In vivo intracellular metabolite dynamics estimation by sequential monte carlo filter

2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007

Volumn , Issue , 2007, Pages 387-394

  Yang, Jing ^a   Kadirkamanathan, Visakan ^a   Billings, Stephen A ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EXTRACELLULAR METABOLITES; FLUX DISTRIBUTIONS; INTRACELLULAR METABOLITE CONCENTRATION; INTRACELLULAR METABOLITES; INTRACELLULAR VOLUMES; LOW CONCENTRATION LEVELS; SEQUENTIAL MONTE-CARLO FILTER; STATISTICAL ESTIMATION;

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; BIOMOLECULES; ESTIMATION; METABOLITES; MONTE CARLO METHODS;

ENZYME ACTIVITY;

EID: 56349163039     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (45)

1. J. E. Bailey, "Toward a science of metabolic engineering," Science, vol. 252, pp. 1668-1675, 1991. (Pubitemid 21917084)
2. G. N. Stephanopoulos, A. A. Aristidou, and J. Nielsen, Metabolic Engineering - Principles and Methodologies. San Diego, USA: Academic Press, 1998.
3. C. H. Schilling, S. Schuster, B. O. Palsson, and R. Heinrich, "Metabolic pathway analysis: basic concepts and scientific applications in the postgenomic era," Biotechnol. Prog., vol. 15, pp. 296-303, 1999. (Pubitemid 29270673)
4. J. A. Papin, N. D. Price, S. J. Wiback, D. A. Fell, and B. O. Palsson, "Metabolic pathways in the post-genomic era," Trends in Biochemical Sciences, vol. 28, pp. 250-258, 2003.
5. A. Varma and B. O. Palsson, "Metabolic flux balancing: basic concepts, scientific and practical use," Bio/Technology., vol. 12, pp. 994-998, 1994.
6. A. Marx, A. A. de Graaf, W. Wiechert, L. Eggeling, and H. Sahm, "Determination of the fluxes in the central metabolism of corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing," Biotechnol. Bioeng., vol. 49, pp. 111-129, 1996. (Pubitemid 26011765)
7. K. Schmidt, J. Nielsen, and J. Villadsen, "Quantitative analysis of metabolic fluxes in Escherichia coli using two-dimensional NMR spectroscopy and complete isotopomer models," J. Biotechnol., vol. 71, no. 1-3, pp. 175-189, 1999. (Pubitemid 29354248)
8. K. Schmidt, L. C. Nørregaard, B. Pedersen, A. Meissner, J. O. Duus, J. O. Nielsen, and J. Villadsen, "Quantification of intracellular metabolic fluxes from fractional enrichment and 13C-13C coupling constraints on the isotopomer distribution in labeled biomass components," Metab. Eng., vol. 1, no. 2, pp. 166-179, 1999. (Pubitemid 129501847)
9. W. Wiechert and A. A. de Graaf, "Bidirectional reaction steps in metabolic networks: I. modeling and simulation of carbon isotope labeling experiments," Biotechnol. Bioeng., vol. 55, no. 1, pp. 101-117, 1997. (Pubitemid 27246856)
10. W. Wiechert, C. Siefke, A. A. de Graaf, and A. Marx, "Bidirectional reaction steps in metabolic networks: II. flux estimation and statistical analysis," Biotechnol. Bioeng., vol. 55, no. 1, pp. 118-135, 1997. (Pubitemid 27246857)
11. H. Kacser and J. A. Burns, "The control of flux," Symp. Soc. Exp. Biol., vol. 27, pp. 65-104, 1973.
12. H. Kacser, J. A. Burns, and D. A. Fell, "The control of flux," Bioch. Soc. Trans., vol. 23, pp. 341-366, 1995.
13. D. A. Fell, Understanding the Control of Metabolism. Miami: Portland Press, 1997.
14. H. V. Westerhoff, "The silicon cell, not dead but live!" Metab. Eng., vol. 3, pp. 207-210, 2001. (Pubitemid 32748164)
15. O. Fiehn, "Metabolomics - the link between phenotypes and genotypes," Plant Mol. Biol., vol. 48, pp. 155-171, 2002.
16. O. Fiehn, J. Kopka, P. Dormann, T. Altmann, R. N. Trethewey, and L. Willmitzer, "Metabolite profiling for plant functional genomics," Nat. Biotechnol., vol. 18, pp. 1142-1143, 2000.
17. D. Weuster-Botz and A. A. de Graaf, "Reaction engineering methods to study intracellular metabolite concentrations," Adv. Biochem. Eng. Biotechnol., vol. 54, pp. 75-108, 1996.
18. U. Theobald, W. Mailinger, M. Baltes, M. Rizzi, and M. Reuss, "Invivo analysis of metabolic dynamics in saccharomyces cerevisiae: I. experimental observations," Biotechnol. Bioeng., vol. 55, pp. 305-316, 1997. (Pubitemid 27291199)
19. A. Buchholz, R. Takors, and C. Wandrey, "Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographicelectrospray ionization tandem mass spectromtric techniques," Anal. Biochem., vol. 295, pp. 129-137, 2001. (Pubitemid 32756965)
20. J. Hurlebaus, A. Buchholz, W. Alt, W. Wiechert, and R. Takors, "MMT - a pathway modeling tool for data from rapid sampling experiments," in silico biol., vol. 2, pp. 467-484, 2002. (Pubitemid 36329189)
21. A. Buchholz, J. Hurlebaus, C. Wandrey, and R. Takors, "Metabolomics: Quantification of intracellular metabolite dynamics," Biomol. Eng., vol. 19, pp. 5-15, 2002. (Pubitemid 34717859)
22. J. B. Russell and G. M. Cook, "Energetics of bacterial growth: balance of anabolic and catabolic reactions," Microbiol. Rev., vol. 59, pp. 48-62, 1995.
23. B. D. Sanwal, "Allosteric controls of amphilbolic pathways in bacteria," Bacteriol Rev., vol. 34, pp. 20-39, 1970.
24. S. Vaseghi, A. Baumeister, M. Rizzi, and M. Reuss, "in vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae," Metabolic Engineering, vol. 1, pp. 128-140, 1999. (Pubitemid 129501844)
25. S. Ostergaard, L. Olsson, and J. Nielsen, "in vivo dynamics of galactose metabolism in saccharomyces cerevisiae: metabolic fluxes and metabolite levels," Biotechnol. Bioeng., vol. 73, pp. 412-425, 2001. (Pubitemid 32493237)
26. M. Rizzi, M. Baltes, U. Theobald, and M. Reuss, "in vivo analysis of metabolic dynamics in saccharomyces cerevisiae: Ii. mathematical model," Biotechnol. Bioeng., vol. 55, pp. 592-608, 2001.
27. D. Visser, G. A. van Zuylen, J. C. van Dam, M. R. Eman, A. PrÖll, C. Ras, L. Wu, W. M. van Gulik, and J. J. Heijnen, "Analysis of in vivo kinetics of glycolysis in aerobic Saccharomyces cerevisiae by application of glucose and ethanol pulses," Biotechnology and Bioengineering, vol. 88, pp. 157-167, 2004. (Pubitemid 39422987)
28. M. West and P. J. Harrison, Bayesian forecasting and dynamic models, 2nd edn. New York: Springer, 1997.
29. R. E. Kalman, "A new approach to linear filtering and prediction problems," J. Basic Eng. - T. ASME., vol. 82, pp. 35-45, 1960.
30. R. E. Kalman and B. R. S., "New results in linear filtering and prediction theory," J. Basic Eng. - T. ASME., vol. 83, pp. 95-107, 1961.
31. S. Arulampalam, S. Maskell, N. Gordon, and T. Clapp, "A tutorial on particle filters for on-line nonlinear/non-Gaussian Bayesian tracking," IEEE Trans. Signal Process., vol. 50, pp. 174-188, 2002. (Pubitemid 34291500)
32. A. Doucet, N. de Freitas, and N. Gordon, Eds., Sequential Monte Carlo Methods in Practice. Springer-Verlag, 2001.
33. J. Liu and R. Chen, "Sequential Monte Carlo methods for dynamic systems," J. Amer. Statist. Assoc., vol. 93, pp. 1032-1044, 1998.
34. M. K. Pitt and N. Shephard, "Filtering via simulation: Auxiliary particle filters," J. Amer. Statist. Assoc., vol. 94, pp. 590-599, 1999.
35. N. Metropolis and S. Ulam, "The monte carlo method," J. Amer. Statist. Assoc., vol. 44, pp. 335-341, 1949.
36. A. Doucet, S. Godsill, and C. Andrieu, "On sequential Monte Carlo sampling methods for Bayesian filtering," Statistics and Computing, vol. 10, pp. 197-208, 2000.
37. G. B. Fogel and D. W. Corne, Eds., Evolutionary computation in bioinformatics. Morgan Kaufmann, 2003.
38. J. Yang, S. Wongsa, V. Kadirkamanathan, S. A. Billings, and P. C. Wright, "Metabolic flux estimation - a self-adaptive evolutionary algorithm with singular value decomposition," IEEE/ACM Trans. Computational biology and Bioinformatics, in press.
39. -, "Self-adaptive evolutionary algorithm based methods for quantification in metabolic systems," in 2004 IEEE Symp. on Computational Intelligence in Bioinformatics and Computational Biology, 2004, pp. 260-267. (Pubitemid 40498012)
40. A. Krogh, M. Brown, I. S. Mian, K. Sjolander, and D. Haussler, "Hidden markov models in computational biology: Applications to protein modeling, Tech. Rep. UCSC-CRL-93-32, 1993.
41. I. Tsigelny, Y. Sharikov, and L. F. T. Eyck, "Hidden markov modelsbased system (HMMSPECTR) for detecting structural homologies on the basis of sequential information," Protein Eng. Des. Sel., vol. 15, no. 5, pp. 347-352, 2002. (Pubitemid 34601725)
42. O. EbenhÖh and R. Heinrich, "Evolutionary optimization of metabolic pathways. theoretical reconstruction of the stoichiometry of atp and nadh producing systems," Bull. Math. Biol., no. 63, pp. 21-55, 2001. (Pubitemid 32577423)
43. K. Schmidt and S. H. Issacs, "An evolutionary algorithm for initial state and parameter estimation in complex biochemical models," in Preprints of the 6th Int. Conf. on computer applications in biotechnology, Garmisch-Partenkirchen, Germany, 1995.
44. L. Wu, W. A. van Winden, W. M. van Gulik, and J. J. Heijnen, "Application of metabolome data in functional genomics: A conceptual strategy," Metab. Eng., vol. 7, pp. 302-310, 2005. (Pubitemid 41225447)
45. A. Kong, J. S. Liu, and W. H. Wong, "Sequential imputations and bayesian missing data problems," Journal of American Statistical Association, vol. 89, pp. 278-288, 1994.