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Volumn 25, Issue 6, 2009, Pages 780-786

Benchmarks for identification of ordinary differential equations from time series data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MICHAELIS MENTEN KINETICS; ORDINARY DIFFERENTIAL EQUATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUALITY CONTROL; STATISTICAL ANALYSIS; SYSTEMS BIOLOGY; TIME SERIES ANALYSIS;

EID: 62549093118     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp050     Document Type: Article
Times cited : (35)

References (34)
  • 1
    • 0000122278 scopus 로고
    • Statistical construction of chemical reaction mechanisms from measured time-series
    • Arkin,A.P. and Ross,J. (1995) Statistical construction of chemical reaction mechanisms from measured time-series. J. Phys. Chem., 99, 970-979.
    • (1995) J. Phys. Chem , vol.99 , pp. 970-979
    • Arkin, A.P.1    Ross, J.2
  • 2
    • 13444304325 scopus 로고    scopus 로고
    • NCBI GEO: Mining millions of expression profiles-database and tools
    • Barrett,T. et al. (2005) NCBI GEO: Mining millions of expression profiles-database and tools. Nucleic Acids Res., 33, D562-D566.
    • (2005) Nucleic Acids Res , vol.33
    • Barrett, T.1
  • 3
    • 34547175927 scopus 로고    scopus 로고
    • Automated reverse engineering of nonlinear dynamical systems
    • Bongard,J. and Lipson,H. (2007) Automated reverse engineering of nonlinear dynamical systems. Proc. Natl Acad. Sci. USA, 104, 9943-9948.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9943-9948
    • Bongard, J.1    Lipson, H.2
  • 4
    • 33745616528 scopus 로고    scopus 로고
    • Identification of biochemical networks by S-tree based genetic programming
    • Cho,D.Y. et al. (2006) Identification of biochemical networks by S-tree based genetic programming. Bioinformatics, 22, 1631-16340.
    • (2006) Bioinformatics , vol.22 , pp. 1631-16340
    • Cho, D.Y.1
  • 5
    • 33749340654 scopus 로고    scopus 로고
    • Parameter estimation in biochemical systems models with alternating regression
    • Chou,I.C. et al. (2006) Parameter estimation in biochemical systems models with alternating regression. Theor. Biol. Med. Model 3, 25.
    • (2006) Theor. Biol. Med. Model , vol.3 , pp. 25
    • Chou, I.C.1
  • 6
    • 3142617691 scopus 로고    scopus 로고
    • Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
    • Crampin,E.J. et al. (2004) Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog. Biophy. Mol. Biol., 86, 77-112.
    • (2004) Prog. Biophy. Mol. Biol , vol.86 , pp. 77-112
    • Crampin, E.J.1
  • 7
    • 33745726568 scopus 로고    scopus 로고
    • Inference of scale-free networks from gene expression time series
    • Daisuke,T. and Horton,P. (2006) Inference of scale-free networks from gene expression time series. J. Bioinform. Comput. Biol., 4, 503-514.
    • (2006) J. Bioinform. Comput. Biol , vol.4 , pp. 503-514
    • Daisuke, T.1    Horton, P.2
  • 9
    • 33947647274 scopus 로고    scopus 로고
    • Gennemark,P. and Wedelin,D. (2007) Efficient algorithms for ordinary differential equation model identification of biological systems. IET Syst. Biol., 1, 120-129.
    • Gennemark,P. and Wedelin,D. (2007) Efficient algorithms for ordinary differential equation model identification of biological systems. IET Syst. Biol., 1, 120-129.
  • 10
    • 33847314052 scopus 로고    scopus 로고
    • Parameter estimation using Simulated Annealing for S-system models of biochemical networks
    • Gonzalez,O.R. et al. (2007) Parameter estimation using Simulated Annealing for S-system models of biochemical networks. Bioinformatics 23, 480-486.
    • (2007) Bioinformatics , vol.23 , pp. 480-486
    • Gonzalez, O.R.1
  • 11
    • 0030002954 scopus 로고    scopus 로고
    • Rules for coupled expression of regulator and effector genes in inducible circuits
    • Hlavacek,W.S. and Savageau,M.A. (1996) Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol., 255, 121-139.
    • (1996) J. Mol. Biol , vol.255 , pp. 121-139
    • Hlavacek, W.S.1    Savageau, M.A.2
  • 12
    • 34247882020 scopus 로고    scopus 로고
    • Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks
    • Karnaukhov,A.V. et al. (2007) Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks. Biophys. J., 92, 3459-3473.
    • (2007) Biophys. J , vol.92 , pp. 3459-3473
    • Karnaukhov, A.V.1
  • 13
    • 0037461033 scopus 로고    scopus 로고
    • Dynamic modeling of genetic networks using genetic algorithm and S-system
    • Kikuchi,S. et al. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics, 19, 643-650.
    • (2003) Bioinformatics , vol.19 , pp. 643-650
    • Kikuchi, S.1
  • 14
    • 20144387371 scopus 로고    scopus 로고
    • Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
    • Kimura,S. et al. (2005) Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 21, 1154-1163.
    • (2005) Bioinformatics , vol.21 , pp. 1154-1163
    • Kimura, S.1
  • 15
    • 33644557151 scopus 로고    scopus 로고
    • CadC-mediated activation of the cadBA promoter in Escherichia coli
    • Kuper,C. and Jung,K. (2005) CadC-mediated activation of the cadBA promoter in Escherichia coli. J. Mol. Microbiol. Biotechnol., 10, 26-39.
    • (2005) J. Mol. Microbiol. Biotechnol , vol.10 , pp. 26-39
    • Kuper, C.1    Jung, K.2
  • 16
    • 34249732527 scopus 로고    scopus 로고
    • Kutalik,Z. et al. (2007) S-system parameter estimation for noisy metabolic profiles using newton-flow analysis. IET Syst. Biol., 1, 174-180.
    • Kutalik,Z. et al. (2007) S-system parameter estimation for noisy metabolic profiles using newton-flow analysis. IET Syst. Biol., 1, 174-180.
  • 17
    • 41949109225 scopus 로고    scopus 로고
    • Inference of biochemical network models in S-system using multiobjective optimization approach
    • Liu,P.K. and Wang,F.S. (2008) Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics 24, 1085-1092.
    • (2008) Bioinformatics , vol.24 , pp. 1085-1092
    • Liu, P.K.1    Wang, F.S.2
  • 18
    • 0035221090 scopus 로고    scopus 로고
    • Development of a system for the inference of large scale genetic networks
    • Maki,Y. et al. (2001) Development of a system for the inference of large scale genetic networks. Pac. Symp. Biocomput., 446-458.
    • (2001) Pac. Symp. Biocomput , pp. 446-458
    • Maki, Y.1
  • 19
    • 33748511015 scopus 로고    scopus 로고
    • An automated procedure for the extraction of metabolic network information from time series data
    • Marino,S. and Voit,E.O. (2006) An automated procedure for the extraction of metabolic network information from time series data. J. Bioinform. Comput. Biol., 4, 665-691.
    • (2006) J. Bioinform. Comput. Biol , vol.4 , pp. 665-691
    • Marino, S.1    Voit, E.O.2
  • 20
    • 33644555826 scopus 로고    scopus 로고
    • Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series
    • McKinney,B.A. et al. (2006) Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 73, 021912.
    • (2006) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys , vol.73 , pp. 021912
    • McKinney, B.A.1
  • 21
    • 2942694772 scopus 로고    scopus 로고
    • Artificial gene networks for objective comparison of analysis algorithms
    • Mendes,P. et al. (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics, 19 (Suppl. 2), ii122-ii129.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Mendes, P.1
  • 22
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • Moles,C.G. et al. (2003) Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res. 13, 2467-2474.
    • (2003) Genome Res , vol.13 , pp. 2467-2474
    • Moles, C.G.1
  • 23
    • 51049117937 scopus 로고    scopus 로고
    • Models from experiments: Combinatorial drug perturbations of cancer cells
    • Nelander,S. et al. (2008) Models from experiments: Combinatorial drug perturbations of cancer cells. Mol. Syst. Biol., 4, 216.
    • (2008) Mol. Syst. Biol , vol.4 , pp. 216
    • Nelander, S.1
  • 24
    • 2142825110 scopus 로고    scopus 로고
    • Adverse events after smallpox immunizations are associated with alterations in systemic cytokine levels
    • Rock,M.T. et al. (2004) Adverse events after smallpox immunizations are associated with alterations in systemic cytokine levels. J. Infect Dis., 189, 8.
    • (2004) J. Infect Dis , vol.189 , pp. 8
    • Rock, M.T.1
  • 25
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen,M. et al. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA., 99, 10555-10560.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 10555-10560
    • Ronen, M.1
  • 27
    • 0042155152 scopus 로고    scopus 로고
    • Numerical data fitting in dynamical systems: A practical introduction with applications and software
    • Donald,H. and Pardalos,P.M, eds, Kluwer Academic, Dordrecht
    • Schittkowski,K. (2002) Numerical data fitting in dynamical systems: A practical introduction with applications and software. In Applied Optimization. Donald,H. and Pardalos,P.M. (eds.), vol. 77. Kluwer Academic, Dordrecht.
    • (2002) Applied Optimization , vol.77
    • Schittkowski, K.1
  • 28
    • 16344385431 scopus 로고    scopus 로고
    • Evolutionary optimization with data collocation for reverse engineering of biological networks
    • Tsai,K.Y. and Wang,F.S. (2005) Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics, 21, 1180-1188.
    • (2005) Bioinformatics , vol.21 , pp. 1180-1188
    • Tsai, K.Y.1    Wang, F.S.2
  • 29
    • 33746895132 scopus 로고    scopus 로고
    • Parameter reconstruction for biochemical networks using interval analysis
    • Tucker,W. and Moulton,V. (2006) Parameter reconstruction for biochemical networks using interval analysis, Reliable Computing, 12, 389-402.
    • (2006) Reliable Computing , vol.12 , pp. 389-402
    • Tucker, W.1    Moulton, V.2
  • 30
    • 34547118379 scopus 로고    scopus 로고
    • Estimating parameters for generalized mass action models using constraint propagation
    • Tucker,W. et al. (2007) Estimating parameters for generalized mass action models using constraint propagation. Math. Bioscience, 208, 607-620.
    • (2007) Math. Bioscience , vol.208 , pp. 607-620
    • Tucker, W.1
  • 32
    • 4444351989 scopus 로고    scopus 로고
    • Decoupling dynamical systems for pathway identification from metabolic profiles
    • Voit,E.O. and Almeida,J. (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics, 20, 1670-1681.
    • (2004) Bioinformatics , vol.20 , pp. 1670-1681
    • Voit, E.O.1    Almeida, J.2
  • 33
    • 0034104824 scopus 로고    scopus 로고
    • Coarse-grained reverse engineering of genetic regulatory networks
    • Wahde,M. and Hertz,J. (2000) Coarse-grained reverse engineering of genetic regulatory networks. Biosystems, 55, 129-136.
    • (2000) Biosystems , vol.55 , pp. 129-136
    • Wahde, M.1    Hertz, J.2
  • 34
    • 0035958144 scopus 로고    scopus 로고
    • Hybrid differential evolution for problems of kinetic parameter estimation and dynamic optimization of an ethanol fermentation process
    • Wang,F.S. et al. (2001) Hybrid differential evolution for problems of kinetic parameter estimation and dynamic optimization of an ethanol fermentation process. Ind. Eng. Chem. Res., 40, 2876-2885.
    • (2001) Ind. Eng. Chem. Res , vol.40 , pp. 2876-2885
    • Wang, F.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.