
, pp. 539-595
-
-
Heinrich, R.1
Holzhütter, H.-G.2
Schuster, S.3
-
15
-
-
77954184815
-
Understanding the Control of Metabolism, Portland Press
-
D. Fell, Understanding the Control of Metabolism, Portland Press, London (1997).
-
(1997)
London
-
-
Fell, D.1
-
16
-
-
0031824204
-
The modeling of metabolic systems. structure, control and optimality
-
R. Heinrich and S. Schuster, The modeling of metabolic systems. structure, control and optimality. BioSystems 47, 61-77 (1998).
-
(1998)
BioSystems
, vol.47
, pp. 61-77
-
-
Heinrich, R.1
Schuster, S.2
-
17
-
-
77954208467
-
Self-Organization in Nonequilibrium System, John Wiley & Sons
-
G. Nicolis and I. Prigogine, Self-Organization in Nonequilibrium System, John Wiley & Sons, New York, 1977.
-
(1977)
New York
-
-
Nicolis, G.1
Prigogine, I.2
-
19
-
-
0037316239
-
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
-
H. Ma and A.-P. Zeng, Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2), 270-277 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 270-277
-
-
Ma, H.1
Zeng, A.-P.2
-
20
-
-
34547658908
-
Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source
-
B. H. Junker, J. Lonien, L. E. Heady, A. Rogers, and J. Schwender, Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source. Phytochemistry 68, 2232-2242 (2007).
-
(2007)
Phytochemistry
, vol.68
, pp. 2232-2242
-
-
Junker, B.H.1
Lonien, J.2
Heady, L.E.3
Rogers, A.4
Schwender, J.5
-
21
-
-
33144474263
-
Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae
-
S Rossell, CC van der Weijden, A Lindenbergh, A van Tuijl, C Francke, BM Bakker, and HV Westerhoff, Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103(7), 2166-2171 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, Issue.7
, pp. 2166-2171
-
-
Rossell, S.1
van der Weijden, C.C.2
Lindenbergh, A.3
van Tuijl, A.4
Francke, C.5
Bakker, B.M.6
Westerhoff, H.V.7
-
22
-
-
32944461132
-
Regulation of metabolic networks: Understanding metabolic complexity in the systems biology era
-
L. J. Sweetlove and A. R. Fernie, Regulation of metabolic networks: Understanding metabolic complexity in the systems biology era. New Phytol. 168, 9-24 (2005).
-
(2005)
New Phytol
, vol.168
, pp. 9-24
-
-
Sweetlove, L.J.1
Fernie, A.R.2
-
23
-
-
34547684426
-
Computational approaches to the topology, stability and dynamics of metabolic networks
-
R. Steuer, Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68(16-18), 2139-2151 (2007).
-
(2007)
Phytochemistry
, vol.68
, Issue.16-18
, pp. 2139-2151
-
-
Steuer, R.1
-
24
-
-
33846061120
-
13C-based flux analysis
-
doi:10. 1038/msb4100109
-
13C-based flux analysis. Mol. Syst. Biol. 2, 62 (2006); doi:10.1038/msb4100109.
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 62
-
-
Sauer, U.1
-
25
-
-
0035160371
-
A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations
-
L. M. Raamsdonk, B. Teusink, D. Broadhurst, N. Zhang, A. Hayes, M. C.Walsh, J. A. Berden, K. M. Brindle, D. B. Kell, J. J. Rowland, H. V. Westerhoff, K. van Dam, and S. G. Oliver, A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19, 45-50 (2001).
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 45-50
-
-
Raamsdonk, L.M.1
Teusink, B.2
Broadhurst, D.3
Zhang, N.4
Hayes, A.5
Walsh, M.C.6
Berden, J.A.7
Brindle, K.M.8
Kell, D.B.9
Rowland, J.J.10
Westerhoff, H.V.11
van Dam, K.12
Oliver, S.G.13
-
26
-
-
0035252567
-
Silent genes given voice
-
A. Cornish-Bowden and M. L. Cárdenas, Silent genes given voice. Nature 409, 571-572 (2001).
-
(2001)
Nature
, vol.409
, pp. 571-572
-
-
Cornish-Bowden, A.1
Cárdenas, M.L.2
-
27
-
-
0033156024
-
Use and limitations of modular metabolic control analysis in medicine and biotechnology
-
S. Schuster, Use and limitations of modular metabolic control analysis in medicine and biotechnology. Metab. Eng. 1, 232-242 (1999).
-
(1999)
Metab. Eng.
, vol.1
, pp. 232-242
-
-
Schuster, S.1
-
28
-
-
28844488320
-
The energy-less red blood cell is lost: Erythrocyte enzyme abnormalities of glycolysis
-
R. vanWijk and W.W. van Solinge, The energy-less red blood cell is lost: Erythrocyte enzyme abnormalities of glycolysis. Blood 106(13), 4034-4042 (2005).
-
(2005)
Blood
, vol.106
, Issue.13
, pp. 4034-4042
-
-
vanWijk, R.1
van Solinge, W.W.2
-
29
-
-
0036851376
-
In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism
-
N. Jamshidi, S. J.Wiback, and B. Ø. Palsson, In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism. Gen. Res. 12 (11), 1687-1692 (2002).
-
(2002)
Gen. Res.
, vol.12
, Issue.11
, pp. 1687-1692
-
-
Jamshidi, N.1
Wiback, S.J.2
Palsson, B.Ø.3
-
30
-
-
34548860112
-
The Edinburgh human metabolic network reconstruction and its functional analysis
-
H. Ma, A. Sorokin, A. Mazein, A. Selkov, E. Selkov, O. Demin, and I. Goryanin, The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol. 3, 135 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 135
-
-
Ma, H.1
Sorokin, A.2
Mazein, A.3
Selkov, A.4
Selkov, E.5
Demin, O.6
Goryanin, I.7
-
31
-
-
10244255126
-
Optimization of regulatory architectures in metabolic reaction networks
-
V. Hatzimanikatis, C. A. Floudas, and J. E. Bailey, Optimization of regulatory architectures in metabolic reaction networks. Biotechnol. Bioeng. 52(4), 485-500 (1996).
-
(1996)
Biotechnol. Bioeng.
, vol.52
, Issue.4
, pp. 485-500
-
-
Hatzimanikatis, V.1
Floudas, C.A.2
Bailey, J.E.3
-
32
-
-
0032485838
-
Application of mathematical tools for metabolic design of microbial ethanol production
-
V. Hatzimanikatis, M. Emmerling, U. Sauer, and J. E. Bailey, Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol. Bioeng. 58(2-3), 154-161 (1998).
-
(1998)
Biotechnol. Bioeng.
, vol.58
, Issue.2-3
, pp. 154-161
-
-
Hatzimanikatis, V.1
Emmerling, M.2
Sauer, U.3
Bailey, J.E.4
-
33
-
-
0031933027
-
Mathematical modeling and analysis in biochemical engineering: Past accomplishments and future opportunities
-
J. E. Bailey, Mathematical modeling and analysis in biochemical engineering: Past accomplishments and future opportunities. Biotech. Prog. 14, 8-20 (1998).
-
(1998)
Biotech. Prog.
, vol.14
, pp. 8-20
-
-
Bailey, J.E.1
-
34
-
-
0004218135
-
-
Academic Press, Elsevier Science New York
-
G. N. Stephanopoulos, A. A. Aristidou, and J. Nielsen, Metabolic Engineering: Principles and Methodologies, Academic Press, Elsevier Science, New York, 1998.
-
(1998)
Metabolic Engineering: Principles and Methodologies
-
-
Stephanopoulos, G.N.1
Aristidou, A.A.2
Nielsen, J.3
-
35
-
-
5044237367
-
Exploiting biological complexity for strain improvement through systems biology
-
G. N. Stephanopoulos, H. Alper, and J. Moxley, Exploiting biological complexity for strain improvement through systems biology. Nat. Biotechnol. 22, 1261-1267 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1261-1267
-
-
Stephanopoulos, G.N.1
Alper, H.2
Moxley, J.3
-
36
-
-
0014894547
-
Computer applications to biochemical kinetics
-
D. Garfinkel, L. Garfinkel, M. Pring, S. B. Green, and B. Chance, Computer applications to biochemical kinetics. Annu. Rev. Biochem. 39, 473-498 (1970).
-
(1970)
Annu. Rev. Biochem.
, vol.39
, pp. 473-498
-
-
Garfinkel, D.1
Garfinkel, L.2
Pring, M.3
Green, S.B.4
Chance, B.5
-
37
-
-
0036336088
-
Mathematical modeling of plant metabolic pathways
-
J. A. Morgan and D. Rhodes, Mathematical modeling of plant metabolic pathways. Metab. Eng. 4, 80-89 (2002).
-
(2002)
Metab. Eng.
, vol.4
, pp. 80-89
-
-
Morgan, J.A.1
Rhodes, D.2
-
39
-
-
34547683486
-
Experimental mathematical approaches to modeling plant metabolic networks
-
R. Rios-Estepa and B. M. Lange, Experimental and mathematical approaches to modeling plant metabolic networks. Phytochemistry 68(16-18), 2351-2374 (2007).
-
(2007)
Phytochemistry
, vol.68
, Issue.16-18
, pp. 2351-2374
-
-
Rios-Estepa, R.1
Lange, B.M.2
-
40
-
-
0033031386
-
E-Cell: Software environment for whole-cell simulation
-
K. Hashimoto M. Tomita, K. Takahashi, T. S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, and C. A. Hutchison III, E-Cell: Software environment for whole-cell simulation. Bioinformatics 15(1), 72-84 (1999).
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 72-84
-
-
Hashimoto, K.1
Tomita, M.2
Takahashi, K.3
Shimizu, T.S.4
Matsuzaki, Y.5
Miyoshi, F.6
Saito, K.7
Tanida, S.8
Yugi, K.9
Venter, J.C.10
Hutchison C.A. III11
-
41
-
-
0142219725
-
Quantitative cell biology with the virtual cell
-
B. M. Slepchenko, J. C. Schaff, I. Macara, and L. M. Loew, Quantitative cell biology with the virtual cell. TRENDS Cell Biol. 13(11), 570-577 (2003).
-
(2003)
TRENDS Cell Biol
, vol.13
, Issue.11
, pp. 570-577
-
-
Slepchenko, B.M.1
Schaff, J.C.2
Macara, I.3
Loew, L.M.4
-
42
-
-
4544227574
-
Toward large-scale modeling of the microbial cell for computer simulation
-
N. Ishii, M. Robert, Y. Nakayama, A. Kanai, and M. Tomita, Toward large-scale modeling of the microbial cell for computer simulation. J. Biotechnol. 113, 281-294 (2004).
-
(2004)
J. Biotechnol.
, vol.113
, pp. 281-294
-
-
Ishii, N.1
Robert, M.2
Nakayama, Y.3
Kanai, A.4
Tomita, M.5
-
43
-
-
4444332930
-
Applications note: A general computational model of mitochondrial metabolism in a whole organelle scale
-
K Yugi and M. Tomita, Applications note: A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 20(11), 1795-1796 (2004).
-
(2004)
Bioinformatics
, vol.20
, Issue.11
, pp. 1795-1796
-
-
Yugi, K.1
Tomita, M.2
-
44
-
-
42949164125
-
Formulating genome-scale kinetic models in the post-genome era
-
N. Jamshidi and B. Ø. Palsson, Formulating genome-scale kinetic models in the post-genome era. Mol. Syst. Biol. 4, 171 (2008).
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 171
-
-
Jamshidi, N.1
Palsson, B.Ø.2
-
45
-
-
0034609791
-
The large-scale organization of metabolic networks
-
H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási, The large-scale organization of metabolic networks. Nature 407, 651-654 (2000).
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabási, A.-L.5
-
46
-
-
0033764169
-
The small world of metabolism
-
D. A. Fell and A. Wagner, The small world of metabolism. Nat. Biotechnol. 18, 1121-1122 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 1121-1122
-
-
Fell, D.A.1
Wagner, A.2
-
47
-
-
0036013593
-
Statistical mechanics of complex networks
-
R. Albert and A.-L. Barabási, Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47-97 (2002).
-
(2002)
Rev. Mod. Phys.
, vol.74
, pp. 47-97
-
-
Albert, R.1
Barabási, A.-L.2
-
48
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
A.-L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
49
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
J. Förster, I. Famili, P. Fu, B. O. Palsson, and J. Nielsen, Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Gen. Res. 13, 244-253 (2003).
-
(2003)
Gen. Res.
, vol.13
, pp. 244-253
-
-
Förster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
51
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
N. C. Duarte, S. A. Becker, N. Jamshidi, I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, and B. Ø. Palsson, Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 104(6), 1777-1782 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.6
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
Vo, T.D.6
Srivas, R.7
Palsson, B.Ø.8
-
52
-
-
0035823264
-
The small world inside large metabolic networks
-
A.Wagner and D. A. Fell, The small world inside large metabolic networks. Proc. R. Soc. Lond. B. 268, 1803-1810 (2001).
-
(2001)
Proc. R. Soc. Lond. B.
, vol.268
, pp. 1803-1810
-
-
Wagner, A.1
Fell, D.A.2
-
54
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A.-L. Barabási, Hierarchical organization of modularity in metabolic networks. Science 297, 1551-1555 (2002).
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabási, A.-L.5
-
55
-
-
0038281450
-
Hierarchical analysis of dependency in metabolic networks
-
J. Gagneur, D. B. Jackson, and G. Casari, Hierarchical analysis of dependency in metabolic networks. Bioinformatics 19(8), 1027-1034 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1027-1034
-
-
Gagneur, J.1
Jackson, D.B.2
Casari, G.3
-
56
-
-
0034721164
-
Error and attack tolerance of complex networks
-
R. Albert, H. Jeong, and A.-L. Barabási, Error and attack tolerance of complex networks. Nature 406, 378-382 (2000).
-
(2000)
Nature
, vol.406
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabási, A.-L.3
-
57
-
-
0346463223
-
Essentially and damage in metabolic networks
-
N. Lemke, F. Herédia, C. K. Barcellos, A.N. dos Reis, and J. C. M. Mombach, Essentially and damage in metabolic networks. Bioinformatics 20(1), 115-119 (2004).
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 115-119
-
-
Lemke, N.1
Herédia, F.2
Barcellos, C.K.3
dos Reis, A.N.4
Mombach, J.C.M.5
-
58
-
-
33748475897
-
On the analysis and interpretation of correlations in metabolomic data
-
R. Steuer, On the analysis and interpretation of correlations in metabolomic data. Brief. Bioinform. 7(2), 151-158 (2006).
-
(2006)
Brief. Bioinform.
, vol.7
, Issue.2
, pp. 151-158
-
-
Steuer, R.1
-
59
-
-
0002013127
-
Stability of complex reaction networks
-
S. A. Rice and I. Prigogine, eds., John Wiley & Sons, New York
-
B. L. Clarke, Stability of complex reaction networks, in Advances in Chemical Physics, S. A. Rice and I. Prigogine, eds., John Wiley & Sons, New York, 1980, pp. 1-215.
-
(1980)
Advances in Chemical Physics
, pp. 1-215
-
-
Clarke, B.L.1
-
60
-
-
0023714694
-
Stoichiometric network analysis
-
B. L. Clarke, Stoichiometric network analysis. Cell Biophys. 12, 237-253 (1988).
-
(1988)
Cell Biophys
, vol.12
, pp. 237-253
-
-
Clarke, B.L.1
-
61
-
-
0028108519
-
Metabolic flux balancing: Basic concepts, scientific and practical use
-
A. Varma and B. Ø. Palsson, Metabolic flux balancing: Basic concepts, scientific and practical use. Bio/Technology (now Nat. Biotechnol.) 12, 994-998 (1994).
-
(1994)
Bio/Technology (now Nat. Biotechnol. )
, vol.12
, pp. 994-998
-
-
Varma, A.1
Palsson, B.Ø.2
-
62
-
-
0023709196
-
Metabolic control theory: A structural approach
-
C. Reder, Metabolic control theory: A structural approach. J. Theoret. Biol. 135, 175-201 (1988).
-
(1988)
J. Theoret. Biol.
, vol.135
, pp. 175-201
-
-
Reder, C.1
-
63
-
-
0034625143
-
The Escherichia coli mg1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
J. S. Edwards and B. Ø. Palsson, The Escherichia coli mg1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97(10), 5528-5533 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, Issue.10
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.Ø.2
-
64
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
J. Stelling, S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles, Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190-193 (2002).
-
(2002)
Nature
, vol.420
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
65
-
-
0036188159
-
Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
-
S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch, and T. Dandekar, Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18(2), 351-361 (2002).
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 351-361
-
-
Schuster, S.1
Pfeiffer, T.2
Moldenhauer, F.3
Koch, I.4
Dandekar, T.5
-
66
-
-
0036350955
-
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy
-
J. A. Papin, N. D. Price, J. S. Edwards, and B. O. Palsson, The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215, 67-82 (2002).
-
(2002)
J. Theor. Biol.
, vol.215
, pp. 67-82
-
-
Papin, J.A.1
Price, N.D.2
Edwards, J.S.3
Palsson, B.O.4
-
67
-
-
0037727678
-
Metabolic pathways in the post-genome era
-
J. A. Papin, N. D. Price, S. J.Wiback, D. A. Fell, and B. Ø. Palsson, Metabolic pathways in the post-genome era. Trends Biochem. Sci. 28, 250-258 (2003).
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 250-258
-
-
Papin, J.A.1
Price, N.D.2
Wiback, S.J.3
Fell, D.A.4
Palsson, B.Ø.5
-
68
-
-
0142186707
-
Network-based analysis of metabolic regulation in the human red blood cell
-
N. D. Price, J. L. Reed, J. A Papin, S. J.Wiback, and B. O. Palsson, Network-based analysis of metabolic regulation in the human red blood cell. J. Theor. Biol. 225, 185-194 (2003).
-
(2003)
J. Theor. Biol.
, vol.225
, pp. 185-194
-
-
Price, N.D.1
Reed, J.L.2
Papin, J.A.3
Wiback, S.J.4
Palsson, B.O.5
-
69
-
-
0344824417
-
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
-
I. Famili, J. Förster, J. Nielsen, and B. Ø. Palsson, Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 100(23), 13134-13139 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, Issue.23
, pp. 13134-13139
-
-
Famili, I.1
Förster, J.2
Nielsen, J.3
Palsson, B.Ø.4
-
70
-
-
0033136116
-
Towards metabolic phenomics: Analysis of genomic data using flux balances
-
C. H. Schilling, J. S. Edwards, and B. Ø. Palsson, Towards metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol. Prog. 15, 288-295 (1999).
-
(1999)
Biotechnol. Prog.
, vol.15
, pp. 288-295
-
-
Schilling, C.H.1
Edwards, J.S.2
Palsson, B.Ø.3
-
71
-
-
0033764285
-
The challenges of in silico biology
-
B. Ø. Palsson, The challenges of in silico biology. Nat. Biotechnol. 18, 1147-1150 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 1147-1150
-
-
Palsson, B.Ø.1
-
72
-
-
0035989610
-
In silico biology through "omics"
-
B. Ø. Palsson, In silico biology through "omics". Nat. Biotechnol. 20, 649-650 (2002).
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 649-650
-
-
Palsson, B.Ø.1
-
73
-
-
1542288938
-
Global organization of metabolic fluxes in the bacterium Escherichia coli
-
E. Almaas, B. Kovacs, T. Vicsek, Z. N. Oltvai, and A.-L. Barabási, Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427, 839-843 (2004).
-
(2004)
Nature
, vol.427
, pp. 839-843
-
-
Almaas, E.1
Kovacs, B.2
Vicsek, T.3
Oltvai, Z.N.4
Barabási, A.-L.5
-
74
-
-
3242795003
-
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
-
H.-G. Holzhütter, The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 271(14), 2905-2922 (2004).
-
(2004)
Eur. J. Biochem.
, vol.271
, Issue.14
, pp. 2905-2922
-
-
Holzhütter, H.-G.1
-
75
-
-
0034995375
-
Complex biology with no parameters
-
J. E. Bailey, Complex biology with no parameters. Nat. Biotechnol. 19, 503-504 (2001).
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 503-504
-
-
Bailey, J.E.1
-
77
-
-
0009377452
-
On chemical kinetics of a certain class
-
M. Feinberg, On chemical kinetics of a certain class. Arch. Rational Mech. Anal. 46(1), 1-41 (1972).
-
(1972)
Arch. Rational Mech. Anal.
, vol.46
, Issue.1
, pp. 1-41
-
-
Feinberg, M.1
-
78
-
-
0016038059
-
Dynamics of open chemical systems and the algebraic structure of the underlying reaction network
-
M. Feinberg and F. J. M. Horn, Dynamics of open chemical systems and the algebraic structure of the underlying reaction network. Chem. Eng. Sci. 29(3), 775-787 (1974).
-
(1974)
Chem. Eng. Sci.
, vol.29
, Issue.3
, pp. 775-787
-
-
Feinberg, M.1
Horn, F.J.M.2
-
79
-
-
0001364051
-
The existence and uniqueness of steady states for a class of chemical reaction networks
-
M. Feinberg, The existence and uniqueness of steady states for a class of chemical reaction networks. Arch. Rational Mech. Anal. 132(4), 311-370 (1995).
-
(1995)
Arch. Rational Mech. Anal.
, vol.132
, Issue.4
, pp. 311-370
-
-
Feinberg, M.1
-
80
-
-
33744744785
-
Understanding bistability in complex enzyme-driven reaction networks
-
G. Craciun, Y. Tang, and M. Feinberg, Understanding bistability in complex enzyme-driven reaction networks. Proc. Natl. Acad. Sci. USA 103(23), 8697-8702 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, Issue.23
, pp. 8697-8702
-
-
Craciun, G.1
Tang, Y.2
Feinberg, M.3
-
81
-
-
36749119634
-
Stability analysis of a model reaction network using graph theory
-
B. L. Clarke, Stability analysis of a model reaction network using graph theory. J. Chem. Phys. 60(4), 1493-1501 (1974).
-
(1974)
J. Chem. Phys.
, vol.60
, Issue.4
, pp. 1493-1501
-
-
Clarke, B.L.1
-
82
-
-
0039673412
-
Stability of topologically similar chemical networks
-
B. L. Clarke, Stability of topologically similar chemical networks. J. Chem. Phys. 62(9), 3726- 3738 (1975).
-
(1975)
J. Chem. Phys.
, vol.62
, Issue.9
, pp. 3726-3738
-
-
Clarke, B.L.1
-
83
-
-
0011748894
-
Bistability in chemical reaction networks: Theory and application to the peroxidase reaction
-
B. D. Agunda and B. L. Clarke, Bistability in chemical reaction networks: Theory and application to the peroxidase reaction. J. Chem. Phys. 87(6), 3461-3469 (1987).
-
(1987)
J. Chem. Phys.
, vol.87
, Issue.6
, pp. 3461-3469
-
-
Agunda, B.D.1
Clarke, B.L.2
-
84
-
-
33747061013
-
Structural kinetic modeling of metabolic networks
-
R. Steuer, T. Gross, J. Selbig, and B. Blasius, Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. USA 103(32), 11868-11873 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, Issue.32
, pp. 11868-11873
-
-
Steuer, R.1
Gross, T.2
Selbig, J.3
Blasius, B.4
-
85
-
-
0033662290
-
Tendency modeling: A new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae
-
D. Visser, R. van der Heijden, K. Mauch, M. Reuss, and S. Heijnen, Tendency modeling: A new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae. Metab. Eng. 2(3), 252-275 (2000).
-
(2000)
Metab. Eng.
, vol.2
, Issue.3
, pp. 252-275
-
-
Visser, D.1
van der Heijden, R.2
Mauch, K.3
Reuss, M.4
Heijnen, S.5
-
86
-
-
6044260198
-
Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics
-
D. Visser, J. W. Schmid, K.Mauch, M. Reuss, and J. J. Heijnen, Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. Metab. Eng. 6(4), 378-390 (2004).
-
(2004)
Metab. Eng.
, vol.6
, Issue.4
, pp. 378-390
-
-
Visser, D.1
Schmid, J.W.2
Mauch, K.3
Reuss, M.4
Heijnen, J.J.5
-
87
-
-
18244406832
-
Inferring dynamic properties of biochemical reaction networks from structural knowledge
-
E. Klipp, W. Liebermeister, and C. Wierling, Inferring dynamic properties of biochemical reaction networks from structural knowledge. Gen. Inform. Ser. 15(1), 125-137 (2004).
-
(2004)
Gen. Inform. Ser.
, vol.15
, Issue.1
, pp. 125-137
-
-
Klipp, E.1
Liebermeister, W.2
Wierling, C.3
-
88
-
-
27244440301
-
Biochemical networks with uncertain parameters
-
W. Liebermeister and E. Klipp, Biochemical networks with uncertain parameters. IEE Proc. Syst. Biol. 152(3), 97-107 (2005).
-
(2005)
IEE Proc. Syst. Biol.
, vol.152
, Issue.3
, pp. 97-107
-
-
Liebermeister, W.1
Klipp, E.2
-
89
-
-
35448974147
-
Something from nothing- bridging the gap between constraint-based and kinetic modeling
-
K. Smallbone, E. Simeonidis, D. S. Broomhead, and D. B Kell, Something from nothing- bridging the gap between constraint-based and kinetic modeling. FEBS J. 274(21), 5576-5585 (2007).
-
(2007)
FEBS J
, vol.274
, Issue.21
, pp. 5576-5585
-
-
Smallbone, K.1
Simeonidis, E.2
Broomhead, D.S.3
Kell, D.B.4
-
91
-
-
33846899178
-
In silico biology: from simulation to understanding
-
M. Kollmann and V. Sourjik, In silico biology: from simulation to understanding. Curr. Biol. 17, R132-134 (2007).
-
(2007)
Curr. Biol.
, vol.17
-
-
Kollmann, M.1
Sourjik, V.2
-
92
-
-
0035478586
-
The virtual cell: A Software environment for computational cell biology
-
L. M. Loew and J. C. Schaff, The virtual cell: A Software environment for computational cell biology. Trends Biotechnol. 19(10), 401-406 (2001).
-
(2001)
Trends Biotechnol
, vol.19
, Issue.10
, pp. 401-406
-
-
Loew, L.M.1
Schaff, J.C.2
-
93
-
-
33746927955
-
News views: International alliances for quantitative modeling in systems biology
-
H. Kitano, News and views: International alliances for quantitative modeling in systems biology. Mol. Syst. Biol. 11, E1-E2 (2005).
-
(2005)
Mol. Syst. Biol.
, vol.11
-
-
Kitano, H.1
-
94
-
-
0014258550
-
Self-oscillations in glycolysis
-
E. E. Selkov, Self-oscillations in glycolysis. Eur. J. Biochem. 4, 79-86 (1968).
-
(1968)
Eur. J. Biochem.
, vol.4
, pp. 79-86
-
-
Selkov, E.E.1
-
95
-
-
0023049002
-
Oscillatory response of photosynthesis in leaves to environmental perturbations: A mathematical model
-
C. Giersch, Oscillatory response of photosynthesis in leaves to environmental perturbations: A mathematical model. Arch. Biochem. Biophys. 245(1), 263-270 (1986).
-
(1986)
Arch. Biochem. Biophys.
, vol.245
, Issue.1
, pp. 263-270
-
-
Giersch, C.1
-
96
-
-
77954194051
-
The Regulation of Cellular Systems, Chapman & Hall
-
R. Heinrich and S. Schuster, The Regulation of Cellular Systems, Chapman & Hall, New York (1996).
-
(1996)
New York
-
-
Heinrich, R.1
Schuster, S.2
-
97
-
-
17444373396
-
Validation of metabolic models: Concepts, tools, and problems
-
Era, B. N. Kholodenko and H. V.Westerhoff, eds., Horizon Bioscience
-
W. Wiechert and R. Takors, Validation of metabolic models: Concepts, tools, and problems, in Metabolic Engineering in the Post Genomic Era, B. N. Kholodenko and H. V.Westerhoff, eds., Horizon Bioscience, 2004, pp. 277-320.
-
(2004)
Metabolic Engineering in the Post Genomic
, pp. 277-320
-
-
Wiechert, W.1
Takors, R.2
-
98
-
-
0037376655
-
Sniffers buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
J. J. Tyson, K. C. Chen, and B. Novak, Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231 (2003).
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
99
-
-
33644807093
-
Feedback dynamics and cell function: Why systems biology is called systems biology
-
O. Wolkenhauer and M. Mesarovic, Feedback dynamics and cell function: Why systems biology is called systems biology. Mol Biosyst. 1(1), 14-16 (2005).
-
(2005)
Mol Biosyst
, vol.1
, Issue.1
, pp. 14-16
-
-
Wolkenhauer, O.1
Mesarovic, M.2
-
100
-
-
0001277376
-
The kinetics of the enzyme-substrate compound of peroxidase
-
B. Chance, The kinetics of the enzyme-substrate compound of peroxidase. J. Biol. Chem. 151 (2), 553-577 (1943).
-
(1943)
J. Biol. Chem.
, vol.151
, Issue.2
, pp. 553-577
-
-
Chance, B.1
-
101
-
-
0035846723
-
Full-scale model of glycolysis in Saccharomyces cerevisiae
-
F. Hynne, S. Danø, and P. G. Sørensen, Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. 94, 121-163 (2001).
-
(2001)
Biophys. Chem.
, vol.94
, pp. 121-163
-
-
Hynne, F.1
Danø, S.2
Sørensen, P.G.3
-
102
-
-
0036789480
-
Monte Carlo simulations of enzyme reactions in two dimensions: Fractal kinetics and spatial segregation
-
H. Berry, Monte Carlo simulations of enzyme reactions in two dimensions: Fractal kinetics and spatial segregation. Biophys. J. 83(4), 1891-1901 (2002).
-
(2002)
Biophys. J.
, vol.83
, Issue.4
, pp. 1891-1901
-
-
Berry, H.1
-
103
-
-
34547177356
-
Stochastic fluctuations in metabolic pathways
-
E. Levine and T. Hwa, Stochastic fluctuations in metabolic pathways. Proc. Natl. Acad. Sci. USA 104(22), 9224-9229 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.22
, pp. 9224-9229
-
-
Levine, E.1
Hwa, T.2
-
104
-
-
0003381877
-
Metabolic control mechanisms: A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells
-
B. Chance, D. Garfinkel, J. Higgins, and B. Hess, Metabolic control mechanisms: A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells. J. Biol. Chem. 235(8), 2426-2439 (1960).
-
(1960)
J. Biol. Chem.
, vol.235
, Issue.8
, pp. 2426-2439
-
-
Chance, B.1
Garfinkel, D.2
Higgins, J.3
Hess, B.4
-
105
-
-
0001736256
-
Metabolic control mechanisms VII. A detailed computer model of the glycolytic pathway in ascites cells
-
D. Garfinkel and B. Hess, Metabolic control mechanisms. VII. A detailed computer model of the glycolytic pathway in ascites cells. J. Biol. Chem. 239, 971-983 (1964).
-
(1964)
J. Biol. Chem.
, vol.239
, pp. 971-983
-
-
Garfinkel, D.1
Hess, B.2
-
106
-
-
0014291683
-
A kinetic model of metabolism essential to differentiation in Dictyostelium discoideum
-
B. Wright,W. Simon, and T.Walsh, A kinetic model of metabolism essential to differentiation in Dictyostelium discoideum. Proc. Natl. Acad. Sci. 60, 644-651 (1968).
-
(1968)
Proc. Natl. Acad. Sci.
, vol.60
, pp. 644-651
-
-
Wright, B.1
Simon, W.2
Walsh, T.3
-
107
-
-
0015071185
-
A simulation study of brain compartments: Metabolism of glutamate and related substances in mouse brain
-
C. J. van den Berg and D. Garfinkel, A simulation study of brain compartments: Metabolism of glutamate and related substances in mouse brain. Biochem. J. 123, 211-218 (1971).
-
(1971)
Biochem. J.
, vol.123
, pp. 211-218
-
-
van den Berg, C.J.1
Garfinkel, D.2
-
108
-
-
0017306757
-
The regulatory principles of glycolysis in erythrocytes in vivo and in vitro. a minimal comprehensive model describing steady states, quasi-steady states and time-dependent processes
-
T. A. Rapoport, R. Heinrich, and S. M. Rapoport, The regulatory principles of glycolysis in erythrocytes in vivo and in vitro. a minimal comprehensive model describing steady states, quasi-steady states and time-dependent processes. Biochem J. (1976).
-
(1976)
Biochem J
-
-
Rapoport, T.A.1
Heinrich, R.2
Rapoport, S.M.3
-
110
-
-
0013393433
-
A mathematical model of leaf carbon metabolism
-
B. D. Hahn, A mathematical model of leaf carbon metabolism. Ann. Botany 54, 325-339 (1984).
-
(1984)
Ann. Botany
, vol.54
, pp. 325-339
-
-
Hahn, B.D.1
-
111
-
-
0021874741
-
Mathematical modeling of metabolic pathways affected by an enzyme deficiency A mathematical model of glycolysis in normal and pyruvate-kinase-deficient red blood cells
-
H. G. Holzhütter, G. Jacobasch, and A. Bisdorff, Mathematical modeling of metabolic pathways affected by an enzyme deficiency. A mathematical model of glycolysis in normal and pyruvate-kinase-deficient red blood cells. Eur. J. Biochem. 149(1), 101-111 (1985).
-
(1985)
Eur. J. Biochem.
, vol.149
, Issue.1
, pp. 101-111
-
-
Holzhütter, H.G.1
Jacobasch, G.2
Bisdorff, A.3
-
112
-
-
17844394123
-
A mathematical model of the Calvin cycle: Analysis of the steady state
-
B. D. Hahn, A mathematical model of the Calvin cycle: Analysis of the steady state. Ann. Botany 57, 639-653 (1986).
-
(1986)
Ann. Botany
, vol.57
, pp. 639-653
-
-
Hahn, B.D.1
-
113
-
-
0024288428
-
A mathematical model of the Calvin photosynthesis cycle
-
G. Petterson and U. Ryde-Petterson, A mathematical model of the Calvin photosynthesis cycle. Eur. J. Biochem. 175, 661-672 (1988).
-
(1988)
Eur. J. Biochem.
, vol.175
, pp. 661-672
-
-
Petterson, G.1
Ryde-Petterson, U.2
-
114
-
-
0024842144
-
Metabolic dynamics in the human red cell Part I-A comprehensive kinetic model
-
A. Joshi and B. O. Palsson, Metabolic dynamics in the human red cell. Part I-A comprehensive kinetic model. J. Theor. Biol. 141(4), 515-528 (1989).
-
(1989)
J. Theor. Biol.
, vol.141
, Issue.4
, pp. 515-528
-
-
Joshi, A.1
Palsson, B.O.2
-
115
-
-
0025400371
-
Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae
-
J. L. Galazzo and J. E. Bailey, Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae. Enzyme Microb. Technol. 12(3), 162- 172 (1990).
-
(1990)
Enzyme Microb. Technol.
, vol.12
, Issue.3
, pp. 162-172
-
-
Galazzo, J.L.1
Bailey, J.E.2
-
116
-
-
0026662512
-
Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum (I). The basis for model construction
-
B. E. Wright, M. H. Butler, and K. R. Albe, Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. (I). The basis for model construction. J. Biol. Chem. 267(5), 3101- 3105 (1992).
-
(1992)
J. Biol. Chem.
, vol.267
, Issue.5
, pp. 3101-3105
-
-
Wright, B.E.1
Butler, M.H.2
Albe, K.R.3
-
117
-
-
0028086220
-
Carbohydrate metabolism in Dictyostelium discoideum: I Model construction
-
B. E. Wright and K. R. Albe, Carbohydrate metabolism in Dictyostelium discoideum: I. Model construction. J. Theor. Biol. 169(3), 231-241 (1994).
-
(1994)
J. Theor. Biol.
, vol.169
, Issue.3
, pp. 231-241
-
-
Wright, B.E.1
Albe, K.R.2
-
118
-
-
0028290762
-
Steady-state modeling of metabolic flux between the tricarboxylic cycle and the glyoxylate bypass in Escherichia coli
-
E. M. T. El-Mansi, G. C. Dawson, and C. F. A. Bryce, Steady-state modeling of metabolic flux between the tricarboxylic cycle and the glyoxylate bypass in Escherichia coli. CABIOS (now Bioinformatics) 10(3), 295-299 (1994).
-
(1994)
CABIOS (now Bioinformatics)
, vol.10
, Issue.3
, pp. 295-299
-
-
El-Mansi, E.M.T.1
Dawson, G.C.2
Bryce, C.F.A.3
-
119
-
-
0028927063
-
Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations Application to enzyme deficiencies of red blood cells
-
R. Schuster and H. G. Holzhütter, Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations. Application to enzyme deficiencies of red blood cells. Eur. J. Biochem. 229(2), 403-418 (1995).
-
(1995)
Eur. J. Biochem.
, vol.229
, Issue.2
, pp. 403-418
-
-
Schuster, R.1
Holzhütter, H.G.2
-
120
-
-
0343907200
-
In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II
-
M. Rizzi, M. Baltes, U. Theobald, and M. Reuss, In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol. Bioeng. 55, 592-608 (1997).
-
(1997)
Mathematical model. Biotechnol. Bioeng.
, vol.55
, pp. 592-608
-
-
Rizzi, M.1
Baltes, M.2
Theobald, U.3
Reuss, M.4
-
121
-
-
0033857139
-
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
-
B. Teusink, J. Passarge, C. A. Reijenga, E. Esgalhado, C. C. van der Weijden, M. Schepper, M. C. Walsh, B. M. Bakker, K. van Dam, H. V. Westerhoff, and J. L. Snoep, Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem. 267(17), 5313-5329 (2000).
-
(2000)
Eur. J. Biochem.
, vol.267
, Issue.17
, 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
Walsh, M.C.7
Bakker, B.M.8
van Dam, K.9
Westerhoff, H.V.10
Snoep, J.L.11
-
122
-
-
0033107539
-
In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae
-
S. Vaseghi, A. Baumeister, M. Rizzi, and M. Reuss, In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab Eng 1(2), 128-140 (1999).
-
(1999)
Metab Eng
, vol.1
, Issue.2
, pp. 128-140
-
-
Vaseghi, S.1
Baumeister, A.2
Rizzi, M.3
Reuss, M.4
-
123
-
-
0033567930
-
Model of 2 3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: Computer simulation and metabolic control analysis
-
P. J. Mulquiney and P.W. Kuchel, Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: Computer simulation and metabolic control analysis. Biochem. J. 342 (3), 597-604 (1999).
-
(1999)
Biochem. J.
, vol.342
, Issue.3
, pp. 597-604
-
-
Mulquiney, P.J.1
Kuchel, P.W.2
-
125
-
-
0034826582
-
Computer modeling and experimental evidence for two steady states in the photosynthetic Calvin cycle
-
M. G. Poolman, H. Ölcer, J. C. Lloyd, C. A. Raines, and D. A. Fell, Computer modeling and experimental evidence for two steady states in the photosynthetic Calvin cycle. Eur. J. Biochem. 268, 2810-2816 (2001).
-
(2001)
Eur. J. Biochem.
, vol.268
, pp. 2810-2816
-
-
Poolman, M.G.1
Ölcer, H.2
Lloyd, J.C.3
Raines, C.A.4
Fell, D.A.5
-
126
-
-
0034088868
-
Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations
-
J. Wolf, J. Passarge, O. J. G. Somsen, J. L. Snoep, R. Heinrich, and H. V. Westerhoff, Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys. J. 78, 1145-1153 (2000).
-
(2000)
Biophys. J.
, vol.78
, pp. 1145-1153
-
-
Wolf, J.1
Passarge, J.2
Somsen, O.J.G.3
Snoep, J.L.4
Heinrich, R.5
Westerhoff, H.V.6
-
127
-
-
0035448427
-
Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data
-
J. M. Rohwer and F. C. Botha, Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445 (2001).
-
(2001)
Biochem. J.
, vol.358
, pp. 437-445
-
-
Rohwer, J.M.1
Botha, F.C.2
-
128
-
-
0035365847
-
An integrated study of threonine-pathway enzyme kinetics in Escherichia coli
-
C. Chassagnole, B. Raïs, E. Quentin, D. A. Fell, and J. P. Mazat, An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem. J. 356 (2), 415-423 (2001).
-
(2001)
Biochem. J.
, vol.356
, Issue.2
, pp. 415-423
-
-
Chassagnole, C.1
Raïs, B.2
Quentin, E.3
Fell, D.A.4
Mazat, J.P.5
-
129
-
-
0037025146
-
Dynamic modeling of the central carbon metabolism of Escherichia coli
-
C. Chassagnole, N. Noisommit-Rizzi, J. W. Schmid, K. Mauch, and M. Reuss, Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79(1), 53-73 (2002).
-
(2002)
Biotechnol. Bioeng.
, vol.79
, Issue.1
, pp. 53-73
-
-
Chassagnole, C.1
Noisommit-Rizzi, N.2
Schmid, J.W.3
Mauch, K.4
Reuss, M.5
-
130
-
-
0036229317
-
Metabolic engineering of lactic acid bacteria, the combined approach: Kinetic modeling, metabolic control and experimental analysis
-
M. H. N. Hoefnagel, M. J. C. Starrenburg, D. E. Martens, J. Hugenholtz, M. Kleerebezem, I. I Van Swam, R. Bongers, H. V.Westerhoff, and J. L. Snoep, Metabolic engineering of lactic acid bacteria, the combined approach: Kinetic modeling, metabolic control and experimental analysis. Microbiology, 148(4), 1003-1013 (2002).
-
(2002)
Microbiology
, vol.148
, Issue.4
, pp. 1003-1013
-
-
Hoefnagel, M.H.N.1
Starrenburg, M.J.C.2
Martens, D.E.3
Hugenholtz, J.4
Kleerebezem, M.5
Van Swam, I.I.6
Bongers, R.7
Westerhoff, H.V.8
Snoep, J.L.9
-
131
-
-
0141815496
-
Mathematical modeling of the urea cycle
-
A. D. Maher, P.W. Kuchel, F. Ortega, P. de Atauri, J. Centelles, and M. Cascante, Mathematical modeling of the urea cycle. A numerical investigation into substrate channelling. Eur. J. Biochem. 270(19), 3953-3961 (2003).
-
(2003)
A numerical investigation into substrate channelling. Eur. J. Biochem.
, vol.270
, Issue.19
, pp. 3953-3961
-
-
Maher, A.D.1
Kuchel, P.W.2
Ortega, F.3
de Atauri, P.4
Centelles, J.5
Cascante, M.6
-
133
-
-
23444449142
-
Integrative model of the response of yeast to osmotic shock
-
E. Klipp, B. Nordlander, R. Krüger, P. Gennemark, and S. Hohmann, Integrative model of the response of yeast to osmotic shock. Nat. Biotechnol. 23(8), 975-982 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, Issue.8
, pp. 975-982
-
-
Klipp, E.1
Nordlander, B.2
Krüger, R.3
Gennemark, P.4
Hohmann, S.5
-
134
-
-
77954183900
-
Mathematical modeling of potato tuber carbohydrate metabolism
-
H. Assmus, Mathematical modeling of potato tuber carbohydrate metabolism. Ph.D. thesis, Oxford Brookes University (2005).
-
(2005)
Ph. D. thesis, Oxford Brookes University
-
-
Assmus, H.1
-
135
-
-
35348928051
-
Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: A numerical simulation using an evolutionary algorithm
-
X.-G. Zhu, E. de Sturler, and S. P. Long, Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: A numerical simulation using an evolutionary algorithm. Plant Physiol. 145(2), 513-526 (2007).
-
(2007)
Plant Physiol
, vol.145
, Issue.2
, pp. 513-526
-
-
Zhu, X.-G.1
de Sturler, E.2
Long, S.P.3
-
136
-
-
34548297895
-
Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology
-
F. Wu, F. Yang, KC Vinnakota, and DA Beard, Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology. J. Biol. Chem. 282(34), 24525-24537 (2007).
-
(2007)
J. Biol. Chem.
, vol.282
, Issue.34
, pp. 24525-24537
-
-
Wu, F.1
Yang, F.2
Vinnakota, K.C.3
Beard, D.A.4
-
137
-
-
49949089863
-
Hemet: Mathematical model of biochemical pathways for simulation and prediction of hepatocyte metabolism
-
C. De Maria, D. Grassini, F. Vozzi, B. Vinci, A. Landi, A. Ahluwalia, and G. Vozzi, Hemet: Mathematical model of biochemical pathways for simulation and prediction of hepatocyte metabolism. Comput. Methods Programs Biomed. (2008).
-
(2008)
Comput. Methods Programs Biomed.
-
-
De Maria, C.1
Grassini, D.2
Vozzi, F.3
Vinci, B.4
Landi, A.5
Ahluwalia, A.6
Vozzi, G.7
-
138
-
-
0037197159
-
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
-
S. Klamt, S. Schuster, and E. D. Gilles, Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng. 77(7), 734-751 (2002).
-
(2002)
Biotechnol. Bioeng.
, vol.77
, Issue.7
, pp. 734-751
-
-
Klamt, S.1
Schuster, S.2
Gilles, E.D.3
-
141
-
-
33744544180
-
Fractal reaction kinetics
-
DOI:101126/science.241.4873.1620
-
R. Kopelman, Fractal reaction kinetics. Science 241(4873), 1620-1626 (1988); DOI:10.1126/ science.241.4873.1620.
-
(1988)
Science
, vol.241
, Issue.4873
, pp. 1620-1626
-
-
Kopelman, R.1
-
142
-
-
0002862462
-
Enzyme kinetics in vitro and in vivo: Michaelis-Menten revisited
-
doi:10. 1016/S1569-2582(06)80007-3
-
M. A. Savageau, Enzyme kinetics in vitro and in vivo: Michaelis-Menten revisited. Principles Med. Biol. 4(1), 93-146 (1995); doi:10.1016/S1569-2582(06)80007-3.
-
(1995)
Principles Med. Biol.
, vol.4
, Issue.1
, pp. 93-146
-
-
Savageau, M.A.1
-
143
-
-
33748977501
-
A systematic investigation of the rate laws valid in intracellular environments
-
R. Grima and S. Schnell. A systematic investigation of the rate laws valid in intracellular environments. Biophys. Chem. 124(124), 1-10 (2006).
-
(2006)
Biophys. Chem.
, vol.124
, Issue.124
, pp. 1-10
-
-
Grima, R.1
Schnell, S.2
-
144
-
-
0031853923
-
Development of fractal kinetic theory for enzyme-catalysed reactions and implications for the design of biochemical pathways
-
M. A. Savageau, Development of fractal kinetic theory for enzyme-catalysed reactions and implications for the design of biochemical pathways. BioSystems 47(1-2), 9-36 (1998).
-
(1998)
BioSystems
, vol.47
, Issue.1-2
, pp. 9-36
-
-
Savageau, M.A.1
-
145
-
-
0014649230
-
Biochemical systems analysis I. Some mathematical properties of the rate law for the component enzymatic reactions
-
M. A. Savageau, Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J. Theor. Biol. 25, 365-369 (1969).
-
(1969)
J. Theor. Biol.
, vol.25
, pp. 365-369
-
-
Savageau, M.A.1
-
146
-
-
0014658880
-
Biochemical systems analysis II. The steady-state solutions for an n-pool system using a power-law approximation
-
M. A. Savageau, 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).
-
(1969)
J. Theor. Biol.
, vol.25
, pp. 370-379
-
-
Savageau, M.A.1
-
148
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
D. E. Koshland, Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44(2), 98-104 (1958).
-
(1958)
Proc. Natl. Acad. Sci. USA
, vol.44
, Issue.2
, pp. 98-104
-
-
Koshland, D.E.1
-
149
-
-
0036286631
-
Energy balance for analysis of complex metabolic networks
-
D. A. Beard, S. Liang, and H. Qian, Energy balance for analysis of complex metabolic networks. Biophys. J. 83(1), 79-86 (2002).
-
(2002)
Biophys. J.
, vol.83
, Issue.1
, pp. 79-86
-
-
Beard, D.A.1
Liang, S.2
Qian, H.3
-
150
-
-
33745433792
-
Putative regulatory sites unraveled by networkembedded thermodynamic analysis of metabolome data
-
A. Kümmel, S. Panke, and M. Heinemann, Putative regulatory sites unraveled by networkembedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2 (2006).
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Kümmel, A.1
Panke, S.2
Heinemann, M.3
-
151
-
-
36248990302
-
Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks
-
A. Hoppe, S. Hoffmann, and H.-G. Holzhütter, Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst. Biol. 1, 23 (2007).
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 23
-
-
Hoppe, A.1
Hoffmann, S.2
Holzhütter, H.-G.3
-
152
-
-
0000870544
-
Die Kinetik der Invertin-Wirkung (the kinetics of invertase activity)
-
L. Michaelis and M. L. Menten, Die Kinetik der Invertin-Wirkung (the kinetics of invertase activity). Biochem. Z. 49, 333-369 (1913).
-
(1913)
Biochem. Z.
, vol.49
, pp. 333-369
-
-
Michaelis, L.1
Menten, M.L.2
-
153
-
-
0000292524
-
A note on the kinetics of enzyme action
-
G. E. Briggs and J. B. S. Haldane, A note on the kinetics of enzyme action. Biochem. J. 19, 338- 339 (1925).
-
(1925)
Biochem. J.
, vol.19
, pp. 338-339
-
-
Briggs, G.E.1
Haldane, J.B.S.2
-
154
-
-
0001705279
-
Theorie generale de l'action de quelques diastases
-
V. Henri, Theorie generale de l'action de quelques diastases. Comptes Rend. Acad. Sci. Paris 135, 916-919 (1902).
-
(1902)
Comptes Rend. Acad. Sci. Paris
, vol.135
, pp. 916-919
-
-
Henri, V.1
-
156
-
-
34047240610
-
Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation
-
A. Ciliberto, F. Capuani, and J. J. Tyson2, Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput. Biol. 3(3), e45 (2007).
-
(2007)
PLoS Comput. Biol.
, vol.3
, Issue.3
-
-
Ciliberto, A.1
Capuani, F.2
Tyson2, J.J.3
-
158
-
-
50549159930
-
The kinetics of enzyme-catalyzed reactions with two or more substrates or products I. Nomenclature and rate equations
-
W. W. Cleland. The kinetics of enzyme-catalyzed reactions with two or more substrates or products. I. Nomenclature and rate equations. Biochim. Biophys. Acta. 67, 104-137 (1963).
-
(1963)
Biochim. Biophys. Acta
, vol.67
, pp. 104-137
-
-
Cleland, W.W.1
-
159
-
-
50549188738
-
The kinetics of enzyme-catalyzed reactions With two or more substrates or products II. Inhibition: Nomenclature and theory
-
W. W. Cleland, The kinetics of enzyme-catalyzed reactions With two or more substrates or products. II. Inhibition: Nomenclature and theory. Biochim. Biophys. Acta. 67, 173-187 (1963).
-
(1963)
Biochim. Biophys. Acta
, vol.67
, pp. 173-187
-
-
Cleland, W.W.1
-
160
-
-
50549155520
-
The kinetics of enzyme-catalyzed reactions with two or more substrates or products III. Prediction of initial velocity and inhibition patterns by inspection
-
W. W. Cleland, The kinetics of enzyme-catalyzed reactions with two or more substrates or products. III. Prediction of initial velocity and inhibition patterns by inspection. Biochim. Biophys. Acta. 67, 188-196 (1963).
-
(1963)
Biochim. Biophys. Acta
, vol.67
, pp. 188-196
-
-
Cleland, W.W.1
-
161
-
-
33846617808
-
Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
-
W. Liebermeister and E. Klipp, Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints. Theor. Biol. Med. Modeling 3(42) (2006).
-
(2006)
Theor. Biol. Med. Modeling
, vol.3
, Issue.42
-
-
Liebermeister, W.1
Klipp, E.2
-
162
-
-
46649094809
-
Detailed enzyme kinetics in terms of biochemical species: Study of citrate synthase
-
D. A. Beard, K. C. Vinnakota, and F. Wu, Detailed enzyme kinetics in terms of biochemical species: Study of citrate synthase. PLoS ONE 3(3), e1825 (2008).
-
(2008)
PLoS ONE
, vol.3
, Issue.3
-
-
Beard, D.A.1
Vinnakota, K.C.2
Wu, F.3
-
164
-
-
33747155081
-
Evaluation of a simplified generic bi-substrate rate equation for computational systems biology
-
J. M. Rohwer, A. J. Hanekom, C. Crous, J. L. Snoep, and J.-H. S. Hofmeyr, Evaluation of a simplified generic bi-substrate rate equation for computational systems biology. IEE Proc.-Syst. Biol. 153(5), 338-341 (2006).
-
(2006)
IEE Proc. -Syst. Biol.
, vol.153
, Issue.5
, pp. 338-341
-
-
Rohwer, J.M.1
Hanekom, A.J.2
Crous, C.3
Snoep, J.L.4
Hofmeyr, J.-H.5
-
165
-
-
33747185335
-
Generic kinetic equations for modeling multisubstrate reactions in computational systems biology
-
A. J. Hanekom, Generic kinetic equations for modeling multisubstrate reactions in computational systems biology. Master's thesis, Stellenbosch University (2006).
-
(2006)
Master's thesis, Stellenbosch University
-
-
Hanekom, A.J.1
-
166
-
-
0000832972
-
Evidence for a negative-feedback mechanismin the biosynthesis of isoleucine
-
H. E. Umbarger, Evidence for a negative-feedback mechanismin the biosynthesis of isoleucine. Science 123, 848 (1956).
-
(1956)
Science
, vol.123
, pp. 848
-
-
Umbarger, H.E.1
-
167
-
-
0009376148
-
Isoleucine and valine metabolism in Escherichia coli VIII. The formation of acetolactate
-
H. E. Umbarger and B. Brown, Isoleucine and valine metabolism in Escherichia coli. VIII. The formation of acetolactate. J. Biol. Chem. 233, 1156-1160 (1958).
-
(1958)
J. Biol. Chem.
, vol.233
, pp. 1156-1160
-
-
Umbarger, H.E.1
Brown, B.2
-
168
-
-
73649152457
-
Allosteric proteins and cellular control systems
-
J. Monod, J.-P. Changeux, and F. Jacob, Allosteric proteins and cellular control systems. J. Mol. Biol. 306-329 (1963).
-
(1963)
J. Mol. Biol
, pp. 306-329
-
-
Monod, J.1
Changeux, J.-P.2
Jacob, F.3
-
169
-
-
0014026169
-
Control of the activity of Escherichia coli carbamoyl phosphate synthetase by antagonistic allosteric effectors
-
A. Pi/'erard, Control of the activity of Escherichia coli carbamoyl phosphate synthetase by antagonistic allosteric effectors. Science 154, 1572-1573 (1966).
-
(1966)
Science
, vol.154
, pp. 1572-1573
-
-
Pierard, A.1
-
170
-
-
0014668125
-
Regulation of branched biosynthetic pathways in bacteria
-
P. Datta, Regulation of branched biosynthetic pathways in bacteria. Science 165, 556-562 (1969).
-
(1969)
Science
, vol.165
, pp. 556-562
-
-
Datta, P.1
-
171
-
-
34548724489
-
The evolution of genetic networks by non-adaptive processes
-
doi:10. 1038/nrg2192
-
M. Lynch, The evolution of genetic networks by non-adaptive processes. Nat. Rev. Genet. 8, 803-813 (2007); doi:10.1038/nrg2192.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 803-813
-
-
Lynch, M.1
-
172
-
-
84889389880
-
Systems Biology in Practice: Concepts, Implementation and Application, Wiley-VCH Verlag GmbH
-
E. Klipp, R. Herwig, A. Kowald, C. Wierling, and H. Lehrach, Systems Biology in Practice: Concepts, Implementation and Application, Wiley-VCH Verlag GmbH, Weinheim, 2005.
-
(2005)
Weinheim
-
-
Klipp, E.1
Herwig, R.2
Kowald, A.3
Wierling, C.4
Lehrach, H.5
-
173
-
-
0003043542
-
The possible effects of the aggregation of the molecules of hemoglobin on its dissociation curves
-
A. V. Hill, The possible effects of the aggregation of the molecules of hemoglobin on its dissociation curves. J. Physiol. (Lond) 40, 4-7 (1910).
-
(1910)
J. Physiol. (Lond)
, vol.40
, pp. 4-7
-
-
Hill, A.V.1
-
174
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
J. Monod, J. Wyman, and J. P. Changeux, On the nature of allosteric transitions: A plausible model. J. Mol. Biol. 12, 88-118 (1965).
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
175
-
-
20344370764
-
Allosteric mechanisms of signal transduction
-
J.-P. Changeux and S. J. Edelstein, Allosteric mechanisms of signal transduction. Science, 308 (5727), 1424-1428 (2005).
-
(2005)
Science
, vol.308
, Issue.5727
, pp. 1424-1428
-
-
Changeux, J.-P.1
Edelstein, S.J.2
-
176
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
D. E. Koshland, G. Némethy, and D. Filmer, Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5(1), 365-368 (1966).
-
(1966)
Biochemistry
, vol.5
, Issue.1
, pp. 365-368
-
-
Koshland, D.E.1
Némethy, G.2
Filmer, D.3
-
177
-
-
33745075591
-
Tools for kinetic modeling of biochemical networks
-
R. Alves, F. Antunes, and A. Salvador, Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. 24(6), 667-672 (2006).
-
(2006)
Nat. Biotechnol.
, vol.24
, Issue.6
, pp. 667-672
-
-
Alves, R.1
Antunes, F.2
Salvador, A.3
-
178
-
-
33845368513
-
Copasi-A complex pathway simulator
-
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer, Copasi-A complex pathway simulator. Bioinformatics 22, 3067-3074 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
179
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
A. Funahashi, N. Tanimura, M. Morohashi, and H. Kitano, CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1, 159-162 (2003).
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
180
-
-
3042595010
-
Cellware-Multi-algorithmic software for computational systems biology
-
P. Dhar, T. C. Meng, S. Somani, L. Ye, A. Sairam, Z. Hao, A. Krishnan, and K. Sakharkar, Cellware-Multi-algorithmic software for computational systems biology. Bioinformatics 20(8), 1319-1321 (2004).
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1319-1321
-
-
Dhar, P.1
Meng, T.C.2
Somani, S.3
Ye, L.4
Sairam, A.5
Hao, Z.6
Krishnan, A.7
Sakharkar, K.8
-
181
-
-
0347511691
-
Next generation simulation tools: The systems biology workbench and BioSPICE integration
-
Herbert M Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano, Next generation simulation tools: The systems biology workbench and BioSPICE integration. OMICS 7(4), 355-372 (2003).
-
(2003)
OMICS
, vol.7
, Issue.4
, pp. 355-372
-
-
Sauro, H.M.1
Hucka, M.2
Finney, A.3
Wellock, C.4
Bolouri, H.5
Doyle, J.6
Hiroaki Kitano, H.7
-
182
-
-
32544443964
-
Systems biology toolbox for Matlab: A computational platform for research in systems biology
-
H. Schmidt and M. Jirstrand, Systems biology toolbox for Matlab: A computational platform for research in systems biology. Bioinformatics 22(4), 514-515 (2006).
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 514-515
-
-
Schmidt, H.1
Jirstrand, M.2
-
183
-
-
47649105109
-
The systems biology research tool: Evolvable open-source software
-
J. Wright and A.Wagner, The systems biology research tool: Evolvable open-source software. BMC Syst. Biol. 2, 55 (2008).
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 55
-
-
Wright, J.1
Wagner, A.2
-
184
-
-
14744280370
-
A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness
-
Y. Gibon, O. E. Blaesing, J. Hannemann, P. Carillo, M. Hoehne, J. H. M. Hendriks N. Palacios, J. Cross, J. Selbig, and M. Stitt, A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 16, 3304-3325 (2004).
-
(2004)
Plant Cell
, vol.16
, pp. 3304-3325
-
-
Gibon, Y.1
Blaesing, O.E.2
Hannemann, J.3
Carillo, P.4
Hoehne, M.5
Hendriks, J.H.M.6
Palacios, N.7
Cross, J.8
Selbig, J.9
Stitt, M.10
-
185
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
N. Le Novére, A. Finney, M. Hucka, U. S. Bhalla, F. Campagne, J. Collado-Vides, E. J. Crampin, M. Halstead, E. Klipp, P. Mendes, P. Nielsen, H. Sauro, B. Shapiro, J. L. Snoep, H. D. Spence, and B. L. Wanner, Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509-1515 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1509-1515
-
-
Le Novére, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.J.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
Nielsen, P.11
Sauro, H.12
Shapiro, B.13
Snoep, J.L.14
Spence, H.D.15
Wanner, B.L.16
-
186
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
M. Kanehisa and S. Goto. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28(1), 27-30 (2000).
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
187
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
Database issue
-
M. Kanehisa, S. Goto, M. Hattori, K. F Aoki-Kinoshita, M. Itoh, S. Kawashima, T. Katayama, M. Araki, and M. Hirakawa, From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34(Database issue), D354-D357 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
188
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Database issue
-
M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi, KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36(Database issue), D480-D484 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
189
-
-
38549117301
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Database issue
-
R. Caspi, H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C.Walk, P. Zhang, and P. D. Karp, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36(Database issue), D623-D631 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Kaipa, P.4
Krummenacker, M.5
Latendresse, M.6
Paley, S.7
Rhee, S.Y.8
Shearer, A.G.9
Tissier, C.10
Walk, T.C.11
Zhang, P.12
Karp, P.D.13
-
190
-
-
34250191844
-
B. de Bono, M. Gillespie, B. Jassal, S. Lewis, L. Matthews, G. Wu, E. Birney, and L. Stein, Reactome: A knowledge base of biologic pathways and processes
-
I. Vastrik, P. D'Eustachio, E. Schmidt, G. Joshi-Tope, G. Gopinath, D. Croft, B. de Bono, M. Gillespie, B. Jassal, S. Lewis, L. Matthews, G. Wu, E. Birney, and L. Stein, Reactome: A knowledge base of biologic pathways and processes. Genome Biol 8(3), R39 (2007).
-
(2007)
Genome Biol
, vol.8
, Issue.3
-
-
Vastrik, I.1
D'Eustachio, P.2
Schmidt, E.3
Joshi-Tope, G.4
Gopinath, G.5
Croft, D.6
-
191
-
-
0345863907
-
BRENDA, the enzyme database: Updates and major new developments
-
Database issue
-
I. Schomburg, A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and D. Schomburg, BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res 32 (Database issue), D431-D433 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Schomburg, I.1
Chang, A.2
Ebeling, C.3
Gremse, M.4
Heldt, C.5
Huhn, G.6
Schomburg, D.7
-
192
-
-
33846114132
-
Brenda amenda and frenda: The enzyme information system in 2007
-
Database issue
-
J. Barthelmes, C. Ebeling, A. Chang, I. Schomburg, and D. Schomburg, Brenda, amenda and frenda: The enzyme information system in 2007. Nucleic Acids Res. 35(Database issue), D511- D514 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Barthelmes, J.1
Ebeling, C.2
Chang, A.3
Schomburg, I.4
Schomburg, D.5
-
193
-
-
34249889888
-
Storing and annotating of kinetic data
-
I. Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, AndreasWeidemann, and Ulrike Wittig, Storing and annotating of kinetic data. In Silico Biol. 7(2 Suppl), S37-S44 (2007).
-
(2007)
In Silico Biol
, vol.7
, Issue.2 SUPPL
-
-
Rojas, I.1
Golebiewski, M.2
Kania, R.3
Krebs, O.4
Mir, S.5
Weidemann, A.6
Ulrike Wittig, U.7
-
194
-
-
63349104913
-
SABIORK: A database for biochemical reactions and their kinetics
-
I. Rojas, M. Golebiewski, R. Kania, O. Krebs, S. Mir, A. Weidemann, and U. Wittig, SABIORK: A database for biochemical reactions and their kinetics. BMC Syst. Biol., 1(Suppl 1), S6 (2007).
-
(2007)
BMC Syst. Biol.
, vol.1
, Issue.SUPPL 1
-
-
Rojas, I.1
Golebiewski, M.2
Kania, R.3
Krebs, O.4
Mir, S.5
Weidemann, A.6
Wittig, U.7
-
195
-
-
8844259501
-
Thermodynamics of enzyme-catalyzed reactions- A database for quantitative biochemistry
-
R. N. Goldberg, Y. B. Tewari, and T. N. Bhat. Thermodynamics of enzyme-catalyzed reactions- A database for quantitative biochemistry. Bioinformatics 20(16), 2874-2877 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 16-2877
-
-
Goldberg, R.N.1
Tewari, Y.B.2
Bhat, T.N.3
-
196
-
-
33644877164
-
Biomodels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
doi:10. 1093/nar/gkj092
-
N. Le Novére, B. Bornstein, A. Broicher,M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, J. L. Snoep, and M. Hucka, Biomodels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689-D691 (2006); doi:10.1093/nar/gkj092.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Le Novére, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
197
-
-
4544344218
-
Web-based kinetic modeling using JWS online
-
B. G. Olivier and J. L. Snoep, Web-based kinetic modeling using JWS online. Bioinformatics 20, 2143-2144 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 2143-2144
-
-
Olivier, B.G.1
Snoep, J.L.2
-
198
-
-
2442595958
-
CellML: Its future, present and past
-
C. M. Lloyd, M. D. B. Halstead, and P. F. Nielsen, CellML: Its future, present and past. Prog. Biophys. Mol. Biol. 85(2-3); 433-450 (2004).
-
(2004)
Prog. Biophys. Mol. Biol
, vol.85
, Issue.2-3
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.B.2
Nielsen, P.F.3
-
199
-
-
34047119230
-
Toward a curated CellML model repository
-
D. Nickerson, C. Stevens, M. Halstead, P. Hunter, and P. Nielsen, Toward a curated CellML model repository. Conf. Proc. IEEE Eng. Med. Biol. Soc. 1, 4237-4240 (2006).
-
(2006)
Conf. Proc. IEEE Eng. Med. Biol. Soc.
, vol.1
, pp. 4237-4240
-
-
Nickerson, D.1
Stevens, C.2
Halstead, M.3
Hunter, P.4
Nielsen, P.5
-
200
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
M. Hucka, A. Finney, H. M. Sauro,H. Bolouri, J. C.Doyle, H.Kitano,A. P. Arkin,B. J.Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin,W. J. Hedley, T.C.Hodgman, J.-H.Hofmeyr, P. J.Hunter,N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novà {currency sign}re, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness,Y.Nakayama,M. R.Nelson, P. F.Nielsen,T. Sakurada, J. C. Schaff,B.E. Shapiro,T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J.Wagner, J.Wang, and S. B. M. L. Forum, The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524-531 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles13
-
201
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project
-
M. Hucka, A. Finney, B. J. Bornstein, S. M. Keating, B. E. Shapiro, J. Matthews, B. L. Kovitz, M. J. Schilstra, A. Funahashi, J. C. Doyle, and H. Kitano, Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project. Syst. Biol. (Stevenage) 1(1), 41-53 (2004).
-
(2004)
Syst. Biol. (Stevenage)
, vol.1
, Issue.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.J.3
Keating, S.M.4
Shapiro, B.E.5
Matthews, J.6
Kovitz, B.L.7
Schilstra, M.J.8
Funahashi, A.9
Doyle, J.C.10
Kitano, H.11
-
202
-
-
0035105106
-
Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems
-
U. Roessner, A. Luedemann, D. Brust, O. Fiehn, T. Linke, L. Willmitzer, and A. R. Fernie, Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11-29 (2001).
-
(2001)
Plant Cell
, vol.13
, pp. 11-29
-
-
Roessner, U.1
Luedemann, A.2
Brust, D.3
Fiehn, O.4
Linke, T.5
Willmitzer, L.6
Fernie, A.R.7
-
203
-
-
0024831970
-
Metabolite levels in specific cells and subcellular compartments of plant leaves
-
M. Stitt, R. M. Lilley, R. Gerhardt, and H. W Heldt, Metabolite levels in specific cells and subcellular compartments of plant leaves. Methods Enzymol. 174, 221-335 (1989).
-
(1989)
Methods Enzymol
, vol.174
, pp. 221-335
-
-
Stitt, M.1
Lilley, R.M.2
Gerhardt, R.3
Heldt, H.W.4
-
204
-
-
0344962433
-
Single cell technology
-
J. Kehr, Single cell technology. Curr. Opin. Plant Biol. 6, 617-621 (2003).
-
(2003)
Curr. Opin. Plant Biol.
, vol.6
, pp. 617-621
-
-
Kehr, J.1
-
205
-
-
0035999896
-
Sensitive and high throughput metabolite assays for inorganic pyrophosphate, ADPGlc, nucleotide phosphates, and glycolytic intermediates based on a novel enzymic cycling system
-
Y. Gibon, H. Vigeolas, A. Tiessen, P. Geigenberger, and M. Stitt, Sensitive and high throughput metabolite assays for inorganic pyrophosphate, ADPGlc, nucleotide phosphates, and glycolytic intermediates based on a novel enzymic cycling system. Plant J. 30, 221-235 (2002).
-
(2002)
Plant J
, vol.30
, pp. 221-235
-
-
Gibon, Y.1
Vigeolas, H.2
Tiessen, A.3
Geigenberger, P.4
Stitt, M.5
-
206
-
-
77954198424
-
-
http://www.genomicglossaries.com/content/omes.asp.
-
-
-
-
207
-
-
0033757963
-
Metabolite profiling for plant functional genomics
-
O. Fiehn, J. Kopka, P. Dörmann, T. Altmann, R. T. Trethewey, and L. Willmitzer, Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18, 1157-1161 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 1157-1161
-
-
Fiehn, O.1
Kopka, J.2
Dörmann, P.3
Altmann, T.4
Trethewey, R.T.5
Willmitzer, L.6
-
208
-
-
0034959944
-
Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks
-
O. Fiehn, Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks. Comp. Funct. Genom. 2, 155-168 (2001).
-
(2001)
Comp. Funct. Genom.
, vol.2
, pp. 155-168
-
-
Fiehn, O.1
-
209
-
-
0036042222
-
Metabolomics and machine learning: Explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules
-
D. B. Kell, Metabolomics and machine learning: Explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules. Mol. Biol. Rep. 29, 237-241 (2002).
-
(2002)
Mol. Biol. Rep.
, vol.29
, pp. 237-241
-
-
Kell, D.B.1
-
210
-
-
0037295057
-
Deciphering metabolic networks
-
O. Fiehn and W. Weckwerth, Deciphering metabolic networks. Eur. J. Biochem. 270, 579-588 (2003).
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 579-588
-
-
Fiehn, O.1
Weckwerth, W.2
-
211
-
-
84889317778
-
Metabolome Analysis: An Introduction
-
John Wiley & Sons, Hoboken NJ
-
S. G. Villas-Boas, U. Roessner, M. Hansen, J. Smedsgaard, and J. Nielsen, Metabolome Analysis: An Introduction, John Wiley & Sons, Hoboken, NJ, 2007.
-
(2007)
-
-
Villas-Boas, S.G.1
Roessner, U.2
Hansen, M.3
Smedsgaard, J.4
Nielsen, J.5
-
212
-
-
0345701915
-
Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles
-
C. Wagner, M. Sefkow, and J. Kopka, Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62, 887-900 (2003).
-
(2003)
Phytochemistry
, vol.62
, pp. 887-900
-
-
Wagner, C.1
Sefkow, M.2
Kopka, J.3
-
213
-
-
0036404889
-
Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry
-
A. Aharoni, C. H. R. de Vos, H. A. Verhoeven, C. A. Maliepaard, G. Kruppa, R. J. Bino, and D. B. Goodenowe, Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. Omics 6, 217-234 (2002).
-
(2002)
Omics
, vol.6
, pp. 217-234
-
-
Aharoni, A.1
de Vos, C.H.R.2
Verhoeven, H.A.3
Maliepaard, C.A.4
Kruppa, G.5
Bino, R.J.6
Goodenowe, D.B.7
-
214
-
-
33947503169
-
Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry
-
B. Luo, K. Groenke, R. Takors, C. Wandrey, and M. Oldiges, Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J. Chromatogr. A 1147, 153-164 (2007).
-
(2007)
J. Chromatogr. A
, vol.1147
, pp. 153-164
-
-
Luo, B.1
Groenke, K.2
Takors, R.3
Wandrey, C.4
Oldiges, M.5
-
215
-
-
0035902992
-
Amino acid analysis in five pooled single plant cell samples using capillary electrophoresis coupled to laser-induced fluorescence detection
-
K. Arlt, S. Brandt, and J. Kehr, Amino acid analysis in five pooled single plant cell samples using capillary electrophoresis coupled to laser-induced fluorescence detection. J. Chromatogr. A 926, 319-325 (2001).
-
(2001)
J. Chromatogr. A
, vol.926
, pp. 319-325
-
-
Arlt, K.1
Brandt, S.2
Kehr, J.3
-
216
-
-
19944398727
-
A proposed framework for the description of plant metabolomics experiments and their results
-
H. Jenkins, N. Hardy, M. Beckmann, J. Draper, A. R. Smith, J. Taylor, O. Fiehn, R. Goodacre, R. J. Bino, R. Hall, J. Kopka, G. A. Lane, B. M. Lange, J. R. Liu, P. Mendes, B. J. Nikolau, S. G. Oliver, N.W. Paton, S. Rhee S, U. Roessner-Tunali, K. Saito, J. Smedsgaard, L.W. Sumner, T. Wang, S. Walsh, E. S. Wurtele, and D. B. Kell, A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 22, 1601-1606 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1601-1606
-
-
Jenkins, H.1
Hardy, N.2
Beckmann, M.3
Draper, J.4
Smith, A.R.5
Taylor, J.6
Fiehn, O.7
Goodacre, R.8
Bino, R.J.9
Hall, R.10
Kopka, J.11
Lane, G.A.12
Lange, B.M.13
Liu, J.R.14
Mendes, P.15
Nikolau, B.J.16
Oliver, S.G.17
Paton, N.W.18
Rhee, S.19
Roessner-Tunali, S.U.20
Saito, K.21
Smedsgaard, J.22
Sumner, L.W.23
Wang, T.24
Walsh, S.25
Wurtele, E.S.26
Kell, D.B.27
more..
-
217
-
-
32044454046
-
Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation
-
K. Morgenthal, W. Weckwerth, and R. Steuer, Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation. BioSystems 83(2-3), 108-117 (2006).
-
(2006)
BioSystems
, vol.83
, pp. 23-117
-
-
Morgenthal, K.1
Weckwerth, W.2
Steuer, R.3
-
218
-
-
40549100747
-
Metabolomics data analysis, visualization, and integration
-
D. Edwards, ed., Humana Press, Towota, NJ
-
L. W. Summer, E. Urbanczyk-Wochniak, and C. D. Broekling, Metabolomics data analysis, visualization, and integration, in Plant Bioinformatics-Methods and Protocols, D. Edwards, ed., Humana Press, Towota, NJ, 2007, pp. 409-436.
-
(2007)
Plant Bioinformatics-Methods and Protocols
, pp. 409-436
-
-
Summer, L.W.1
Urbanczyk-Wochniak, E.2
Broekling, C.D.3
-
219
-
-
33747620056
-
-
R. A. Notebaart, F. H. J. van Enckevort, C. Francke, R. J. Siezen, and B. Teusink, Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinform. 7, 296 (2006).
-
(2006)
BMC Bioinform
, vol.7
, pp. 296
-
-
Notebaart, R.A.1
van Enckevort, F.H.J.2
Francke, C.3
Siezen, R.J.4
Teusink, B.5
-
220
-
-
0033580813
-
Systems properties of the Haemophilus influenzae Rd metabolic genotype
-
J. S. Edwards and B. Ø. Palsson, Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274, 17410-17416 (1999).
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17410-17416
-
-
Edwards, J.S.1
Palsson, B.Ø.2
-
221
-
-
34547888003
-
A genome-scale, constraint based approach to systems biology of human metabolism
-
M. L. Mo, N. Jamshidi, and B. Ø. Palsson, A genome-scale, constraint based approach to systems biology of human metabolism. Mol. BioSystems 3, 598-603 (2007).
-
(2007)
Mol. BioSystems
, vol.3
, pp. 598-603
-
-
Mo, M.L.1
Jamshidi, N.2
Palsson, B.Ø.3
-
222
-
-
43049156566
-
Human metabolic network reconstruction and its impact on drug discovery and development
-
H. Ma and I. Goryanin, Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov. Today 13(9-10), 402-408 (2008).
-
(2008)
Drug Discov. Today
, vol.13
, Issue.9-10
, pp. 402-408
-
-
Ma, H.1
Goryanin, I.2
-
223
-
-
67649855560
-
Global network properties
-
B. H. Junker and F. Schreiber, eds., John Wiley & Sons, Inc
-
R. Steuer and G. Zamora López, Global network properties. Analysis of Biological Networks, Wiley Series on Bioinformatics: Computational Techniques and Engineering. B. H. Junker and F. Schreiber, eds., John Wiley & Sons, Inc. 2008.
-
(2008)
Analysis of Biological Networks, Wiley Series on Bioinformatics: Computational Techniques and Engineering
-
-
Steuer, R.1
Zamora López, G.2
-
224
-
-
34447551397
-
Structural functional analysis of cellular networks with CellNetAnalyzer
-
S. Klamt, J. Saez-Rodriguez, and E. D. Gilles, Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1, 2 (2007).
-
(2007)
BMC Syst. Biol.
, vol.1
, Issue.2
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Gilles, E.D.3
-
225
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA toolbox
-
doi:101038/nprot. 2007.99
-
S. A. Becker, A. M. Feist, M. L. Mo, G. Hannum, B. O. Palsson, and M. J. Herrgard, Quantitative prediction of cellular metabolism with constraint-based models: The COBRA toolbox. Nat. Protocols 2(3), 727-738 (2007); doi:10.1038/nprot.2007.99.
-
(2007)
Nat. Protocols
, vol.2
, Issue.3
, 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
-
226
-
-
0344052685
-
Metatool: For studying metabolic networks
-
T. Pfeiffer, I. Sánchez-Valdenebro, J. C. Nunõ, F. Montero, and S. Schuster, Metatool: For studying metabolic networks. Bioinformatics 15(3), 251-257 (1999).
-
(1999)
Bioinformatics
, vol.15
, Issue.3
, pp. 251-257
-
-
Pfeiffer, T.1
Sánchez-Valdenebro, I.2
Nunõ, J.C.3
Montero, F.4
Schuster, S.5
-
227
-
-
33747856186
-
Metatool 5 0: Fast and flexible elementary modes analysis
-
A. von Kamp and S. Schuster, Metatool 5.0: Fast and flexible elementary modes analysis. Bioinformatics 22(15), 1930-1931 (2006).
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1930-1931
-
-
von Kamp, A.1
Schuster, S.2
-
228
-
-
25444515956
-
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
-
R. Schwarz, P. Musch, A. von Kamp, B. Engels, H. Schirmer, S. Schuster, and T. Dandekar, YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 6, 135 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.135
-
-
Schwarz, R.1
Musch, P.2
von Kamp, A.3
Engels, B.4
Schirmer, H.5
Schuster, S.6
Dandekar, T.7
-
229
-
-
35248849697
-
Integrated network reconstruction, visualization and analysis using YANAsquare
-
R. Schwarz, C. Liang, C. Kaleta, M. Kühnel, E. Hoffmann, S. Kuznetsov, M. Hecker, G. Griffiths, S. Schuster, and T. Dandekar, Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 8, 313 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 313
-
-
Schwarz, R.1
Liang, C.2
Kaleta, C.3
Kühnel, M.4
Hoffmann, E.5
Kuznetsov, S.6
Hecker, M.7
Griffiths, G.8
Schuster, S.9
Dandekar, T.10
-
230
-
-
33645536317
-
SNA-a toolbox for the stoichiometric analysis of metabolic networks
-
Robert Urbanczik, SNA-a toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics 7, 129 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 129
-
-
Urbanczik, R.1
-
231
-
-
17544366029
-
Expa: A program for calculating extreme pathways in biochemical reaction networks
-
S. L. Bell and B. Ø. Palsson, Expa: A program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21(8), 1739-1740 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1739-1740
-
-
Bell, S.L.1
Palsson, B.Ø.2
-
232
-
-
47649132045
-
Pathwayanalyser: A systems biology tool for flux analysis of metabolic pathways
-
K. Raman and N. Chandra, Pathwayanalyser: A systems biology tool for flux analysis of metabolic pathways. Nature Precedings, 2008.
-
(2008)
Nature Precedings
-
-
Raman, K.1
Chandra, N.2
-
233
-
-
0038281453
-
Observing and interpreting correlations in metabolomic networks
-
R. Steuer, J. Kurths, O. Fiehn, and W. Weckwerth, Observing and interpreting correlations in metabolomic networks. Bioinformatics 19(8), 1019-1026 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1019-1026
-
-
Steuer, R.1
Kurths, J.2
Fiehn, O.3
Weckwerth, W.4
-
234
-
-
20344365760
-
The origin of correlations in metabolomics data
-
D. Camacho, A. de la Fuente, and P. Mendes, The origin of correlations in metabolomics data. Metabolomics 1, 53-63 (2005).
-
(2005)
Metabolomics
, vol.1
, pp. 53-63
-
-
Camacho, D.1
de la Fuente, A.2
Mendes, P.3
-
235
-
-
0033136109
-
Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era
-
C. H. Schilling, S. Schuster, B. O. Palsson, and R. Heinrich, Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296-303 (1999).
-
(1999)
Biotechnol. Prog.
, vol.15
, pp. 296-303
-
-
Schilling, C.H.1
Schuster, S.2
Palsson, B.O.3
Heinrich, R.4
-
236
-
-
0000029295
-
On elementary flux modes in biochemical reaction systems at steady state
-
S. Schuster and C. Hilgetag, On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2, 165-182 (1994).
-
(1994)
J. Biol. Syst.
, vol.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
237
-
-
0033080396
-
Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
-
S. Schuster, T. Dandekar, and D. A. Fell, Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. TIBTECH 17, 53-60 (1999).
-
(1999)
TIBTECH
, vol.17
, pp. 53-60
-
-
Schuster, S.1
Dandekar, T.2
Fell, D.A.3
-
238
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic systems
-
S. Schuster, D. A. Fell, and T. Dandekar, A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic systems. Nat. Biotechnol. 18, 326- 332 (2000).
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
239
-
-
0037308505
-
Two approaches for metabolic pathway analysis?
-
S. Klamt and J. Stelling, Two approaches for metabolic pathway analysis? Trends Biotechnol. 21(2), 64-69 (2003).
-
(2003)
Trends Biotechnol
, vol.21
, Issue.2
, pp. 64-69
-
-
Klamt, S.1
Stelling, J.2
-
240
-
-
3342925846
-
Comparison of network-based pathway analysis methods
-
J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, and B. Ø. Palsson, Comparison of network-based pathway analysis methods. Trends Biotechnol. 22(8), 400-405 (2004).
-
(2004)
Trends Biotechnol
, vol.22
, Issue.8
, pp. 400-405
-
-
Papin, J.A.1
Stelling, J.2
Price, N.D.3
Klamt, S.4
Schuster, S.5
Palsson, B.Ø.6
-
241
-
-
0037317848
-
Elementary modes analysis of photosynthate metabolism in the chloroplast stroma
-
M. G. Poolman, D. A. Fell, and C. A. Raines, Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 270, 430-439 (2003).
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 430-439
-
-
Poolman, M.G.1
Fell, D.A.2
Raines, C.A.3
-
242
-
-
1042269472
-
Minimal cut sets in biochemical reaction networks
-
S. Klamt and E. D. Gilles, Minimal cut sets in biochemical reaction networks. Bioinformatics 20(2), 226-234 (2004).
-
(2004)
Bioinformatics
, vol.20
, Issue.2
, pp. 226-234
-
-
Klamt, S.1
Gilles, E.D.2
-
243
-
-
32144453095
-
Generalized concept of minimal cut sets in biochemical networks
-
S. Klamt, Generalized concept of minimal cut sets in biochemical networks. Biosystems 83(2-3), 233-247 (2006).
-
(2006)
Biosystems
, vol.83
, Issue.2-3
, pp. 233-247
-
-
Klamt, S.1
-
244
-
-
16344381707
-
Application of Petri net theory for modeling and validation of the sucrose breakdown pathway in the potato tuber
-
I. Koch, B. H. Junker, and M. Heiner. Application of Petri net theory for modeling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7), 1219- 1226 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1219-1226
-
-
Koch, I.1
Junker, B.H.2
Heiner, M.3
-
245
-
-
41549107955
-
Modularization of biochemical networks based on classification of Petri net t-invariants
-
E. Grafahrend-Belau, F. Schreiber, M. Heiner, A. Sackmann, B. H. Junker, S. Grunwald, A. Speer, K. Winder, and I. Koch, Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinform. 9, 90 (2008).
-
(2008)
BMC Bioinform
, vol.9
, pp. 90
-
-
Grafahrend-Belau, E.1
Schreiber, F.2
Heiner, M.3
Sackmann, A.4
Junker, B.H.5
Grunwald, S.6
Speer, A.7
Winder, K.8
Koch, I.9
-
246
-
-
34447557916
-
Principles of optimal metabolic network operation
-
J. Nielsen, Principles of optimal metabolic network operation. Mol. Syst. Biol. 3, 126 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 126
-
-
Nielsen, J.1
-
247
-
-
39449095000
-
Stoichiometric modeling of cell metabolism
-
F. Llaneras and J. Pico, Stoichiometric modeling of cell metabolism. J. Biosci. Bioeng. 105(1), 1-11 (2008).
-
(2008)
J. Biosci. Bioeng.
, vol.105
, Issue.1
, pp. 1-11
-
-
Llaneras, F.1
Pico, J.2
-
248
-
-
0034741983
-
13C metabolic flux analysis
-
13C metabolic flux analysis. Metab. Eng. 3, 195-206 (2001).
-
(2001)
Metab. Eng.
, vol.3
, pp. 195-206
-
-
Wiechert, W.1
-
249
-
-
0032977883
-
Lessons from metabolic engineering for functional genomics and drug discovery
-
J. E. Bailey, Lessons from metabolic engineering for functional genomics and drug discovery. Nat. Biotechnol. 17, 616-618 (1999).
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 616-618
-
-
Bailey, J.E.1
-
250
-
-
2942530586
-
Chloroplast proteomics: Potentials and challenges
-
S. Baginsky and W. Gruissem, Chloroplast proteomics: Potentials and challenges. J. Exp. Bot. 55, 1213-1220 (2004).
-
(2004)
J. Exp. Bot.
, vol.55
, pp. 1213-1220
-
-
Baginsky, S.1
Gruissem, W.2
-
251
-
-
0041864127
-
In vivo measurement of fluxes through metabolic pathways: The missing link in functional genomics and pharmaceutical research
-
M. K. Hellerstein, In vivo measurement of fluxes through metabolic pathways: The missing link in functional genomics and pharmaceutical research. Annu. Rev. Nutr. 23, 379-402 (2003).
-
(2003)
Annu. Rev. Nutr.
, vol.23
, pp. 379-402
-
-
Hellerstein, M.K.1
-
252
-
-
10644266747
-
Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds
-
J. Schwender, F. Goffman, J. B. Ohlrogge, and Y. Shachar-Hill, Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. Nature 432, 779-782 (2004).
-
(2004)
Nature
, vol.432
, pp. 779-782
-
-
Schwender, J.1
Goffman, F.2
Ohlrogge, J.B.3
Shachar-Hill, Y.4
-
253
-
-
14744267531
-
Flux an important, but neglected, component of functional genomics
-
A. R. Fernie, P. Geigenberger, and M. Stitt. Flux an important, but neglected, component of functional genomics. Curr. Opin. Plant Biol. 8, 174-182 (2005).
-
(2005)
Curr. Opin. Plant Biol.
, vol.8
, pp. 174-182
-
-
Fernie, A.R.1
Geigenberger, P.2
Stitt, M.3
-
254
-
-
34547658908
-
Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source
-
B. H. Junker, J. Lonien, L. E. Heady, A. Rogers, and J. Schwender, Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source. Phytochemistry 68, 2232-2242 (2007).
-
(2007)
Phytochemistry
, vol.68
, pp. 2232-2242
-
-
Junker, B.H.1
Lonien, J.2
Heady, L.E.3
Rogers, A.4
Schwender, J.5
-
256
-
-
0035121892
-
Fructose 2 6-bisphosphate activates pyrophosphate:fructose-6-phosphate 1-phosphotransferase and increases triose phosphate to hexose phosphate cycling in heterotrophic cells
-
A. R. Fernie, A. Roscher, R. G. Ratcliffe, and N. J. Kruger, Fructose 2,6-bisphosphate activates pyrophosphate:fructose-6-phosphate 1-phosphotransferase and increases triose phosphate to hexose phosphate cycling in heterotrophic cells. Planta 212, 250-263 (2001).
-
(2001)
Planta
, vol.212
, pp. 250-263
-
-
Fernie, A.R.1
Roscher, A.2
Ratcliffe, R.G.3
Kruger, N.J.4
-
257
-
-
12344253235
-
Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression
-
B. H. Junker, R. Wuttke, A. Tiessen, P. Geigenberger, U. Sonnewlad, L. Willmitzer, and A. R. Fernie, Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Mol. Biol. 56, 91-110 (2004).
-
(2004)
Plant Mol. Biol.
, vol.56
, pp. 91-110
-
-
Junker, B.H.1
Wuttke, R.2
Tiessen, A.3
Geigenberger, P.4
Sonnewlad, U.5
Willmitzer, L.6
Fernie, A.R.7
-
258
-
-
0031554635
-
Bidirectional reaction steps in metabolic networks. Part I: Modeling and simulation of carbon isotope labelling experiments. Biotechnol
-
W. Wiechert and A. A. de Graaf, Bidirectional reaction steps in metabolic networks. Part I: Modeling and simulation of carbon isotope labelling experiments. Biotechnol. Bioeng. 55, 101- 117 (1997).
-
(1997)
Bioeng
, vol.55
, pp. 101-117
-
-
Wiechert, W.1
de Graaf, A.A.2
-
259
-
-
0031554628
-
Bidirectional reaction steps in metabolic networks. Part II: Fluxestimation and statistical analysis
-
W. Wiechert, C. Siefke, A. A. de Graaf, and A. Marx, Bidirectional reaction steps in metabolic networks. Part II: Fluxestimation and statistical analysis. Biotechnol. Bioeng. 55, 118-135 (1997).
-
(1997)
Biotechnol. Bioeng.
, vol.55
, pp. 118-135
-
-
Wiechert, W.1
Siefke, C.2
de Graaf, A.A.3
Marx, A.4
-
260
-
-
0343267841
-
Bidirectional reaction steps in metabolic networks. Part III: Explicit solution and analysis of isotopomer labeling systems
-
W. Wiechert, M. Möllney, N. Isermann, M. Wurzel, and A. A. de Graaf, Bidirectional reaction steps in metabolic networks. Part III: Explicit solution and analysis of isotopomer labeling systems. Biotechnol. Bioeng. 66, 69-85 (1999).
-
(1999)
Biotechnol. Bioeng.
, vol.66
, pp. 69-85
-
-
Wiechert, W.1
Möllney, M.2
Isermann, N.3
Wurzel, M.4
de Graaf, A.A.5
-
261
-
-
4243829380
-
Bidirectional reaction steps in metabolic networks. Part III: Optimal design of isotopomer labeling experiments
-
M. Möllney, W. Wiechert, D. Kownatzki, and A. A. de Graaf, Bidirectional reaction steps in metabolic networks. Part III: Optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66, 86-103 (1999).
-
(1999)
Biotechnol. Bioeng.
, vol.66
, pp. 86-103
-
-
Möllney, M.1
Wiechert, W.2
Kownatzki, D.3
de Graaf, A.A.4
-
262
-
-
0034741985
-
A universal framework for 13C metabolic flux analysis
-
W. Wiechert, M. Möllney, S. Petersen, and A. A. de Graaf, A universal framework for 13C metabolic flux analysis. Metab. Eng. 3, 265-283 (2001).
-
(2001)
Metab. Eng.
, vol.3
, pp. 265-283
-
-
Wiechert, W.1
Möllney, M.2
Petersen, S.3
de Graaf, A.A.4
-
263
-
-
34547655298
-
Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13c labeling and comprehensive bondomer balancing
-
G. Sriram, D. B. Fulton, and J. V. Shanks, Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13c labeling and comprehensive bondomer balancing. Phytochemistry 68, 2243-2257 (2007).
-
(2007)
Phytochemistry
, vol.68
, pp. 2243-2257
-
-
Sriram, G.1
Fulton, D.B.2
Shanks, J.V.3
-
264
-
-
0026204952
-
Mass isotopomer analysis: Theoretical and practical considerations
-
W.-N. P. Lee, L. O. Byerley, E. A. Bergner, and J. Edmond, Mass isotopomer analysis: Theoretical and practical considerations. Biol. Mass Spectrom. 20, 451-458 (1991).
-
(1991)
Biol. Mass Spectrom.
, vol.20
, pp. 451-458
-
-
Lee, W.-N.1
Byerley, L.O.2
Bergner, E.A.3
Edmond, J.4
-
265
-
-
0029146299
-
13C-labeling of proteinogenic amino acids-an efficient analytical tool to investigate intermediary metabolism
-
13C-labeling of proteinogenic amino acids-an efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232, 433- 448 (1995).
-
(1995)
Eur. J. Biochem.
, vol.232
, pp. 433-448
-
-
Szyperski, T.1
-
266
-
-
25444489844
-
13C-glucose experiments
-
U. Sauer, N. Zamboni, and E. Fischer, FiatFlux-a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinform. 6, e209 (2005).
-
(2005)
BMC Bioinform
, vol.6
-
-
Sauer, U.1
Zamboni, N.2
Fischer, E.3
-
267
-
-
33644853940
-
Measuring multiple fluxes through plant metabolic networks
-
R. G. Ratcliffe and Y. Shachar-Hill, Measuring multiple fluxes through plant metabolic networks. Plant J. 45, 490-511 (2006).
-
(2006)
Plant J
, vol.45
, pp. 490-511
-
-
Ratcliffe, R.G.1
Shachar-Hill, Y.2
-
268
-
-
44949161995
-
Metabolic flux analysis in plants: From intelligent design to rational engineering
-
I. G. L. Libourel and Y. Shachar-Hill, Metabolic flux analysis in plants: From intelligent design to rational engineering. Annu. Rev. Plant Biol. 59, 625-650 (2008).
-
(2008)
Annu. Rev. Plant Biol.
, vol.59
, pp. 625-650
-
-
Libourel, I.G.L.1
Shachar-Hill, Y.2
-
269
-
-
0001635921
-
A kinetic study of the assimilation of [15N]-ammonia and the synthesis of amino acids in an exponentially growing culture of Candida utilis
-
A. P. Sims and B. F. Folkes, A kinetic study of the assimilation of [15N]-ammonia and the synthesis of amino acids in an exponentially growing culture of Candida utilis. Proc. Roy. Soc. Lond. B. Biol. Sci. 159, 479-502 (1964).
-
(1964)
Proc. Roy. Soc. Lond. B. Biol. Sci.
, vol.159
, pp. 479-502
-
-
Sims, A.P.1
Folkes, B.F.2
-
270
-
-
4143116713
-
Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in 13C labeled isotopes
-
U. Roessner-Tunali, J. Liu, A. Leisse, I. Balbo, A. Perez-Melis, L.Willmitzer, and A. R. Fernie, Kinetics of labelling of organic and amino acids in potato tubers by gas chromatography-mass spectrometry following incubation in 13C labeled isotopes. Plant J. 39, 668-679 (2004).
-
(2004)
Plant J
, vol.39
, pp. 668-679
-
-
Roessner-Tunali, U.1
Liu, J.2
Leisse, A.3
Balbo, I.4
Perez-Melis, A.5
Willmitzer, L.6
Fernie, A.R.7
-
271
-
-
34547675713
-
GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling
-
J. Huege, R. Sulpice, Y. Gibon, J. Lisec, K. Koehl, and J. Kopka, GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling. Phytochemistry 68, 2258-2272 (2007).
-
(2007)
Phytochemistry
, vol.68
, pp. 2258-2272
-
-
Huege, J.1
Sulpice, R.2
Gibon, Y.3
Lisec, J.4
Koehl, K.5
Kopka, J.6
-
272
-
-
0018501521
-
An atlas of cellular oscillators
-
P. E. Rapp, An atlas of cellular oscillators. J. Exp. Biol. 81, 281-306 (1979).
-
(1979)
J. Exp. Biol.
, vol.81
, pp. 281-306
-
-
Rapp, P.E.1
-
273
-
-
0016829888
-
Stabilization of energy charge, generation of oscillation and multiple steady states in energy metabolism as a result of purely stoichiometric regulation
-
E. E. Selkov, Stabilization of energy charge, generation of oscillation and multiple steady states in energy metabolism as a result of purely stoichiometric regulation. Eur. J. Biochem. 59, 151-157 (1975).
-
(1975)
Eur. J. Biochem.
, vol.59
, pp. 151-157
-
-
Selkov, E.E.1
-
274
-
-
0033581959
-
Sustained oscillations in living cells
-
S. Danø, P. G. Sørensen, and F. Hynne, Sustained oscillations in living cells. Nature 402, 320-322 (1999).
-
(1999)
Nature
, vol.402
, pp. 320-322
-
-
Danø, S.1
Sørensen, P.G.2
Hynne, F.3
-
275
-
-
0001349267
-
Control of phosphate turnover as a rate-limiting factor and possible source of oscillations in photosynthesis, a mathematical model
-
A. Laisk and D. A.Walker, Control of phosphate turnover as a rate-limiting factor and possible source of oscillations in photosynthesis, a mathematical model. Proc. R. Soc. London B 227, 281-302 (1986).
-
(1986)
Proc. R. Soc. London B
, vol.227
, pp. 281-302
-
-
Laisk, A.1
Walker, D.A.2
-
276
-
-
0025859085
-
Identification of possible two-reactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways
-
U. Ryde-Petterson, Identification of possible two-reactant sources of oscillations in the Calvin photosynthesis cycle and ancillary pathways. Eur. J. Biochem. 198, 613-619 (1991).
-
(1991)
Eur. J. Biochem.
, vol.198
, pp. 613-619
-
-
Ryde-Petterson, U.1
-
278
-
-
77954210246
-
Biochemical Oscillations Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behaviour, Cambridge University Press, Cambridge
-
A. Goldbeter, Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behaviour, Cambridge University Press, Cambridge, United Kingdom (1997).
-
(1997)
United Kingdom
-
-
Goldbeter, A.1
-
279
-
-
15044341917
-
Cellular oscillators: Rhythmic gene expression and metabolism
-
U. Schibler and F. Naef, Cellular oscillators: Rhythmic gene expression and metabolism. Curr. Opin. Cell. Biol. 17, 223-229 (2005).
-
(2005)
Curr. Opin. Cell. Biol.
, vol.17
, pp. 223-229
-
-
Schibler, U.1
Naef, F.2
-
280
-
-
0032531818
-
Calcium a life and death signal
-
M. J. Berridge, M. D. Bootman, and P. Lipp, Calcium a life and death signal. Nature 395, 645-648 (1998).
-
(1998)
Nature
, vol.395
, pp. 645-648
-
-
Berridge, M.J.1
Bootman, M.D.2
Lipp, P.3
-
281
-
-
33746463692
-
The temporal architecture of eukaryotic growth
-
D. Lloyd and D. Murray, The temporal architecture of eukaryotic growth. FEBS Lett. 580(12), 2830-2835 (2005).
-
(2005)
FEBS Lett
, vol.580
, Issue.12
, pp. 2830-2835
-
-
Lloyd, D.1
Murray, D.2
-
282
-
-
34248598677
-
Redox rhythmicity: Clocks at the core of temporal coherence
-
D. Lloyd and D. B. Murray, Redox rhythmicity: Clocks at the core of temporal coherence. BioEssays 29(5), 465-473 (2007).
-
(2007)
BioEssays
, vol.29
, Issue.5
, pp. 465-473
-
-
Lloyd, D.1
Murray, D.B.2
-
283
-
-
0037079015
-
Computational approaches to cellular rhythms
-
A. Goldbeter, Computational approaches to cellular rhythms. Nature 420, 238-245 (2002).
-
(2002)
Nature
, vol.420
, pp. 238-245
-
-
Goldbeter, A.1
-
284
-
-
0025826876
-
Modeling the cell division cycle: cdc2 and cyclin interactions
-
J. J. Tyson, Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl. Acad. Sci. USA 88, 7328-7332 (1991).
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 7328-7332
-
-
Tyson, J.J.1
-
286
-
-
0033555859
-
Emergent properties of networks of biological signaling pathways
-
U. S. Bhalla and R. Iyengar, Emergent properties of networks of biological signaling pathways. Science 283, 381-387 (1999).
-
(1999)
Science
, vol.283
, pp. 381-387
-
-
Bhalla, U.S.1
Iyengar, R.2
-
287
-
-
0037605637
-
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible
-
J. E. Ferrell, Jr., and W. Xiong, Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. Chaos 11(1), 227-236 (2001).
-
(2001)
Chaos
, vol.11
, Issue.1
, pp. 227-236
-
-
Ferrell J.E., Jr.1
Xiong, W.2
-
288
-
-
0033230728
-
Multistability: A Major Means of differentiation and evolution in biological systems
-
M. Laurent and N. Kellershohn, Multistability: A Major Means of differentiation and evolution in biological systems. Trends Biochem Sci. 24(11), 418-422 (1999).
-
(1999)
Trends Biochem Sci
, vol.24
, Issue.11
, pp. 418-422
-
-
Laurent, M.1
Kellershohn, N.2
-
289
-
-
0034676456
-
Feedback control of intercellular signaling in development
-
M. Freeman. Feedback control of intercellular signaling in development. Nat. Rev. 408, 313-319 (2000).
-
(2000)
Nat. Rev.
, vol.408
, pp. 313-319
-
-
Freeman, M.1
-
291
-
-
35949018382
-
Ergodic theory of chaos and strange attractors
-
J. P. Eckmann and D. Ruelle, Ergodic theory of chaos and strange attractors. Rev. Mod. Phys. 57(3), 617-656 (1985).
-
(1985)
Rev. Mod. Phys.
, vol.57
, Issue.3
, pp. 617-656
-
-
Eckmann, J.P.1
Ruelle, D.2
-
294
-
-
0031213576
-
Studies on glycolysis-I Multiple steady states in bacterial glycolysis
-
V. Hatzimanikatis and J. E. Bailey, Studies on glycolysis-I. Multiple steady states in bacterial glycolysis. Chem. Eng. Sci. 52(15), 2579-2588 (1997).
-
(1997)
Chem. Eng. Sci.
, vol.52
, Issue.15
, pp. 2579-2588
-
-
Hatzimanikatis, V.1
Bailey, J.E.2
-
295
-
-
32044432602
-
Metabolic homeostasis in the human erythrocyte: In silico analysis
-
P. de Atauri, M. J. Ramírez, P.W. Kuchel, J. Carreras, and M. Cascante, Metabolic homeostasis in the human erythrocyte: In silico analysis. Biosystems 83(2-3), 118-124 (2006).
-
(2006)
Biosystems
, vol.83
, Issue.2-3
, pp. 118-124
-
-
de Atauri, P.1
Ramírez, M.J.2
Kuchel, P.W.3
Carreras, J.4
Cascante, M.5
-
296
-
-
36248952170
-
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
-
S. Grimbs, J. Selbig, S. Bulik, H.-G. Holzhütter, and R. Steuer, The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Mol. Syst. Biol. 3, 146 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 146
-
-
Grimbs, S.1
Selbig, J.2
Bulik, S.3
Holzhütter, H.-G.4
Steuer, R.5
-
297
-
-
84951134408
-
The theory of oscillating reactions
-
J. Higgins, The theory of oscillating reactions. Ind. Eng. Chem. 59, 18-62 (1967).
-
(1967)
Ind. Eng. Chem.
, vol.59
, pp. 18-62
-
-
Higgins, J.1
-
298
-
-
0015012526
-
Chemical instabilities and sustained oscillations
-
R. Lefever and G. Nicolis, Chemical instabilities and sustained oscillations. J. Theor. Biol. 30 (2), 267-284 (1971).
-
(1971)
J. Theor. Biol.
, vol.30
, Issue.2
, pp. 267-284
-
-
Lefever, R.1
Nicolis, G.2
-
299
-
-
32844460213
-
Generalized models as an universal approach to the analysis of nonlinear dynamical systems
-
T. Gross and U. Feudel, Generalized models as an universal approach to the analysis of nonlinear dynamical systems. Phys. Rev. E 73, 016205 (2006).
-
(2006)
Phys. Rev. E
, vol.73
, pp. 016205
-
-
Gross, T.1
Feudel, U.2
-
300
-
-
33846796117
-
Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture
-
M. R. Roussel and D. Lloyd, Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture. FEBS J. 274(4), 1011-1018 (2007).
-
(2007)
FEBS J
, vol.274
, Issue.4
, pp. 1011-1018
-
-
Roussel, M.R.1
Lloyd, D.2
-
301
-
-
0032556477
-
Slowly reverting enzyme inactivation: A mechanism for generating long-lived damped oscillations
-
M. R. Roussel, Slowly reverting enzyme inactivation: A mechanism for generating long-lived damped oscillations. J. Theor. Biol. 195, 233-244 (1998).
-
(1998)
J. Theor. Biol.
, vol.195
, pp. 233-244
-
-
Roussel, M.R.1
-
302
-
-
0000320504
-
Birhythmicity, chaos, and other patterns of temporal selforganization in a multiply regulated biochemical system
-
O. Delcroly and A. Goldbeter, Birhythmicity, chaos, and other patterns of temporal selforganization in a multiply regulated biochemical system. Proc. Natl. Acad. Sci. USA 79, 6917-6921 (1982).
-
(1982)
Proc. Natl. Acad. Sci. USA
, vol.79
, pp. 6917-6921
-
-
Delcroly, O.1
Goldbeter, A.2
-
303
-
-
0021189377
-
Transitions between oscillatory modes in a glycolytic model system
-
M. Markus and B. Hess, Transitions between oscillatory modes in a glycolytic model system. Proc. Natl. Acad. Sci. USA 81, 4394-4398 (1984).
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 4394-4398
-
-
Markus, M.1
Hess, B.2
-
305
-
-
0015173025
-
Oscillatory phenomena in biochemistry
-
B. Hess and A. Boiteux, Oscillatory phenomena in biochemistry. Ann. Rev. Biochem. 40, 237- 258 (1971).
-
(1971)
Ann. Rev. Biochem.
, vol.40
, pp. 237-258
-
-
Hess, B.1
Boiteux, A.2
-
306
-
-
0015419716
-
Dissipative structures for an allosteric model: Application to glycolytic oscillations
-
A. Goldbeter and R. Lefever, Dissipative structures for an allosteric model: Application to glycolytic oscillations. Biophys. J. 12, 1302-1315 (1972).
-
(1972)
Biophys. J.
, vol.12
, pp. 1302-1315
-
-
Goldbeter, A.1
Lefever, R.2
-
307
-
-
0000498082
-
Control of oscillating glycolysis of yeast by stochastic, periodic, and steady source of substrate: A model and experimental study
-
A. Boiteux, A. Goldbeter, and B. Hess, Control of oscillating glycolysis of yeast by stochastic, periodic, and steady source of substrate: A model and experimental study. Proc. Natl. Acad. Sci. 72(10), 3829-3833 (1975).
-
(1975)
Proc. Natl. Acad. Sci.
, vol.72
, Issue.10
, pp. 3829-3833
-
-
Boiteux, A.1
Goldbeter, A.2
Hess, B.3
-
308
-
-
0019569727
-
Oscillations and control features in glycolysis: Numerical analysis of a comprehensive model
-
Y. Termonia and J. Ross, Oscillations and control features in glycolysis: Numerical analysis of a comprehensive model. Proc. Natl. Acad. Sci. USA 78, 2952-2956 (1981).
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 2952-2956
-
-
Termonia, Y.1
Ross, J.2
-
309
-
-
0032485816
-
Sustained oscillations in glycolysis: An experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations
-
K. Nielsen, P. G. Sørensen, F. Hynne, and H.-G. Busse, Sustained oscillations in glycolysis: An experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations. Biophys. Chem. 72, 49-62 (1998).
-
(1998)
Biophys. Chem.
, vol.72
, pp. 49-62
-
-
Nielsen, K.1
Sørensen, P.G.2
Hynne, F.3
Busse, H.-G.4
-
310
-
-
0034092437
-
How yeast cells synchronize their glycolytic oscillations: A perturbation analytic treatment
-
M. Bier, B. M. Bakker, and H. V. Westerhoff, How yeast cells synchronize their glycolytic oscillations: A perturbation analytic treatment. Biophys. J. 78, 1087-1093 (2000).
-
(2000)
Biophys. J.
, vol.78
, pp. 1087-1093
-
-
Bier, M.1
Bakker, B.M.2
Westerhoff, H.V.3
-
311
-
-
0032077442
-
K. van Dam, and H. V.Westerhoff
-
doi:10. 1016/S0968-0004(98)01205-5
-
B. Teusink, M. C.Walsh, K. van Dam, and H. V.Westerhoff, The danger of metabolic pathways with turbo design. Trends Biochem. Sci. 23(5), 162-169, (1998); doi:10.1016/S0968-0004(98) 01205-5.
-
(1998)
The danger of metabolic pathways with turbo design. Trends Biochem. Sci.
, vol.23
, Issue.5
, pp. 162-169
-
-
Teusink, B.1
Walsh, M.C.2
-
312
-
-
0032441091
-
Glycolysis, turbo design and the endocrine pancreatic cell
-
P. B. Iynedjian, Glycolysis, turbo design and the endocrine pancreatic cell. Trends Biochem. Sci. 23(12), 467-468 (1998).
-
(1998)
Trends Biochem. Sci.
, vol.23
, Issue.12
, pp. 467-468
-
-
Iynedjian, P.B.1
-
314
-
-
0015989446
-
A linear steady-state treatment of enzymatic chains. General properties, control and effector strength
-
R. Heinrich and T. A. Rapoport, A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95 (1974).
-
(1974)
Eur. J. Biochem.
, vol.42
, pp. 89-95
-
-
Heinrich, R.1
Rapoport, T.A.2
-
316
-
-
45949117248
-
Biochemical systems theory and metabolic control theory: 1 Fundamental similarities and differences
-
M. A. Savageau, Biochemical systems theory and metabolic control theory: 1. Fundamental similarities and differences. Math. Biosci. 86, 127-145 (1987).
-
(1987)
Math. Biosci.
, vol.86
, pp. 127-145
-
-
Savageau, M.A.1
-
317
-
-
0027113928
-
Dominance according to metabolic control analysis: Major achievement or house of cards (letter to the editor)
-
M. A. Savageau, Dominance according to metabolic control analysis: Major achievement or house of cards (letter to the editor). J. Theor. Biol. 154, 131-136 (1992).
-
(1992)
J. Theor. Biol.
, vol.154
, pp. 131-136
-
-
Savageau, M.A.1
-
318
-
-
25144492110
-
Approximative kinetics formats used in metabolic network modeling
-
J. J. Heijnen, Approximative kinetics formats used in metabolic network modeling. Biotechnol. Bioeng. 91(5), 535-545 (2005).
-
(2005)
Biotechnol. Bioeng.
, vol.91
, Issue.5
, pp. 535-545
-
-
Heijnen, J.J.1
-
319
-
-
13844280250
-
Stoichiometric foundation of large-scale biochemical system analysis
-
G. Ciobanu and G. Rozenberg, eds. Springer Natural Computing Series, Springer-Verlag, Berlin
-
D. A. Beard, H. Qian, and J. B. Bassingthwaighte, Stoichiometric foundation of large-scale biochemical system analysis, in Modeling in Molecular Biology, G. Ciobanu and G. Rozenberg, eds. Springer Natural Computing Series, Springer-Verlag, Berlin, 2004, pp. 1-19.
-
(2004)
Modeling in Molecular Biology
, pp. 1-19
-
-
Beard, D.A.1
Qian, H.2
Bassingthwaighte, J.B.3
-
320
-
-
1842405351
-
Effects of spatiotemporal variations on metabolic control: Approximate analysis using (log)linear kinetic models
-
J. E. Bailey and V. Hatzimanikatis, Effects of spatiotemporal variations on metabolic control: Approximate analysis using (log)linear kinetic models. Biotechnol. Bioeng. (1997).
-
(1997)
Biotechnol. Bioeng.
-
-
Bailey, J.E.1
Hatzimanikatis, V.2
-
322
-
-
0031018721
-
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates
-
J. Nielsen, Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates. Biochem. J. 321(1), 133-138 (1997).
-
(1997)
Biochem. J.
, vol.321
, Issue.1
, pp. 133-138
-
-
Nielsen, J.1
-
323
-
-
33846647495
-
Bringing metabolic networks to life: Integration of kinetic, metabolic, and proteomic data
-
W. Liebermeister and E. Klipp, Bringing metabolic networks to life: Integration of kinetic, metabolic, and proteomic data. Theor. Biol. Med. Modeling 3(42), (2006).
-
(2006)
Theor. Biol. Med. Modeling
, vol.3
, Issue.42
-
-
Liebermeister, W.1
Klipp, E.2
-
324
-
-
0036860705
-
Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: Decarboxylation rate, oscillations, and multiplicity
-
A.-P. Zeng, J. Modak, and W.-D. Deckwer, Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: Decarboxylation rate, oscillations, and multiplicity. Biotechnol. Prog. 18(6), 1265-1276 (2002).
-
(2002)
Biotechnol. Prog.
, vol.18
, Issue.6
, pp. 1265-1276
-
-
Zeng, A.-P.1
Modak, J.2
Deckwer, W.-D.3
-
325
-
-
34447314196
-
From structure to dynamics of metabolic pathways: Application to the plant mitochondrial TCA cycle
-
R. Steuer, A. Nunes-Nesi, A. R. Fernie, T. Gross, B. Blasius, and J. Selbig, From structure to dynamics of metabolic pathways: Application to the plant mitochondrial TCA cycle. Bioinformatics 23(11), 1378-1385 (2007).
-
(2007)
Bioinformatics
, vol.23
, Issue.11
, pp. 1378-1385
-
-
Steuer, R.1
Nunes-Nesi, A.2
Fernie, A.R.3
Gross, T.4
Blasius, B.5
Selbig, J.6
-
326
-
-
77954178523
-
Stability analysis of metabolic networks
-
M. Kirkilionis, U. Kummer, and I. Stoleriu, eds., Logos Verlag, Berlin
-
I. Stoleriu, Stability analysis of metabolic networks, in M. Kirkilionis, U. Kummer, and I. Stoleriu, eds., 2nd UniNet Workshop: Data, Networks and Dynamics, Logos Verlag, Berlin, 2006.
-
(2006)
2nd UniNet Workshop: Data, Networks and Dynamics
-
-
Stoleriu, I.1
-
327
-
-
0036428761
-
Negative autoregulation speeds the response times of transcription networks
-
N. Rosenfeld, M. Elowitz, and U. Alon, Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323(5), 785-793 (2002).
-
(2002)
J. Mol. Biol.
, vol.323
, Issue.5
, pp. 785-793
-
-
Rosenfeld, N.1
Elowitz, M.2
Alon, U.3
-
328
-
-
0034102066
-
Compartimentation protects trypanosomes from the dangerous design of glycolysis
-
B. M. Bakker, F. I. C. Mensonides, B. Teusink, P. van Hoek, P. A. M. Michels, and H. V. Westerhoff, Compartimentation protects trypanosomes from the dangerous design of glycolysis. PNAS 97(5), 2087-2092 (2000).
-
(2000)
PNAS
, vol.97
, Issue.5
, pp. 2087-2092
-
-
Bakker, B.M.1
Mensonides, F.I.C.2
Teusink, B.3
van Hoek, P.4
Michels, P.A.M.5
Westerhoff, H.V.6
-
329
-
-
34347332311
-
Agenome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 ORFs and thermodynamic information
-
A. M. Feist,C. S.Henry, J. L.Reed, M.Krummenacker,A.R. Joyce, P.D.Karp, L. J. Broadbelt,V. Hatzimanikatis, and B.Ø. Palsson,Agenome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.Ø.9
-
330
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
C. S. Henry, L. J. Broadbelt, and V. Hatzimanikatis, Thermodynamics-based metabolic flux analysis. Biophys J. 92(5), 1792-1805 (2007).
-
(2007)
Biophys J
, vol.92
, Issue.5
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
332
-
-
45549087281
-
Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks
-
A. Kun, B. Papp, and E. Szathmáry, Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks. Gen. Biol. 9(3), R51 (2008).
-
(2008)
Gen. Biol.
, vol.9
, Issue.3
-
-
Kun, A.1
Papp, B.2
Szathmáry, E.3
-
333
-
-
17144409094
-
Long food chains are in general chaotic
-
T. Gross, W. Ebenhöh, and U. Feudel, Long food chains are in general chaotic. Oikos 109, 135-144 (2005).
-
(2005)
Oikos
, vol.109
, pp. 135-144
-
-
Gross, T.1
Ebenhöh, W.2
Feudel, U.3
-
334
-
-
0013770284
-
Passive stability in a metabolic network
-
H. J. Morowitz, W. A. Higinbotham, S. W. Matthysse, and H. Quastler, Passive stability in a metabolic network. J. Theor. Biol. 7(1), 98-111 (1964).
-
(1964)
J. Theor. Biol.
, vol.7
, Issue.1
, pp. 98-111
-
-
Morowitz, H.J.1
Higinbotham, W.A.2
Matthysse, S.W.3
Quastler, H.4
-
335
-
-
45849120994
-
Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
-
C.-S. Chin, V. Chubukov, E. R. Jolly, J. DeRisi, and H. Li, Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 6(6), e146 (2008).
-
(2008)
PLoS Biol
, vol.6
, Issue.6
-
-
Chin, C.-S.1
Chubukov, V.2
Jolly, E.R.3
DeRisi, J.4
Li, H.5
-
336
-
-
0034636310
-
The diversity-stability debate
-
K. S. McCann, The diversity-stability debate. Nature (insight review) 405, 228-233 (2000).
-
(2000)
Nature (insight review)
, vol.405
, pp. 228-233
-
-
McCann, K.S.1
-
337
-
-
0042526388
-
The mutual information: Detecting and evaluating dependencies between variables
-
R. Steuer, J. Kurths, C. O. Daub, J.Weise, and J. Selbig, The mutual information: Detecting and evaluating dependencies between variables. Bioinformatics 18(Suppl. 2), S231-S240 (2002).
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL 2
-
-
Steuer, R.1
Kurths, J.2
Daub, C.O.3
Weise, J.4
Selbig, J.5
-
338
-
-
0019475515
-
The regulation of glycolysis in human erythrocytes The dependence of the glycolytic flux on the ATP concentration
-
F. I. Ataullakhanov, V. M. Vitvitsky, A. M. Zhabotinsky, A. V. Pichugin, O. V. Platonova, B. N. Kholodenko, and L. I. Ehrlich, The regulation of glycolysis in human erythrocytes. The dependence of the glycolytic flux on the ATP concentration. Eur. J. Biochem. 115(2), 359-365 (1981).
-
(1981)
Eur. J. Biochem.
, vol.115
, Issue.2
, pp. 359-365
-
-
Ataullakhanov, F.I.1
Vitvitsky, V.M.2
Zhabotinsky, A.M.3
Pichugin, A.V.4
Platonova, O.V.5
Kholodenko, B.N.6
Ehrlich, L.I.7
-
339
-
-
0024593430
-
Comparison of computer simulations of the f-type and l-type non-oxidative hexose monophosphate shunts with 31PNMR experimental data from human erythrocytes
-
L. M. McIntyre, D. R. Thorburn, W. A. Bubb, and P. W. Kuchel, Comparison of computer simulations of the f-type and l-type non-oxidative hexose monophosphate shunts with 31PNMR experimental data from human erythrocytes. Eur. J. Biochem. 180(2), 399-420 (1989).
-
(1989)
Eur. J. Biochem.
, vol.180
, Issue.2
, pp. 399-420
-
-
McIntyre, L.M.1
Thorburn, D.R.2
Bubb, W.A.3
Kuchel, P.W.4
-
340
-
-
0029876941
-
Application of biochemical systems theory to metabolism in human red blood cells Signal propagation and accuracy of representation
-
T. C. Ni and M. A. Savageau, Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J. Biol. Chem. 271 (14), 7927-7941 (1996).
-
(1996)
J. Biol. Chem.
, vol.271
, Issue.14
, pp. 7927-7941
-
-
Ni, T.C.1
Savageau, M.A.2
-
341
-
-
21544479394
-
Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition
-
Y. Nakayama, A. Kinoshita, and M. Tomita, Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor. Biol. Med. Model. 2(1), 18 (2005).
-
(2005)
Theor. Biol. Med. Model.
, vol.2
, Issue.1
, pp. 18
-
-
Nakayama, Y.1
Kinoshita, A.2
Tomita, M.3
-
342
-
-
21644449850
-
Erythrocyte osmotic fragility and oxidative stress in experimental hypothyroidis
-
N. Dariyerli, S. Toplan, M. C. Akyolcu, H. Hatemi, G, and Yigit, Erythrocyte osmotic fragility and oxidative stress in experimental hypothyroidis. Endocrine 25(1), 1-5 (2004).
-
(2004)
Endocrine
, vol.25
, Issue.1
, pp. 1-5
-
-
Dariyerli, N.1
Toplan, S.2
Akyolcu, M.C.3
Hatemi, H.4
Yigit, G.5
-
344
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
R. N. Gutenkunst, J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers, and J. P. Sethna, Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3(10), 1871-78 (2007).
-
(2007)
PLoS Comput. Biol.
, vol.3
, Issue.10
, pp. 1871-1878
-
-
Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
Brown, K.S.4
Myers, C.R.5
Sethna, J.P.6
-
345
-
-
5644272615
-
Caloric restriction, metabolic rate, and entropy
-
L. Demetrius, Caloric restriction, metabolic rate, and entropy. J. Gerontol. A Biol. Sci. Med. Sci. 59(9), B902-B915 (2004).
-
(2004)
J. Gerontol. A Biol. Sci. Med. Sci.
, vol.59
, Issue.9
-
-
Demetrius, L.1
-
347
-
-
20444411533
-
The silicon cell initiative: Working towards a detailed kinetic description at the cellular level
-
J. L. Snoep, The silicon cell initiative: Working towards a detailed kinetic description at the cellular level. Curr. Opin. Biotechnol. 16, 336-343 (2005).
-
(2005)
Curr. Opin. Biotechnol.
, vol.16
, pp. 336-343
-
-
Snoep, J.L.1
-
348
-
-
35649027901
-
The virtual human: Towards a global systems biology of multiscale, distributed biochemical network models
-
D. B. Kell, The virtual human: Towards a global systems biology of multiscale, distributed biochemical network models. IUBMB Life 59(11), 689 - 695 (2007).
-
(2007)
IUBMB Life
, vol.59
, Issue.11
, pp. 689-695
-
-
Kell, D.B.1
-
349
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
N. Le Novére, A. Finney, M. Hucka, U. S. Bhalla, F. Campagne, J. Collado-Vides, E. J. Crampin, M. Halstead, E. Klipp, P. Mendes, P. Nielsen, H. Sauro, B. Shapiro, J. L. Snoep, H. D. Spence, and B. L. Wanner, Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509-1515 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1509-1515
-
-
Le Novére, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.J.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
Nielsen, P.11
Sauro, H.12
Shapiro, B.13
Snoep, J.L.14
Spence, H.D.15
Wanner, B.L.16
-
350
-
-
17444372421
-
Investigating the dynamic behavior of biochemical networks using model families
-
M. D. Haunschild, B. Freisleben, R. Takors, and W. Wiechert, Investigating the dynamic behavior of biochemical networks using model families. Bioinformatics 21(8), 1617-1625 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1617-1625
-
-
Haunschild, M.D.1
Freisleben, B.2
Takors, R.3
Wiechert, W.4
-
351
-
-
37549069325
-
MetaNetter: Inference and visualization of high-resolution metabolomic networks
-
F. Jourdan, R. Breitling, M. P. Barrett, and D. Gilbert, MetaNetter: Inference and visualization of high-resolution metabolomic networks. Bioinformatics 24(1), 143-145 (2008).
-
(2008)
Bioinformatics
, vol.24
, Issue.1
, pp. 143-145
-
-
Jourdan, F.1
Breitling, R.2
Barrett, M.P.3
Gilbert, D.4
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