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Volumn 736, Issue , 2012, Pages 409-424

Global optimization in systems biology: Stochastic methods and their applications

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL METABOLISM; BIOLOGICAL ACTIVITY; DATA ANALYSIS SOFTWARE; ENZYME ACTIVATION; ESCHERICHIA COLI; EXPERIMENTAL STUDY; GLOBAL OPTIMIZATION; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; STATISTICS; SYSTEMS BIOLOGY;

EID: 84855981944     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-7210-1_24     Document Type: Article
Times cited : (26)

References (47)
  • 1
    • 48749095711 scopus 로고    scopus 로고
    • Computational procedures for optimal experimental design in biological systems
    • Balsa-Canto E, Alonso AA, Banga JR (2008) Computational procedures for optimal experimental design in biological systems. IET Syst Biol 2(4):163-172
    • (2008) IET Syst Biol , vol.2 , Issue.4 , pp. 163-172
    • Balsa-Canto, E.1    Alonso, A.A.2    Banga, J.R.3
  • 2
    • 77949475400 scopus 로고    scopus 로고
    • An iterative identification procedure for dynamic modeling of biochemical networks
    • Balsa-Canto E, Alonso AA, Banga JR (2010) An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst Biol 4:11
    • (2010) BMC Syst Biol , vol.4 , pp. 11
    • Balsa-Canto, E.1    Alonso, A.A.2    Banga, J.R.3
  • 3
    • 41849104688 scopus 로고    scopus 로고
    • Hybrid optimization method with general switching strategy for parameter estimation
    • Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C (2008) Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst Biol 2:26
    • (2008) BMC Syst Biol , vol.2 , pp. 26
    • Balsa-Canto, E.1    Peifer, M.2    Banga, J.R.3    Timmer, J.4    Fleck, C.5
  • 4
    • 14344265463 scopus 로고    scopus 로고
    • Dynamic optimization of single- and multistage systems using a hybrid stochastic-deterministic method
    • Balsa-Canto E, Vassiliadis VS, Banga JR (2005) Dynamic optimization of single- and multistage systems using a hybrid stochastic-deterministic method. Ind Eng Chem Res 44(5): 1514-1523
    • (2005) Ind Eng Chem Res , vol.44 , Issue.5 , pp. 1514-1523
    • Balsa-Canto, E.1    Vassiliadis, V.S.2    Banga, J.R.3
  • 5
    • 73449142148 scopus 로고    scopus 로고
    • Optimal experimental design for parameter estimation of a cell signaling model
    • Bandara S, Sclöder J, Eils R, Bock H, Meyer T (2009) Optimal experimental design for parameter estimation of a cell signaling model. Plos Comput Biol 5(11):1-12
    • (2009) Plos Comput Biol , vol.5 , Issue.11 , pp. 1-12
    • Bandara, S.1    Sclöder, J.2    Eils, R.3    Bock, H.4    Meyer, T.5
  • 6
    • 46349105936 scopus 로고    scopus 로고
    • Optimization in computational systems biology
    • Banga JR (2008) Optimization in computational systems biology. BMC Syst Biol 2:47-53
    • (2008) BMC Syst Biol , vol.2 , pp. 47-53
    • Banga, J.R.1
  • 7
    • 58149232578 scopus 로고    scopus 로고
    • Parameter estimation and optimal experimental design
    • Banga JR, Balsa-Canto E (2008) Parameter estimation and optimal experimental design. Essays Biochem 45:195-210
    • (2008) Essays Biochem , vol.45 , pp. 195-210
    • Banga, J.R.1    Balsa-Canto, E.2
  • 8
    • 77953609496 scopus 로고    scopus 로고
    • Modelling the optimal timing inmetabolic pathway activationuse of pontryagin's maximum principle and role of the golden section
    • BartlM, Li P, Schuster S (2010) Modelling the optimal timing inmetabolic pathway activationuse of pontryagin's maximum principle and role of the golden section. Biosystems 101(1): 67-77
    • (2010) Biosystems , vol.101 , Issue.1 , pp. 67-77
    • Bartlm Li, P.1    Schuster, S.2
  • 9
    • 0037074623 scopus 로고    scopus 로고
    • Advances in simultaneous strategies for dynamic process optimization
    • DOI 10.1016/S0009-2509(01)00376-1, PII S0009250901003761
    • Biegler LT, Cervantes A, Wätcher A (2002) Advances in simulaneous strategies for dynamic process optimization. Chem Eng Sci 57(4):575-593 (Pubitemid 34195938)
    • (2002) Chemical Engineering Science , vol.57 , Issue.4 , pp. 575-593
    • Biegler, L.T.1    Cervantes, A.M.2    Wachter, A.3
  • 10
    • 0002564462 scopus 로고
    • A multiple shooting algorithm for direct solution of optimal control problems
    • Pergamon Press, New York
    • Bock H, Plitt K (1984) A multiple shooting algorithm for direct solution of optimal control problems. In: Proc 9th IFAC World Congress, Pergamon Press, New York, pp 242-247
    • (1984) Proc 9th IFAC World Congress , pp. 242-247
    • Bock, H.1    Plitt, K.2
  • 12
    • 34447501892 scopus 로고    scopus 로고
    • Cancer immunotherapy, mathematical modeling and optimal control
    • DOI 10.1016/j.jtbi.2007.04.003, PII S0022519307001853
    • Castiglione F, Piccoli B (2007) Cancer immunotherapy, mathematical modeling, and optimal control. J Theor Biol 247(4):723-732 (Pubitemid 47081044)
    • (2007) Journal of Theoretical Biology , vol.247 , Issue.4 , pp. 723-732
    • Castiglione, F.1    Piccoli, B.2
  • 13
    • 67049088428 scopus 로고    scopus 로고
    • Dynamic optimization of nonlinear processes with an enhanced scatter search method
    • Egea JA, Balsa-Canto E, Garcia MSG, Banga JR (2009) Dynamic optimization of nonlinear processes with an enhanced scatter search method. Ind Eng Chem Res 48(9):4388-4401
    • (2009) Ind Eng Chem Res , vol.48 , Issue.9 , pp. 4388-4401
    • Egea, J.A.1    Balsa-Canto, E.2    Msg, G.3    Banga, J.R.4
  • 14
    • 69549124230 scopus 로고    scopus 로고
    • An evolutionary method for complex-process optimization
    • Egea JA,Martí R, Banga JR (2010) An evolutionary method for complex-process optimization. Comp Oper Res 37(2):315-324
    • (2010) Comp Oper Res , vol.37 , Issue.2 , pp. 315-324
    • Egea, J.A.1    Martí, R.2    Banga, J.R.3
  • 17
    • 68349101376 scopus 로고    scopus 로고
    • DOTcvpSB, a software toolbox for dynamic optimization in systems biology
    • Hirmajer T, Balsa-Canto E, Banga JR (2009) DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinformatics 10:199-213
    • (2009) BMC Bioinformatics , vol.10 , pp. 199-213
    • Hirmajer, T.1    Balsa-Canto, E.2    Banga, J.R.3
  • 19
    • 33750374139 scopus 로고    scopus 로고
    • Linking data to models: Data regression
    • DOI 10.1038/nrm2030, PII NRM2030
    • Jaqaman K, Danuser G (2006) Linking data to models: data regression. Nat Rev Mol Cell Bio 7(11):813-819 (Pubitemid 44627474)
    • (2006) Nature Reviews Molecular Cell Biology , vol.7 , Issue.11 , pp. 813-819
    • Jaqaman, K.1    Danuser, G.2
  • 20
    • 33645579942 scopus 로고    scopus 로고
    • Role of mathematical modeling on the optimal control of hiv-1 pathogenesis
    • Joly M, Pinto J (2006) Role of mathematical modeling on the optimal control of hiv-1 pathogenesis. AiChe J 52(3):856-884
    • (2006) AiChe J , vol.52 , Issue.3 , pp. 856-884
    • Joly, M.1    Pinto, J.2
  • 22
    • 0036441029 scopus 로고    scopus 로고
    • Prediction of temporal gene expression: Metabolic optimization by re-distribution of enzyme activities
    • DOI 10.1046/j.1432-1033.2002.03223.x
    • Klipp E, Heinrich R, Holzhtte H (2002) Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities. Eur J Biochem 269:5406-5413 (Pubitemid 35365529)
    • (2002) European Journal of Biochemistry , vol.269 , Issue.22 , pp. 5406-5413
    • Klipp, E.1    Heinrich, R.2    Holzhutter, H.-G.3
  • 23
    • 77949385752 scopus 로고    scopus 로고
    • Bacterial adaptation through distributed sensing of metabolic fluxes
    • Kotte O, Zaugg J, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Sys Biol 6:355
    • (2010) Mol Sys Biol , vol.6 , pp. 355
    • Kotte, O.1    Zaugg, J.2    Heinemann, M.3
  • 24
    • 27644457757 scopus 로고    scopus 로고
    • Exploiting optimal control for target-oriented manipulation of (bio)chemical systems: A model-based approach to specific modification of self-organized dynamics
    • DOI 10.1142/S0217979205032498
    • Lebiedz D (2005) Exploiting optimal control for target-oriented manipulation of (bio)chemical systems: A model-based approach to specific modification of self-organized dynamics. Int J Mod Phys B 19 3763-3798 (Pubitemid 41549766)
    • (2005) International Journal of Modern Physics B , vol.19 , Issue.25 , pp. 3763-3798
    • Lebiedz, D.1
  • 25
    • 31144434238 scopus 로고    scopus 로고
    • External optimal control of self-organisation dynamics in a chemotaxis reaction diffusion system
    • Lebiedz D, Maurer H (2004) External optimal control of self-organisation dynamics in a chemotaxis reaction diffusion system. IEE Syst Biol 2:222-229
    • (2004) IEE Syst Biol , vol.2 , pp. 222-229
    • Lebiedz, D.1    Maurer, H.2
  • 26
    • 51749122228 scopus 로고    scopus 로고
    • Dynamical modeling and multi-experiment fitting with PottersWheel
    • Maiwald T, Timmer J (2008) Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics 24(18):2037-2043
    • (2008) Bioinformatics , vol.24 , Issue.18 , pp. 2037-2043
    • Maiwald, T.1    Timmer, J.2
  • 27
    • 0032406131 scopus 로고    scopus 로고
    • Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
    • DOI 10.1093/bioinformatics/14.10.869
    • Mendes P, Kell D (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14(10):869-883 (Pubitemid 29041543)
    • (1998) Bioinformatics , vol.14 , Issue.10 , pp. 869-883
    • Mendes, P.1    Kell, D.B.2
  • 28
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • DOI 10.1101/gr.1262503
    • Moles CG, Mendes P, Banga JR (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13:2467-2474 (Pubitemid 37428271)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2467-2474
    • Moles, C.G.1    Mendes, P.2    Banga, J.R.3
  • 29
    • 70350400430 scopus 로고    scopus 로고
    • Sequential activation of metabolic pathways: A dynamic optimization approach
    • Oyarzun DA, Ingalls B, Middleton R, Kalamatianos D (2009) Sequential activation of metabolic pathways: a dynamic optimization approach. Bull Math Biol 71:1851-1872
    • (2009) Bull Math Biol , vol.71 , pp. 1851-1872
    • Oyarzun, D.A.1    Ingalls, B.2    Middleton, R.3    Kalamatianos, D.4
  • 30
    • 0034546906 scopus 로고    scopus 로고
    • Recent developments and trends in global optimization
    • DOI 10.1016/S0377-0427(00)00425-8, PII S0377042700004258, Numerical analysis 2000 Volume IV: Optimization and nonlinear equations
    • Pardalos P, Romeijn HE, Tuyb H (2000) Recent developments and trends in global optimization. J Comp App Math 124:209-228 (Pubitemid 32003860)
    • (2000) Journal of Computational and Applied Mathematics , vol.124 , Issue.1-2 , pp. 209-228
    • Pardalos, P.M.1    Romeijn, H.E.2    Tuy, H.3
  • 32
    • 70349992872 scopus 로고    scopus 로고
    • Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts the dynamics of stat1 pathway activity
    • Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R (2010) Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts the dynamics of stat1 pathway activity. Cell Signal 22:97-105
    • (2010) Cell Signal , vol.22 , pp. 97-105
    • Rateitschak, K.1    Karger, A.2    Fitzner, B.3    Lange, F.4    Wolkenhauer, O.5    Jaster, R.6
  • 33
    • 33751423943 scopus 로고    scopus 로고
    • Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
    • Rodriguez-Fernandez M, Egea JA, Banga JR (2006) Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics 7:483
    • (2006) BMC Bioinformatics , vol.7 , pp. 483
    • Rodriguez-Fernandez, M.1    Egea, J.A.2    Banga, J.R.3
  • 34
    • 32044474451 scopus 로고    scopus 로고
    • A hybrid approach for efficient and robust parameter estimation in biochemical pathways
    • Rodriguez-Fernandez M, Mendes P, Banga JR (2006) A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems 83(2-3):24
    • (2006) Biosystems , vol.83 , Issue.2-3 , pp. 24
    • Rodriguez-Fernandez, M.1    Mendes, P.2    Banga, J.R.3
  • 35
    • 34548625320 scopus 로고    scopus 로고
    • Optimal control of self-organized dynamics in cellular signal transduction
    • Salby O, Sager S, Shaik O, Kummer U, Lebiedz D (2007) Optimal control of self-organized dynamics in cellular signal transduction. Math Comp Model Dyn 13:487-502
    • (2007) Math Comp Model Dyn , vol.13 , pp. 487-502
    • Salby, O.1    Sager, S.2    Shaik, O.3    Kummer, U.4    Lebiedz, D.5
  • 36
    • 0003509985 scopus 로고
    • Computational mathematics in engineering and applied science: ODEs
    • CRC Press, Inc., Florida, USA
    • Schiesser WE (1994) Computational mathematics in engineering and applied science: ODEs, DAEs, and PDEs. CRC Press, Inc., Florida, USA
    • (1994) DAEs, and PDEs
    • Schiesser, W.E.1
  • 37
    • 32544443964 scopus 로고    scopus 로고
    • Systems Biology Toolbox for MATLAB: A computational platform for research in systems biology
    • DOI 10.1093/bioinformatics/bti799
    • Schmidt H, Jirstrand M (2006) Systems biology toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 22(4):514-515 (Pubitemid 43231434)
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 514-515
    • Schmidt, H.1    Jirstrand, M.2
  • 38
    • 77953296954 scopus 로고    scopus 로고
    • Multi-objective mixed integer strategy for the optimisation of biological networks
    • Sendin JOH, Exler O, Banga JR (2010) Multi-objective mixed integer strategy for the optimisation of biological networks. IET Syst Biol 4(3):236-248
    • (2010) IET Syst Biol , vol.4 , Issue.3 , pp. 236-248
    • Sendin, J.O.H.1    Exler, O.2    Banga, J.R.3
  • 39
    • 33746828943 scopus 로고    scopus 로고
    • Model based optimization of biochemical systems using multiple objectives: A comparison of several solution strategies
    • DOI 10.1080/13873950600723442, PII T6033G5HL6W32704
    • Sendin JOH, Vera J, Torres N, Banga JR (2006) Model based optimization of biochemical systems using multiple objectives: A comparison of several solution strategies. Math Comp Mod Dyn Syst 12(5):469-487 (Pubitemid 44181275)
    • (2006) Mathematical and Computer Modelling of Dynamical Systems , vol.12 , Issue.5 , pp. 469-487
    • Sendin, O.H.1    Vera, J.2    Torres, N.V.3    Banga, J.R.4
  • 40
    • 17044395470 scopus 로고    scopus 로고
    • Reverse engineering of biochemical equations from time-course data by means of genetic programming
    • Sugimoto M, Kikuchi S, Tomita M (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming. BioSystems 80:155-164
    • (2005) BioSystems , vol.80 , pp. 155-164
    • Sugimoto, M.1    Kikuchi, S.2    Tomita, M.3
  • 41
    • 21344487533 scopus 로고    scopus 로고
    • The best solution
    • Sutherland W (2005) The best solution. Nature 435:569
    • (2005) Nature , vol.435 , pp. 569
    • Sutherland, W.1
  • 43
    • 0347601910 scopus 로고    scopus 로고
    • Systemic behavior of cooperative search algorithms
    • Toulouse M, Crainic T, Sansó B (2004) Systemic behavior of cooperative search algorithms. Parallel Comput 30:57-79
    • (2004) Parallel Comput , vol.30 , pp. 57-79
    • Toulouse, M.1    Crainic, T.2    Sansó, B.3
  • 44
    • 0028497977 scopus 로고
    • Solution of a class of multistage dynamic optimization problems. problems without path constraints
    • Vassiliadis VS, Pantelides CC, Sargent RWH (1994) Solution of a class of multistage dynamic optimization problems. 1. problems without path constraints. Ind Eng Chem Res 33(9): 2111-2122
    • (1994) Ind Eng Chem Res , vol.33 , Issue.9 , pp. 2111-2122
    • Vassiliadis, V.S.1    Pantelides, C.C.2    Rwh, S.3
  • 45
    • 0037899231 scopus 로고    scopus 로고
    • Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae
    • DOI 10.1002/bit.10676
    • Vera J, de Atauri P, Torres N, Banga JR (2003) Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by Saccharomyces cerevisiae. Biotechnol Bioeng 83(3):335-343 (Pubitemid 36818434)
    • (2003) Biotechnology and Bioengineering , vol.83 , Issue.3 , pp. 335-343
    • Vera, J.1    De Atauri, P.2    Cascante, M.3    Torres, N.V.4
  • 46
    • 34249279181 scopus 로고    scopus 로고
    • Power-law models of signal transduction pathways
    • DOI 10.1016/j.cellsig.2007.01.029, PII S0898656807000460
    • Vera J, Balsa-Canto E, Wellstead P, Banga JR, Wolkenhauer O (2007) Power-law models of signal transduction pathways. Cell Signal 19:1531-1541 (Pubitemid 46818917)
    • (2007) Cellular Signalling , vol.19 , Issue.7 , pp. 1531-1541
    • Vera, J.1    Balsa-Canto, E.2    Wellstead, P.3    Banga, J.R.4    Wolkenhauer, O.5


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