Exploring the dynamics of large-scale biochemical networks: A computational perspective

Open Bioinformatics Journal

Volumn 5, Issue SPEC.ISS 1, 2011, Pages 4-15

  Steuer, Ralf ^a,b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Dynamical modeling; Metabolism; Systems biology

Indexed keywords

EID: 84859334344     PISSN: None     EISSN: 18750362     Source Type: Journal    
DOI: 10.2174/1875036201105010004     Document Type: Article

References (124)

1. A. Goldbeter, "Computational approaches to cellular rhythms", Nature, vol. 420, pp. 238-245, November 2002.
2. J. Jaeger, S. Surkova, M. Blagov, H. Janssens, D. Kosman, K. N. Kozlov, Manu, E. Myasnikova, C. E. Vanario-Alonso, M. Sam-sonova, D. H. Sharp, and J. Reinitz, "Dynamic control of positional information in the early Drosophila embryo", Nature, vol. 430, pp. 368-371, July 2004.
3. H. Meinhardt, "Computational modelling of epithelial patterning", Curr. Opin. Genet. Dev., vol. 17, pp. 272-280, August 2007.
4. R. Heinrich, B. G. Neel, and T. A. Rapoport, "Mathematical models of protein kinase signal transduction", Mol. Cell., vol. 9, pp. 957-970, May 2002.
5. D. B. Kell, "The virtual human: towards a global systems biology of multiscale, distributed biochemical network models", IUBMB Life, vol. 59, pp. 689-695, November 2007.
6. R. Steuer, "Computational approaches to the topology, stability and dynamics of metabolic networks", Phytochemistry, vol. 68, no. 16-18, pp. 2139-2151, 2007.
7. N. Jamshidi, and B. Ø. Palsson, "Formulating genome-scale kinetic models in the post-genome era", Mol. Syst. Biol., vol. 4, pp.171, 2008.
8. E. Pieroni, S. de la Fuente van Bentem, G. Mancosu, E. Capobi-anco, H. Hirt, and A. de la Fuente, "Protein networking: insights into global functional organization of proteomes", Proteomics, vol. 8, pp. 799-816, February 2008.
9. J. Schellenberger, and B. Ø. Palsson, "Use of randomized sampling for analysis of metabolic networks", J. Biol. Chem., vol. 284, pp. 5457-5461, February 2009.
10. H. V. Westerhoff, A. Kolodkin, R. Conradie, S. J. Wilkinson, F. J. Bruggeman, K. Krab, J. H. van Schuppen, H. Hardin, B. M. Bak-ker, M. J. Mon, K. N. Rybakova, M. Eijken, H. J. P. van Leeuwen, and J. L. Snoep, "Systems biology towards life in silico: mathematics of the control of living cells", J. Math. Biol., vol. 58, pp. 7-34, January 2009.
11. B. Chance, "The kinetics of the enzyme-substrate compound of peroxidase 1943", Adv. Enzymol. Relat. Areas Mol. Biol., vol. 73, pp. 3-23, 1999.
12. D. Garfinkel, L. Garfinkel, M. Pring, S. B. Green, and B. Chance, "Computer applications to biochemical kinetics", Annu. Rev. Bio-chem., vol. 39, pp. 473-498, 1970.
13. D. Garfinkel, "Simulating biochemical activity in physiological systems," Simulation, vol. 28, pp. 193-196, 1977.
14. H. Kitano, "Computational systems biology", Nature, vol. 420, pp. 206-210, November 2002.
15. J. E. Bailey, "Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities", Bio-technol. Prog., vol. 14, no. 1, pp. 8-20, 1998.
16. 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., vol. 3, pp. 1871-1878, Octuber 2007.
17. J. L. Casti, Would-be-worlds: How Simulation Is Changing the Frontiers of Science. John Wiley & Sons Inc, 1998.
18. Y. Lazebnik, "Can a biologist fix a radio?-or, what I learned while studying apoptosis" Cancer Cell., vol. 2, pp. 179-182, September 2002.
19. 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., vol. 15, pp. 221-231, 2003.
20. R. Steuer, and B. H. Junker, "Computational models of metabolism: Stability and regulation in metabolic networks," Adv. Chem. Phys., vol. 142, pp. 105-251, 2009.
21. M. A. Savageau, "Biochemical systems analysis. i. Some mathematical properties of the rate law for the component enzymatic reactions", J. Theor. Biol., vol. 25, pp. 365-369, December 1969.
22. M. A. Savageau, "Biochemical systems analysis. ii. the Steady-state solutions for an n-pool system using a power-law approximation", J. Theor. Biol., vol. 25, pp. 370-379, December 1969.
23. H. Kacser, and J. A. Burns, "The control of flux," Symp. Soc. Exp. Biol., vol. 27, pp. 65-104, 1973.
24. R. Heinrich, and T. A. Rapoport, "A linear steady-state treatment of enzymatic chains. General properties, control and effector strength", Eur. J. Biochem., vol. 42, pp. 89-95, February 1974.
25. A.-L. Barabási, and Z. N. Oltvai, "Network biology: understanding the cell's functional organization", Nat. Rev. Genet., vol. 5, pp. 101-113, February 2004.
26. S. Schuster, A. von Kamp, and M. Pachkov, "Understanding the roadmap of metabolism by pathway analysis" Methods Mol. Biol., vol. 358, pp. 199-226, 2007.
27. B.Ø. Palsson, "Metabolic systems biology", FEBS Lett., vol. 583, pp. 3900-3904, September 2009.
28. H. Knoop, Y. Zilliges, W. Lockau, and R. Steuer, "The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth", Plant Physiol., vol. 154, pp. 410-422, July 2010.
29. S. A. Kauffman, "Metabolic stability and epigenesis in randomly constructed genetic nets" J. Theor. Biol., vol. 22, pp. 437-467, March 1969.
30. S. Bornholdt, "Boolean network models of cellular regulation: prospects and limitations", J. R. Soc. Interface, vol. 5 (Suppl. 1), pp. S85-S94, August 2008.
31. B. N. Kholodenko, "Cell-signalling dynamics in time and space", Nat. Rev. Mol. Cell. Biol., vol. 7, pp. 165-176, March 2006.
32. H. H. McAdams, and A. Arkin, "It's a noisy business! Genetic regulation at the nanomolar scale", Trends Genet., vol. 15, pp. 65-69, February 1999.
33. W. J. Blake, M. Kaern, C. R. Cantor, and J. J. Collins, "Noise in eukaryotic gene expression", Nature, vol. 422, pp. 633-637, April 2003.
34. N. Maheshri, and E. K. O'Shea, "Living with noisy genes: How cells function reliably with inherent variability in gene expression", Annu. Rev. Biophys. Biomol. Struct., vol. 36, pp. 413-434, 2007.
35. A. Sackmann, M. Heiner, and I. Koch, "Application of petri net based analysis techniques to signal transduction pathways", BMC Bioinformatics, vol. 7, pp. 482, 2006.
36. R. Breitling, D. Gilbert, M. Heiner, and R. Orton, "A structured approach for the engineering of biochemical network models, illustrated for signalling pathways" Brief Bioinform., vol. 9, pp. 404-421, September 2008.
37. P. Mendes, and D. Kell, "Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation", Bioinformatics, vol. 14, no. 10, pp. 869-883, 1998.
38. I.-C. Chou, and E. O. Voit, "Recent developments in parameter estimation and structure identification of biochemical and genomic systems", Math. Biosci., vol. 219, pp. 57-83, June 2009.
39. S. Kaplan, A. Bren, A. Zaslaver, E. Dekel, and U. Alon, "Diverse two-dimensional input functions control bacterial sugar genes", Mol. Cell., vol. 29, pp. 786-792, March 2008.
40. R. Albert, "Network inference, analysis, and modeling in systems biology", Plant Cell, vol. 19, pp. 3327-3338, November 2007.
41. S. M. Assmann, and R. Albert, "Discrete dynamic modeling with asynchronous update, or how to model complex systems in the ab-sence of quantitative information" Methods Mol. Biol., vol. 553, pp. 207-225, 2009.
42. T. Gowda, S. Vrudhula, and S. Kim, "Modeling of gene regulatory network dynamics using threshold logic", Ann. N Y Acad. Sci., vol. 1158, pp. 71-81, March 2009.
43. F. Horn, and R. Jackson, "General mass action kinetics," Archiv. Ration. Mech. Anal., vol. 47, pp. 81-116, 1972.
44. M. Feinberg, and F. J. M. Horn, "Dynamics of open chemical systems and the algebraic structure of the underlying reaction network," Chem. Eng. Sci., vol. 29, no. 3, pp. 775-787, 1974.
45. G. Craciun, Y. Tang, and M. Feinberg, "Understanding bistability in complex enzyme-driven reaction networks," Proc. Natl. Acad. Sci. USA, vol. 103, pp. 8697-8702, June 2006.
46. B. L. Clarke, "Stoichiometric network analysis", Cell. Biophys., vol. 12, pp. 237-253, 1988.
47. W. Liebermeister, and E. Klipp, "Biochemical networks with uncertain parameters" Syst. Biol., (Stevenage), vol. 152, pp. 97-107, September 2005.
48. R. Steuer, T. Gross, J. Selbig, and B. Blasius, "Structural kinetic modeling of metabolic networks", Proc. Natl. Acad. Sci. USA, vol. 103, pp. 11868-11873, August 2006.
49. W. Liebermeister, and E. Klipp, "Bringing metabolic networks to life: convenience rate law and thermodynamic constraints", Theor. Biol. Med. Model., vol. 3, p. 41, 2006.
50. W. Liebermeister and E. Klipp, "Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data", Theor. Biol. Med. Model., vol. 3, p. 42, 2006.
51. R. Steuer, A. N. 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, vol. 23, pp. 1378-1385, June 2007.
52. L. Kuepfer, M. Peter, U. Sauer, and J. Stelling, "Ensemble modeling for analysis of cell signaling dynamics", Nat. Biotechnol., vol. 25, pp. 1001-1006, September 2007.
53. S. Grimbs, J. Selbig, S. Bulik, H.-G. Holzhtter, and R. Steuer, "The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks", Mol. Syst. Biol., vol. 3, p.146, 2007.
54. L. M. Tran, M. L. Rizk, and J. C. Liao, "Ensemble modeling of metabolic networks", Biophys. J., vol. 95, pp. 5606-5617, December 2008.
55. J. Schaber, W. Liebermeister, and E. Klipp, "Nested uncertainties in biochemical models", IET Syst. Biol., vol. 3, pp. 1-9, January 2009.
56. H.-M. Kaltenbach, S. Dimopoulos, and J. Stelling, "Systems analysis of cellular networks under uncertainty" FEBS Lett., vol. 583, pp. 3923-3930, October 2009.
57. J. Stelling, S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles, "Metabolic network structure determines key aspects of functionality and regulation", Nature, vol. 420, pp. 190-193, November 2002.
58. A. M. Feist, M. J. Herrgård, I. Thiele, J. L. Reed, and B. Ø. Pals-son, Reconstruction of biochemical networks in microorganisms, Nat. Rev. Microbiol., vol. 7, pp. 129-143, February 2009.
59. L. Wang, I. Birol, and V. Hatzimanikatis, "Metabolic control analysis under uncertainty: framework development and case studies", Biophys. J., vol. 87, pp. 3750-3763, December 2004.
60. K. Smallbone, E. Simeonidis, D. S. Broomhead, and D. B. Kell, "Something from nothing: bridging the gap between constraint-based and kinetic modelling", FEBS J., vol. 274, pp. 5576-5585, November 2007.
61. D. A. Adiamah, J. Handl, and J.-M. Schwartz, "Streamlining the construction of large-scale dynamic models using generic kinetic equations", Bioinformatics, vol. 26, pp. 1324-1331, May 2010.
62. 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", Syst. Biol.,(Stevenage), vol. 153, pp. 338-341, September 2006.
63. S. Bulik, S. Grimbs, C. Huthmacher, J. Selbig, and H. G. Holzhtter, "Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws-a promising method for speeding up the kinetic modelling of complex metabolic networks", FEBS J., vol. 276, pp. 410-424, January 2009.
64. F. Hadlich, S. Noack, and W. Wiechert, "Translating biochemical network models between different kinetic formats", Metab. Eng., vol. 11, pp. 87-100, March 2009.
65. A. Dräger, M. Kronfeld, M. J. Ziller, J. Supper, H. Planatscher, J. B. Magnus, M. Oldiges, O. Kohlbacher, and A. Zell, "Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies", BMC Syst. Biol., vol. 3, p. 5, 2009.
66. W. Liebermeister, J. Uhlendorf, and E. Klipp, "Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation" Bioinformatics, vol. 26, pp. 1528-1534, June 2010.
67. R. A. Alberty, Thermodynamics of Biochemical Reactions. New York: John Wiley & Sons, Inc., 2003.
68. R. N. Goldberg, Y. B. Tewari, and T. N. Bhat, "Thermodynamics of enzyme-catalyzed reactions-a database for quantitative biochemistry", Bioinformatics, vol. 20, pp. 2874-2877, November 2004.
69. C. S. Henry, M. D. Jankowski, L. J. Broadbelt, and V. Hatzimani-katis, "Genome-scale thermodynamic analysis of Escherichia coli metabolism", Biophys. J., vol. 90, pp. 1453-1461, February 2006.
70. 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, "A genome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 ORFs and thermodynamic information", Mol. Syst. Biol., vol. 3, p. 121, 2007.
71. M. D. Jankowski, C. S. Henry, L. J. Broadbelt, and V. Hatzimani-katis, "Group contribution method for thermodynamic analysis of complex metabolic networks", Biophys. J., vol. 95, pp. 1487-1499, August 2008.
72. I. Rojas, M. Golebiewski, R. Kania, O. Krebs, S. Mir, A. Weide-mann, and U. Wittig, "Storing and annotating of kinetic data", In Silico. Biol., vol. 7, no. 2, pp. S37-S44, 2007.
73. A. Chang, M. Scheer, A. Grote, I. Schomburg, and D. Schomburg, "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009", Nucleic Acids Res., vol. 37, pp. D588-D592, January 2009.
74. I. Spasic, E. Simeonidis, H. L. Messiha, N. W. Paton, and D. B. Kell, "Kipar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways", Bioinformatics, vol. 25, pp. 1404-1411, June 2009.
75. Y. Gibon, O. E. Blaesing, J. Hannemann, P. Carillo, M. Höhne, 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, vol. 16, pp. 3304-3325, December 2004.
76. S. Borger, W. Liebermeister, J. Uhlendorf, and E. Klipp, "Automatically generated model of a metabolic network", Genome Inform, vol. 18, pp. 215-224, 2007.
77. 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, vol. 68, no. 16-18, pp. 2232-2242, 2007.
78. S. Sahle, P. Mendes, S. Hoops, and U. Kummer, "A new strategy for assessing sensitivities in biochemical models" Philos. Transact. A. Math. Phys. Eng. Sci., vol. 366, pp. 3619-3631, October 2008.
79. O. Fiehn, "Combining genomics, metabolome analysis, and bio chemical modelling to understand metabolic networks", Comp. Funct. Genomics, vol. 2, no. 3, pp. 155-168, 2001.
80. D. B. Kell, "Metabolomics and systems biology: making sense of the soup", Curr. Opin. Microbiol., vol. 7, pp. 296-307, June 2004.
81. R. Goodacre, S. Vaidyanathan, W. B. Dunn, G. G. Harrigan, and D. B. Kell, "Metabolomics by numbers: acquiring and understanding global metabolite data", Trends Biotechnol., vol. 22, pp. 245-252, May 2004.
82. U. Sauer, "Metabolic networks in motion: 13C-based flux analysis", Mol. Syst. Biol., vol. 2, p. 62, 2006.
83. N. Zamboni, and U. Sauer, "Novel biological insights through metabolomics and 13c-flux analysis", Curr. Opin. Microbiol., vol. 12, pp. 553-558, October 2009.
84. N. Zamboni, S.-M. Fendt, M. Rhl, and U. Sauer, "(13) C-based metabolic flux analysis", Nat. Protoc., vol. 4, no. 6, pp. 878-892, 2009.
85. N. J. Kruger, and R. G. Ratcliffe, "Insights into plant metabolic networks from steady-state metabolic flux analysis", Biochimie, vol. 91, pp. 697-702, June 2009.
86. N. Ishii, K. Nakahigashi, T. Baba, M. Robert, T. Soga, A. Kanai, T. Hirasawa, M. Naba, K. Hirai, A. Hoque, P. Y. Ho, Y. Kakazu, K. Sugawara, S. Igarashi, S. Harada, T. Masuda, N. Sugiyama, T. To-gashi, M. Hasegawa, Y. Takai, K. Yugi, K. Arakawa, N. Iwata, Y. Toya, Y. Nakayama, T. Nishioka, K. Shimizu, H. Mori, and M. Tomita, "Multiple high-throughput analyses monitor the response of E. coli to perturbations", Science, vol. 316, pp. 593-597, April 2007.
87. B. D. Bennett, E. H. Kimball, M. Gao, R. Osterhout, S. J. V. Dien, and J. D. Rabinowitz, "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli", Nat. Chem. Biol., vol. 5, pp. 593-599, August 2009.
88. T. Gross and U. Feudel, "Generalized models as a universal approach to the analysis of nonlinear dynamical systems", Phys. Rev. E. Stat. Nonlin. Soft. Matter. Phys., vol. 73, p. 016205, January 2006.
89. A. Mogilner, R. Wollman, and W. F. Marshall, "Quantitative modeling in cell biology: what is it good for?," Dev. Cell., vol. 11, pp. 279-287, September 2006.
90. 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. L. Novère, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Saku-rada, 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, vol. 19, pp. 524-531, March 2003.
91. N. L. Novere, 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., vol. 23, pp. 1509-1515, December 2005.
92. N. L. Novre, 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., vol. 34, pp. D689-D691, January 2006.
93. C. van Gend, and J. L. Snoep, "Systems biology model databases and resources", Essays Biochem., vol. 45, pp. 223-236, 2008.
94. H.M. Sauro, and F. T. Bergmann, "Standards and ontologies in computational systems biology" Essays Biochem., vol. 45, pp. 211-222, 2008.
95. L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, and N. L. Novre, "Designing and encoding models for synthetic biology", J. R. Soc. Interface, vol. 6, (Suppl. 4), pp. S405-S417, August 2009.
96. B. G. Olivier, and J. L. Snoep, "Web-based kinetic modelling using JWS online", Bioinformatics, vol. 20, pp. 2143-2144, September 2004.
97. 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, vol. 22, pp. 3067-3074, December 2006.
98. P. Mendes, S. Hoops, S. Sahle, R. Gauges, J. Dada, and U. Kum-mer, "Computational modeling of biochemical networks using Co-pasi", Methods Mol. Biol., vol. 500, pp. 17-59, 2009.
99. A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gab-doulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade, and U. Kummer, "Sycamore-a systems biology computational analysis and modeling research environment", Bioinformat-ics, vol. 24, pp. 1463-1464, June 2008.
100. S. Mirschel, K. Steinmetz, M. Rempel, M. Ginkel, and E. D. Gilles, "PROMOT: modular modeling for systems biology", Bioinformat-ics, vol. 25, pp. 687-689, March 2009.
101. M. Arita, "The metabolic world of Escherichia coli is not small", Proc. Natl. Acad. Sci. USA, vol. 101, pp. 1543-1547, February 2004.
102. K. Nakahigashi, Y. Toya, N. Ishii, T. Soga, M. Hasegawa, H. Wa-tanabe, Y. Takai, M. Honma, H. Mori, and M. Tomita, "Systematic phenome analysis of escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism", Mol. Syst. Biol., vol. 5, p. 306, 2009.
103. A. de la Fuente and P. Mendes, "Integrative modelling of gene expression and cell metabolism", Appl. Bioinformatics, vol. 2, no. 2, pp. 79-90, 2003.
104. E. Klipp, B. Nordlander, R. Krüger, P. Gennemark, and S. Hohmann, "Integrative model of the response of yeast to osmotic shock", Nat. Biotechnol., vol. 23, pp. 975-982, August 2005.
105. M. W. Covert, N. Xiao, T. J. Chen, and J. R. Karr, "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli", Bioinformatics, vol. 24, pp. 2044-2050, September 2008.
106. J. Kovac, J. Husse, and H. Oster, "A time to fast, a time to feast: the crosstalk between metabolism and the circadian clock", Mol. Cells, vol. 28, pp. 75-80, August 2009.
107. C. B. Green, J. S. Takahashi, and J. Bass, "The meter of metabolism", Cell, vol. 134, pp. 728-742, September 2008.
108. R. R. Klevecz, J. Bolen, G. Forrest, and D. B. Murray, "A ge-nomewide oscillation in transcription gates DNA replication and cell cycle", Proc. Natl. Acad. Sci. USA, vol. 101, pp. 1200-1205, February 2004.
109. D. Lloyd, and D. B. Murray, "The temporal architecture of eukary-otic growth", FEBS Lett., vol. 580, pp. 2830-2835, May 2006.
110. B. P. Tu, and S. L. McKnight, "Metabolic cycles as an underlying basis of biological oscillations", Nat. Rev. Mol. Cell. Biol., vol. 7, pp. 696-701, September 2006.
111. D. B. Murray, M. Beckmann, and H. Kitano, "Regulation of yeast oscillatory dynamics", Proc. Natl. Acad. Sci. USA, vol. 104, pp. 2241-2246, February 2007.
112. B. P. Tu, R. E. Mohler, J. C. Liu, K. M. Dombek, E. T. Young, R. E. Synovec, and S. L. McKnight, "Cyclic changes in metabolic state during the life of a yeast cell", Proc. Natl. Acad. Sci. USA, vol. 104, pp. 16886-16891, October 2007.
113. B. Teusink, M. C. Walsh, K. van Dam, and H. V. Westerhoff, "The danger of metabolic pathways with turbo design", Trends Biochem. Sci., vol. 23, pp. 162-169, May 1998.
114. R. Scheibe, J. E. Backhausen, V. Emmerlich, and S. Holtgrefe, "Strategies to maintain redox homeostasis during photosynthesis under changing conditions", J. Exp. Bot., vol. 56, pp. 1481-1489, June 2005.
115. R. J. Prill, P. A. Iglesias, and A. Levchenko, "Dynamic properties of network motifs contribute to biological network organization", PLoS Biol., vol. 3, p. e343, November 2005.
116. E. Voit, A. R. Neves, and H. Santos, "The intricate side of systems biology", Proc. Natl. Acad. Sci. USA, vol. 103, pp. 9452-9457, June 2006.
117. A. Ma'ayan, G. A. Cecchi, J. Wagner, A. R. Rao, R. Iyengar, and G. Stolovitzky, "Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks", Proc. Natl. Acad. Sci. USA, vol. 105, pp. 19235-19240, December 2008.
118. J. R. Haanstra, A. van Tuijl, P. Kessler, W. Reijnders, P. A. M. Michels, H. V. Westerhoff, M. Parsons, and B. M. Bakker, "Com-partmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes", Proc. Natl. Acad. Sci. USA, vol. 105, pp. 17718-17723, November 2008.
119. P. Morandini, "Rethinking metabolic control," Plant Sci., vol. 176, pp. 441-451, 2009.
120. V. Baldazzi, D. Ropers, Y. Markowicz, D. Kahn, J. Geiselmann, and H. de Jong, "The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes", PLoS Comput. Biol., vol. 6, no. 6, p. e1000812, 2010.
121. S. Goyal, J. Yuan, T. Chen, J. D. Rabinowitz, and N. S. Wingreen, "Achieving optimal growth through product feedback inhibition in metabolism", PLoS Comput. Biol., vol. 6, no. 6, p. e1000802, 2010.
122. T. Pfeiffer, S. Schuster, and S. Bonhoeffer, "Cooperation and competition in the evolution of ATP-producing pathways", Science, vol. 292, pp. 504-507, April 2001.
123. B. Papp, B. Teusink, and R. A. Notebaart, "A critical view of metabolic network adaptations", HFSP J., vol. 3, pp. 24-35, February 2009.
124. D. Molenaar, R. van Berlo, D. de Ridder, and B. Teusink, "Shifts in growth strategies reflect tradeoffs in cellular economics", Mol. Syst. Biol., vol. 5, p. 323, 2009.