Multi-objective optimization of biological networks for prediction of intracellular fluxes

Advances in Soft Computing

Volumn 49, Issue , 2009, Pages 197-205

  Sendín, José Oscar H ^a   Alonso, Antonio A ^a   Banga, Julio R ^a  

^a INSTITUTO DE INVESTIGACIONES MARINAS   (Spain)

Author keywords

Flux balance analysis; Multi objective optimization; Pareto front

Indexed keywords

EID: 58149112640     PISSN: 16153871     EISSN: 18600794     Source Type: Book Series    
DOI: 10.1007/978-3-540-85861-4_24     Document Type: Conference Paper

References (12)

1. Bonarios, H.P.J., Hatzimanikatis, V., Meesters, K.P.H., de Gooijer, C.D., Schmid, G., Tramper, J.: Metabolic flux analysis of hybridoma cells in different culture media using mass balances. Biotechnology Bioengineering 50, 299-318 (1996)
2. Das, I., Dennis, J.E.: Normal Boundary Intersection: A new method for generating the Pareto surface in nonlinear multicriteria optimization problems. SIAM J. Optimization 8, 631-657 (1998)
3. Dauner, M., Sauer, U.: Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnology Bioengineering 76, 132-143 (2001)
4. Edwards, J.S., Ibarra, R.U., Palsson, B.O.: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology 19(2), 125-130 (2001)
5. Forster, J., Famili, I., Fu, P., Palsson, B.O., Nielssen, J.: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research 13(2), 244-253 (2003)
6. Handl, J., Kell, D.B., Knowles, J.: Multiobjective optimization in bioinformatics and computational biology. IEEE-ACM Transactions on Computational Biology and Bioinformatics 4(2), 279-292 (2007)
7. Nielsen, J.: Principles of optimal metabolic network operation. Molecular Systems Biology 3, 2 (2007)
8. Schuetz, R., Kuepfer, L., Sauer, U.: Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Molecular Systems Biology 3, 119 (2007)
9. Sendín, J.O.H., Vera, J., Torres, N.V., Banga, J.R.: Model-based optimization of biochemical systems using multiple objectives: A comparison of several solution strategies. Mathematical and Computer Modelling of Dynamical Systems 12(5), 469-487 (2006)
10. Sendín, J.O.H., Banga, J.R., Csendes, T.: Extensions of a multistart clustering algorithm for constrained global optimization problems. Industrial & Engineering Chemistry Research (accepted for publication, 2008)
11. van Gulik, W.M., Heijnen, J.J.: A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnology Bioengineering 48, 681-698 (1995)
12. Varma, A., Palsson, B.O.: Metabolic flux balancing: Basic concepts, scientific and practical us. Bio/Technology 12(10), 994-998 (1994)