Determining interconnections in chemical reaction networks

Proceedings of the American Control Conference

Volumn , Issue , 2007, Pages 4872-4877

  Papachristodoulou, Antonis ^a   Recht, Ben ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADDITION REACTIONS; CHEMICAL REACTIONS; NEWTONIAN FLOW; RATE CONSTANTS; REACTION RATES; TIME SERIES ANALYSIS;

CHEMICAL REACTION NETWORKS; DECISION VARIABLE (DV); GENERAL MODEL; MASS-ACTION KINETICS; REACTION NETWORKS; TIME SERIES DATA;

REACTION KINETICS;

EID: 46449093079     PISSN: 07431619     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ACC.2007.4283084     Document Type: Conference Paper

References (23)

1. L. El Ghaoui and H. Lebret, "Robust solutions to least-squares problems with uncertain data," SIAM J. MATRIX ANAL. APPL., vol. 18, no. 4, pp. 1035-1064, 1997.
2. E. J. Crampin, S. Schnell, and P. E. McSharry, "Mathematical and computational techniques to deduce complex biochemical reaction mechanisms," Progress in Biophysics and Molecular Biology, vol. 86, pp. 77-112, 2004.
3. J. Ross, I. Schreiber, and M. O. Vlad, Determination of Complex Reaction Mechanisms: Analysis of Chemical, Biological and Genetic Networks. Oxford University Press, Inc., 2006.
4. T. Chevalier, I. Schreiber, and J. Ross, "Toward a systematic determination of complex reaction mechanisms," J. Phys. Chem., vol. 97, no. 26, pp. 6776-6787, 1993.
5. B. N. Kholodenko, A. Kiyatkin, F. J. Bruggeman, E. D. Sontag, H. V. Westerhoff, and J. B. Hoek, "Untangling the wires: A strategy to trace functional interactions in signalling and gene networks," Proceedings of the National Academy of Sciences, vol. 99, no. 20, pp. 12841-12846, 2002.
6. B. N. Kholodenko and E. D. Sontag, "Determination of functional network structure from local parameter dependence data," 2002. oai:arXiv.org:physics/0205003.
7. W. Vance, A. Arkin, and J. Ross, "Determination of causal connectivities of species in random networks," Proceedings of the National Academy of Sciences, vol. 99, no. 9, pp. 5816-5821, 2002.
8. A. Arkin, P. D. Shen, and J. Ross, "A test case of correlation metric construction of a reaction pathway from measurements," Science, vol. 277, pp. 1275-1279, 1997.
9. J. S. Almeida, "Predictive non-linear modeling of complex data by artificial neural networks," Current Option in Biotechnology, vol. 13, pp. 72-76, 2002.
10. M. Wahde and J. Hertz, "Coarse-grained reverse engineering of genetic regulatory networks," Biosystems, vol. 55, pp. 129-136, 2000.
11. M. K. Stephen Yeung, J. Tegnér, and J. J. Collins, "Reverse engineering gene networks using singular value decomposition and robust regression," Proceedings of the National Academy of Sciences, vol. 99, no. 9, pp. 6163-6168, 2002.
12. F. J. Doyle III, R. K. Pearson, and B. Ogunnaike, Identification and Control of Process Systems Using Volterra Models. Springer, 2001.
13. M. Feinberg, "Lectures on chemical reaction networks," 1979. Lectures delivered at the Mathematics Research Center, University of Wisconsin-Madison.
14. J. I. Yuz and G. C. Goodwin, "On sampled-data models for nonlinear systems," IEEE Transactions on Automatic Control, vol. 50, no. 10, pp. 1477-1485, 2005.
15. L. Ljung, System Identification: Theory for the User. Information and System Sciences, Prentice Hall, Inc., second ed., 1999.
16. S. Boyd and L. Vandenberghe, Convex Optimization. Cambridge University Press, 2004.
17. A. L. Soyster, "Convex programming with set-inclusive constraints and applications to inexact linear programming," Operations Research, vol. 21, pp. 1154-1157, 1973.
18. D. Bertsimas and M. Sim, "The price of robustness," Operations Research, vol. 52, no. 1, pp. 35-53, 2004.
19. A. Papachristodoulou and H. El-Samad, "Algorithms for discriminating between biochemical reaction network models: Towards systematic experimental design," in Proceedings of the American Control Conference, 2007.
20. S. Prajna, "Barrier certificates for nonlinear model validation," Automatica, vol. 42, no. 1, pp. 117-126, 2006.
21. M. A. Savageau, "Biochemical systems analysis: I. some mathematical properties of the rate law for the component enzymatic reactions," Journal of Theoretical Biology, vol. 25, pp. 365-369, 1969.
22. M. A. Savageau, "Biochemical systems analysis: I. the steady-state solutions for an n-pool system using a power law approximation," Journal of Theoretical Biology, vol. 25, pp. 370-379, 1969.
23. E. O. Voit, Computational analysis of biochemical systems: a practical guide for biochemists and molecular biologists. Cambridge University Press, 2000.