Parameter estimation in biochemical systems models with alternating regression

Theoretical Biology and Medical Modelling

Volumn 3, Issue , 2006, Pages

  Chou, I Chun ^a   Martens, Harald ^b   Voit, Eberhard O ^a  

^a Emory University   (United States)

^b NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL MODEL; KINETICS; LINEAR REGRESSION ANALYSIS; REGRESSION ANALYSIS; BIOLOGICAL MODEL; BIOLOGY; STATISTICAL MODEL; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; LINEAR MODELS; MODELS, BIOLOGICAL; MODELS, THEORETICAL;

EID: 33749340654     PISSN: 17424682     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-3-25     Document Type: Article

References (26)

1. Savageau MA: Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 1969, 25:365-369.
2. Savageau MA: Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol 1969, 25:370-379.
3. Savageau MA: Biochemical systems analysis. A study of function and design in molecular biology. Reading, MA, Addison-Wesley; 1976:xvii, 379.
4. Voit EO: Computational analysis of biochemical systems: a practical guide for biochemists and molecular biologists. Cambridge, U.K., Cambridge University Press; 2000:xii, 531.
5. Voit EO, Almeida JS: Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 2004, 20:1670-1681.
6. Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M: Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 2003, 19:643-650.
7. Voit EO: Canonical nonlinear modeling : S-system approach to understanding complexity. New York, Van Nostrand Reinhold; 1991:xii, 365.
8. Torres NV, Voit EO: Pathway analysis and optimization in metabolic engineering. Cambridge, U.K., Cambridge University Press; 2002:xiv, 305.
9. Voit EO, Savageau MA: Power-Law Approach to Modeling Biological-Systems. 3. Methods of Analysis. J Ferment Technol 1982, 60:233-241.
10. de Boor C: A practical guide to splines. In Applied mathematical sciences: 27 New York, Springer-Verlag; 1978:xxiv, 392.
11. de Boor C, Höllig K, Riemenschneider SD: Box splines. In Applied mathematical sciences ; v 98 New York; Hong Kong, Springer-Verlag; 1993:xvii, 200.
12. Green PJ, Silverman BW: Nonparametric regression and generalized linear models: a roughness penalty approach. In Monographs on statistics and applied probability ; 58 1st edition. London; New York, Chapman & Hall; 1994:ix, 182.
13. Seatzu C: A fitting based method for parameter estimation in S-systems. Dynam Systems Appl 2000, 9:77-98.
14. Burden RL, Faires JD: Numerical Analysis. 5th edition. Boston, MA, PWS Publishing Co; 1993:pp. 156-167.
15. Eilers PHC: A perfect smoother. Anal Chem Anal Chem 2003, 75:3631-3636.
16. Tsai KY, Wang FS: Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics 2005, 21:1180-1188.
17. Almeida JS, Voit EO: Neural-network based parameter estimation in complex biomedical system. Genome Inform 2003, 14:114-123.
18. Almeida JS: Predictive non-linear modeling of complex data by artificial neural networks. Curr Opin Biotechnol 2002, 13:72-76.
19. Karjalainen EJ: The Spectrum reconstruction problem: use of alternating regression for unexpected spectral compoments in two-dimensional spectroscopies. Chemom Intell Lab Syst 1989, 7:31-38.
20. Oliveira MR, Branco JA, Croux C, Filzmoser P: Robust redundancy analysis by alternating regression. In Theory and Applications of Recent Robust Methods Edited by: Hubert M, Pison G, Struyf A and Van Aelst S. Basel, Birkhauser; 2004:235-246.
21. Martens H, Naes T: Multivariate Calibration. Chichester, UK, John Wiley & Son Ltd.; 1989:419.
22. Epureanu BI, Greenside HS: Fractal basins of attraction associated with a damped Newton's method. SIAM Rev 1998, 40:102-109.
23. Veflingstad SR, Almeida JS, Voit EO: Priming nonlinear searches for pathway identification. Theor Biol Med Model 2004, 1:8.
24. Marino S, Voit EO: An automated procedure for the extraction of metabolic network information from time series data. J Bioinform Comp Biol in press.
25. Hlavacek WS, Savageau MA: Rules for coupled expression of regulator and effector genes in inducible circuits. J Mol Biol 1996, 255:121-139.
26. Jeong H, Tombor B, Albert R, Oltval ZN, Barabasi AL: The large-scale organization of metabolic networks. Nature 2000, 407:651-654.