Response to temporal parameter fluctuations in biochemical networks

Journal of Theoretical Biology

Volumn 234, Issue 3, 2005, Pages 423-438

  Liebermeister, Wolfram ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Correlated fluctuations; Fourier analysis; Metabolic control analysis; Mode coupling; Resonance; Response coefficient

Indexed keywords

METABOLISM; PHYSIOLOGICAL RESPONSE;

AMPLITUDE MODULATION; ARTICLE; BIOINFORMATICS; CHEMICAL ANALYSIS; CHEMICAL REACTION; CONCENTRATION (PARAMETERS); GLYCOLYSIS; KINETICS; MATHEMATICAL ANALYSIS; OSCILLATION; PARAMETER; PRIORITY JOURNAL; RAMAN SPECTROMETRY; SEASONAL VARIATION; STEADY STATE; STOCHASTIC MODEL; THEORY;

EID: 15244357543     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.12.010     Document Type: Article

References (23)

1. F. Bruggeman, H.V. Westerhoff, J.B. Hoek, and B. Kholodenko Modular response analysis of cellular regulatory networks J. Theor. Biol. 218 2002 507 520
2. O.V. Demin, H.V. Westerhoff, and B.N. Kholodenko Control analysis of stationary forced oscillations J. Phys. Chem. 103 1999 10,695 10,710
3. D.A. Fell Metabolic control analysis a survey of its theoretical and experimental development Biochem. J. 286 1992 313 330
4. D.T. Gillespie Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 1977 2340 2361
5. D.T. Gillespie The chemical Langevin equation J. Chem. Phys. 113 1 2000 297 306
6. R. Heinrich, and C. Reder Metabolic control analysis of relaxation processes J. Theor. Biol. 151 1991 343 350
7. R. Heinrich, and S. Schuster The Regulation of Cellular Systems 1996 Chapman & Hall London
8. T. Höfer, and R. Heinrich A second-order approach to metabolic control analysis J. Theor. Biol 164 1993 85 102
9. Hofmeyer, J.S., 2001. Metabolic control analysis in a nutshell. In: ICSB 2001 Online Proceedings, http://www.icsb2001.org/toc.html.
10. F. Hynne, S. Danø, and P.G. Sørensen Full-scale model of glycolysis in Saccharomyces cerevisiae Biophys. Chem. 94 2001 121 163
11. B.P. Ingalls A frequency domain approach to sensitivity analysis of biochemical systems J. Phys. Chem. B 108 2004 1143 1152
12. B.P. Ingalls, and H.M. Sauro Sensitivity analysis of stoichiometric networks an extension of metabolic control analysis to non-steady state trajectories J. Theor. Biol. 222 1 2003 23 36
13. H.W. Knobloch, and H. Kwakernaak Lineare Kontrolltheorie 1985 Springer Berlin
14. Liebermeister, W., 2004. Analysis of optimal differential gene expression. Ph.D. Thesis, Humboldt-Universität zu Berlin.
15. H. McAdams, and A. Arkin Stochastic mechanisms in gene expression PNAS 94 1997 814
16. L. Nedbal Negative feedback regulation is responsible for the non-linear modulation of photosynthetic activity in plants and cyanobacteria exposed to a dynamic light environment Biochim. Biophys. Acta 1607 2003 5 17
17. B. Olivier, and J. Snoep Web-based kinetic modelling using jws online Bioinformatics 20 13 2004 2143 2144
18. C. Reder Metabolic control a structural approach J. Theor. Biol. 135 1988 175 201
19. K.A. Reijenga, H.V. Westerhoff, B. Kholodenko, and J.K. Snoep Control analysis for autonomously oscillating biochemical networks Biophys. J. 82 2002 99 108
20. I. Rojdestvenski, and M.G. Cottam Diagrammatic approach to the fluctuation correlation matrix in a metabolic system Biosystems 56 2000 63 73
21. R. Steuer, J. Kurths, O. Fiehn, and W. Weckwerth Observing and interpreting correlations in metabolomics networks Bioinformatics 19 8 2003 1019 1026
22. M. Thattai, and A. van Oudenaarden Intrinsic noise in gene regulatory networks PNAS 98 15 2001 8614 8619
23. T. Wilhelm, and R. Heinrich The smallest chemical reaction systems with Hopf-bifurcation J. Math. Chem. 17 1995 1 14