-
1
-
-
0033665572
-
Extending the method of mathematically controlled comparison to include numerical comparisons
-
Alves, R., Savageau, M.A., 2000. Extending the method of mathematically controlled comparison to include numerical comparisons. Bioinformatics 16(9), 786-798.
-
(2000)
Bioinformatics
, vol.16
, Issue.9
, pp. 786-798
-
-
Alves, R.1
Savageau, M.A.2
-
2
-
-
19744368117
-
Dynamic optimization of bioprocesses: Efficient and robust numerical strategies
-
Banga, J., Balsa-Canto, E., Moles, C., Alonso, A., 2005. Dynamic optimization of bioprocesses: Efficient and robust numerical strategies. J. Biotechnol. 117, 407-419.
-
(2005)
J. Biotechnol.
, vol.117
, pp. 407-419
-
-
Banga, J.1
Balsa-Canto, E.2
Moles, C.3
Alonso, A.4
-
3
-
-
33748049452
-
Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states
-
Bilu, Y., Shlomi, T., Barkai, N., Ruppin, E., 2006. Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput. Biol. 2(8), 932-938.
-
(2006)
PLoS Comput. Biol.
, vol.2
, Issue.8
, pp. 932-938
-
-
Bilu, Y.1
Shlomi, T.2
Barkai, N.3
Ruppin, E.4
-
4
-
-
0026050621
-
Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells
-
Brown, G., 1991. Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells. J. Theor. Biol. 153, 195-203.
-
(1991)
J. Theor. Biol.
, vol.153
, pp. 195-203
-
-
Brown, G.1
-
5
-
-
84988041993
-
Timing is everything
-
Campbell, N., 2004. Timing is everything. Nat. Rev. Genet. 5, 405.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 405
-
-
Campbell, N.1
-
6
-
-
18844380444
-
Robustness and fragility of Boolean models for genetic regulatory network
-
Chaves, M., Albert, R., Sontag, E., 2005. Robustness and fragility of Boolean models for genetic regulatory network. J. Theor. Biol. 235, 431-449.
-
(2005)
J. Theor. Biol.
, vol.235
, pp. 431-449
-
-
Chaves, M.1
Albert, R.2
Sontag, E.3
-
9
-
-
0030574071
-
Control analysis of unbranched enzymatic chains in states of maximal activity
-
Heinrich, R., Klipp, E., 1996. Control analysis of unbranched enzymatic chains in states of maximal activity. J. Theor. Biol. 182, 242-252.
-
(1996)
J. Theor. Biol.
, vol.182
, pp. 242-252
-
-
Heinrich, R.1
Klipp, E.2
-
11
-
-
0025923478
-
Mathematical analysis of enzymatic reaction systems using optimization principles
-
Heinrich, R., Schuster, S., Holzhütter, H.G., 1991. Mathematical analysis of enzymatic reaction systems using optimization principles. Eur. J. Biochem. 201, 1-21.
-
(1991)
Eur. J. Biochem.
, vol.201
, pp. 1-21
-
-
Heinrich, R.1
Schuster, S.2
Holzhütter, H.G.3
-
12
-
-
3242795003
-
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
-
Holzhütter, H.-G., 2004. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 271, 2905-2922.
-
(2004)
Eur. J. Biochem.
, vol.271
, pp. 2905-2922
-
-
Holzhütter, H.-G.1
-
13
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
Ibarra, R., Edwards, J., Palsson, B., 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-189.
-
(2002)
Nature
, vol.420
, pp. 186-189
-
-
Ibarra, R.1
Edwards, J.2
Palsson, B.3
-
14
-
-
0035875010
-
Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
-
Kalir, S., McClure, J., Pabbaraju, K., Southward, C., Ronen, M., Leibler, S., Surette, M.G., Alon, U., 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292, 2080-2083.
-
(2001)
Science
, vol.292
, pp. 2080-2083
-
-
Kalir, S.1
McClure, J.2
Pabbaraju, K.3
Southward, C.4
Ronen, M.5
Leibler, S.6
Surette, M.G.7
Alon, U.8
-
15
-
-
0032729822
-
Competition for enzymes in metabolic pathways: Implications for optimal distributions of enzyme concentrations and for the distribution of flux control
-
Klipp, E., Heinrich, R., 1999. Competition for enzymes in metabolic pathways: Implications for optimal distributions of enzyme concentrations and for the distribution of flux control. Biosystems 54, 1-14.
-
(1999)
Biosystems
, vol.54
, pp. 1-14
-
-
Klipp, E.1
Heinrich, R.2
-
16
-
-
0036441029
-
Prediction of temporal gene expression: Metabolic optimization by re-distribution of enzyme activities
-
Klipp, E., Heinrich, R., Holzhütter, H.G., 2002. Prediction of temporal gene expression: Metabolic optimization by re-distribution of enzyme activities. Eur. J. Biochem. 269, 5406-5413.
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 5406-5413
-
-
Klipp, E.1
Heinrich, R.2
Holzhütter, H.G.3
-
17
-
-
84889389880
-
-
New York: Wiley-Vch
-
Klipp, E., Herwig, R., Kowald, A., Wierling, C., Lehrach, H., 2005. Systems Biology in Practice: Concepts, Implementation and Application. Wiley-Vch, New York.
-
(2005)
Systems Biology in Practice: Concepts, Implementation and Application
-
-
Klipp, E.1
Herwig, R.2
Kowald, A.3
Wierling, C.4
Lehrach, H.5
-
18
-
-
33749651702
-
Time ordering of gene coexpression
-
Leng, X., Müller, H.-G., 2006. Time ordering of gene coexpression. Biostatistics 7(4), 569-584.
-
(2006)
Biostatistics
, vol.7
, Issue.4
, pp. 569-584
-
-
Leng, X.1
Müller, H.-G.2
-
19
-
-
0342901749
-
Generalization of the theory of transition times in metabolic pathways: A geometrical approach
-
Llorens, M., Nuno, J., Rodriguez, Y., Melendez-Hevia, E., Montero, F., 1999. Generalization of the theory of transition times in metabolic pathways: A geometrical approach. Biophys. J. 77, 22-36.
-
(1999)
Biophys. J.
, vol.77
, pp. 22-36
-
-
Llorens, M.1
Nuno, J.2
Rodriguez, Y.3
Melendez-Hevia, E.4
Montero, F.5
-
20
-
-
0036708443
-
Dynamic flux balance analysis of diauxic growth in Escherichia coli
-
Mahadevan, R., Edwards, J., Doyle, F., 2002. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83, 1331-1340.
-
(2002)
Biophys. J.
, vol.83
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.2
Doyle, F.3
-
21
-
-
0025317877
-
A generalization of metabolic control analysis to conditions of no proportionality between activity and concentrations of enzymes
-
Meléndez-Hevia, E., Torres, N., Sicilia, J., 1990. A generalization of metabolic control analysis to conditions of no proportionality between activity and concentrations of enzymes. J. Theor. Biol. 142, 443-451.
-
(1990)
J. Theor. Biol.
, vol.142
, pp. 443-451
-
-
Meléndez-Hevia, E.1
Torres, N.2
Sicilia, J.3
-
22
-
-
34447557916
-
Principles of optimal network operation
-
Nielsen, J., 2007. Principles of optimal network operation. Mol. Syst. Biol. 3(126), 00-00.
-
(2007)
Mol. Syst. Biol.
, vol.3
, Issue.126
, pp. 00-00
-
-
Nielsen, J.1
-
23
-
-
38349120985
-
Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells
-
Ou, J., Yamada, T., Nagahis, K., Hirasawa, T., Furusawa, C., Yomo, T., Shimizu, H., 2008. Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells. Mol. Biosyst. 4, 128-134.
-
(2008)
Mol. Biosyst.
, vol.4
, pp. 128-134
-
-
Ou, J.1
Yamada, T.2
Nagahis, K.3
Hirasawa, T.4
Furusawa, C.5
Yomo, T.6
Shimizu, H.7
-
24
-
-
70350391935
-
Optimal metabolic regulation by time varying enzyme activities: A control theoretic approach
-
Stuttgart, Germany
-
Oyarzún, D., Ingalls, B., Kalamatianos, D., 2007. Optimal metabolic regulation by time varying enzyme activities: A control theoretic approach. In: Proceedings of Foundations of Systems Biology & Engineering, Stuttgart, Germany.
-
(2007)
Proceedings of Foundations of Systems Biology & Engineering
-
-
Oyarzún, D.1
Ingalls, B.2
Kalamatianos, D.3
-
25
-
-
0003716450
-
-
(transl. by K.M. Tririgoff), Wiley: New York
-
Pontryagin, L.S., Boltyanskii, V., Gamkrelidze, R., Mischenko, F., 1962. The Mathematical Theory of Optimal Processes. New York, Wiley (transl. by K.M. Tririgoff).
-
(1962)
The Mathematical Theory of Optimal Processes
-
-
Pontryagin, L.S.1
Boltyanskii, V.2
Gamkrelidze, R.3
Mischenko, F.4
-
26
-
-
64849106540
-
PROPT-Matlab Optimal Control Software
-
260 SE Bishop Blvd Ste E, Pullman, WA 99163, USA, February 2009
-
Rutquist, P., Edvall, M., (2009) PROPT-Matlab Optimal Control Software, Tomlab Optimization Inc., 260 SE Bishop Blvd Ste E, Pullman, WA 99163, USA, February 2009.
-
(2009)
Tomlab Optimization Inc.
-
-
Rutquist, P.1
Edvall, M.2
-
27
-
-
0016201107
-
Optimal design of feedback control by inhibition: Steady state considerations
-
Savageau, M.A., 1974. Optimal design of feedback control by inhibition: Steady state considerations. J. Mol. Evol. 4, 139-156.
-
(1974)
J. Mol. Evol.
, vol.4
, pp. 139-156
-
-
Savageau, M.A.1
-
28
-
-
0016788494
-
Optimal design of feedback control by inhibition: Dynamic considerations
-
Savageau, M.A., 1975. Optimal design of feedback control by inhibition: Dynamic considerations. J. Mol. Evol. 5(3), 199-222.
-
(1975)
J. Mol. Evol.
, vol.5
, Issue.3
, pp. 199-222
-
-
Savageau, M.A.1
-
30
-
-
0021776306
-
A theory of alternative designs for biochemical control systems
-
Savageau, M.A., 1985. A theory of alternative designs for biochemical control systems. Biomed. Biochim. Acta 44(6), 875-880.
-
(1985)
Biomed. Biochim. Acta
, vol.44
, Issue.6
, pp. 875-880
-
-
Savageau, M.A.1
-
31
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
Schuetz, R., Kuepfer, L., Sauer, U., 2007. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
32
-
-
43449132092
-
Is maximization of molar yield in metabolic networks favoured by evolution?
-
Schuster, S., Pfeiffer, T., Fell, D., 2008. Is maximization of molar yield in metabolic networks favoured by evolution? J. Theor. Biol. 252(3), 497-504.
-
(2008)
J. Theor. Biol.
, vol.252
, Issue.3
, pp. 497-504
-
-
Schuster, S.1
Pfeiffer, T.2
Fell, D.3
-
33
-
-
0028470795
-
Application of the transition time of metabolic systems as a criterion for optimization of metabolic processes
-
Torres, N., 1994. Application of the transition time of metabolic systems as a criterion for optimization of metabolic processes. Biotechnol. Bioeng. 44, 291-296.
-
(1994)
Biotechnol. Bioeng.
, vol.44
, pp. 291-296
-
-
Torres, N.1
-
35
-
-
33846067658
-
DFBA-LQR: An optimal control approach to flux balance analysis
-
Uygun, K., Matthew, H., Huang, Y., 2006. DFBA-LQR: An optimal control approach to flux balance analysis. Ind. Eng. Chem. Res. 45, 8554-8564.
-
(2006)
Ind. Eng. Chem. Res.
, vol.45
, pp. 8554-8564
-
-
Uygun, K.1
Matthew, H.2
Huang, Y.3
-
36
-
-
0033926217
-
Dynamic optimal control of homeostasis: An integrative systems approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae
-
van Riel, N., Giuseppin, M., Verrips, C., 2000. Dynamic optimal control of homeostasis: An integrative systems approach for modeling of the central nitrogen metabolism in Saccharomyces cerevisiae. Metab. Eng. 2, 14-33.
-
(2000)
Metab. Eng.
, vol.2
, pp. 14-33
-
-
van Riel, N.1
Giuseppin, M.2
Verrips, C.3
-
37
-
-
0028108519
-
Metabolic flux balancing-basic concepts, scientific and practical use
-
Varma, A., Palsson, B., 1994. Metabolic flux balancing-basic concepts, scientific and practical use. Bio-Technology 12(10), 994-998.
-
(1994)
Bio-Technology
, vol.12
, Issue.10
, pp. 994-998
-
-
Varma, A.1
Palsson, B.2
-
38
-
-
0033005128
-
Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries
-
Varner, J., Ramkrishna, D., 1999. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 15, 407-425.
-
(1999)
Biotechnol. Prog.
, vol.15
, pp. 407-425
-
-
Varner, J.1
Ramkrishna, D.2
-
39
-
-
0037899231
-
Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae
-
Vera, J., de Atauri, P., Cascante, M., Torres, N., 2003. Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae. Biotechnol. Bioeng. 83, 335-343.
-
(2003)
Biotechnol. Bioeng.
, vol.83
, pp. 335-343
-
-
Vera, J.1
de Atauri, P.2
Cascante, M.3
Torres, N.4
-
40
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
Zaslaver, A., Mayo, A., Rosenberg, R., Bashkin, P., Sberro, H., Tsalyuk, M., Surette, M., Alon, U., 2004. Just-in-time transcription program in metabolic pathways. Nat. Genet. 36(5), 486-491.
-
(2004)
Nat. Genet.
, vol.36
, Issue.5
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.2
Rosenberg, R.3
Bashkin, P.4
Sberro, H.5
Tsalyuk, M.6
Surette, M.7
Alon, U.8
|