메뉴 건너뛰기




Volumn 3, Issue 11, 2008, Pages

Extended Kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks

Author keywords

[No Author keywords available]

Indexed keywords

JANUS KINASE; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE KINASE; RAF PROTEIN; RAS PROTEIN; STAT PROTEIN;

EID: 56649104989     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003758     Document Type: Article
Times cited : (96)

References (46)
  • 1
    • 41249097444 scopus 로고    scopus 로고
    • Interaction networks for systems biology
    • Bader S, Kühner S, Gavin AC (2008) Interaction networks for systems biology. FEBS Letter 582(8): 1220-4.
    • (2008) FEBS Letter , vol.582 , Issue.8 , pp. 1220-1224
    • Bader, S.1    Kühner, S.2    Gavin, A.C.3
  • 2
    • 0037417886 scopus 로고    scopus 로고
    • Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data based modeling
    • Swameye I, Muller TG, Timmer J, Sandra O, Klingmuller U (2002) Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data based modeling. Proc Natl Acad Sci USA 100(3): 1028-1033.
    • (2002) Proc Natl Acad Sci USA , vol.100 , Issue.3 , pp. 1028-1033
    • Swameye, I.1    Muller, T.G.2    Timmer, J.3    Sandra, O.4    Klingmuller, U.5
  • 3
    • 36248952170 scopus 로고    scopus 로고
    • The stability and robustness of metabolic states: Identifying stabilizihg sites in metabolic networks
    • Grimbs S, Selbig J, Bulik S, Holzhütter HG, Steuer R (2007) The stability and robustness of metabolic states: identifying stabilizihg sites in metabolic networks. Mol Syst Biol 3: 146.
    • (2007) Mol Syst Biol , vol.3 , pp. 146
    • Grimbs, S.1    Selbig, J.2    Bulik, S.3    Holzhütter, H.G.4    Steuer, R.5
  • 4
    • 34548049053 scopus 로고    scopus 로고
    • Mathematical modeling of intracellular signaling pathways
    • Klipp E, Liebermeister W (2006) Mathematical modeling of intracellular signaling pathways. BMC Neurosci 2006; 7(Suppl 1): S10.
    • (2006) BMC Neurosci , vol.7 , Issue.SUPPL. 1
    • Klipp, E.1    Liebermeister, W.2
  • 5
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modeling and analysis of biochemical networks: Mechanism-based models and model-based experiments
    • Natal AW, Riel V (2006) Dynamic modeling and analysis of biochemical networks: mechanism-based models and model-based experiments. Briefings in Bioinformatics 7: 364-374.
    • (2006) Briefings in Bioinformatics , vol.7 , pp. 364-374
    • Natal, A.W.1    Riel, V.2
  • 6
    • 0036789922 scopus 로고    scopus 로고
    • Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
    • Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, et al. (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci USA 99(20): 12841-12846.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.20 , pp. 12841-12846
    • Kholodenko, B.N.1    Kiyatkin, A.2    Bruggeman, F.J.3    Sontag, E.4    Westerhoff, H.V.5
  • 8
    • 33747061013 scopus 로고    scopus 로고
    • Structural kinetic modeling of metabolic networks
    • Steuer R, Gross T, Selbig J, Blasius B (2006) Structural kinetic modeling of metabolic networks. Proc Natl Acad Sci USA 103(32): 11868-11873.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.32 , pp. 11868-11873
    • Steuer, R.1    Gross, T.2    Selbig, J.3    Blasius, B.4
  • 9
    • 20444411533 scopus 로고    scopus 로고
    • the silicon cell initiative: Working towards a detailed kinetic description at the cellular level
    • Snoep JL (2005) the silicon cell initiative: working towards a detailed kinetic description at the cellular level. Curr Opin Biotechnol 16: 336-343.
    • (2005) Curr Opin Biotechnol , vol.16 , pp. 336-343
    • Snoep, J.L.1
  • 10
    • 22344438058 scopus 로고    scopus 로고
    • Electronic Data Sources for Kinetic Models of Cell Signaling
    • HarshaRani GV, Vayttaden SJ, Bhalla US (2005) Electronic Data Sources for Kinetic Models of Cell Signaling. J Biochem 137: 653-657.
    • (2005) J Biochem , vol.137 , pp. 653-657
    • HarshaRani, G.V.1    Vayttaden, S.J.2    Bhalla, U.S.3
  • 11
    • 36248943011 scopus 로고    scopus 로고
    • Dynamic pathway modeling: Feasibility analysis and optimal experimental design
    • Maiwald T, Kreutz C, Pfeifer AC, Bohl S, Klingymüller U, et al. (2007) Dynamic pathway modeling: feasibility analysis and optimal experimental design. Ann N Y Acad Sci 1115: 212-220.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 212-220
    • Maiwald, T.1    Kreutz, C.2    Pfeifer, A.C.3    Bohl, S.4    Klingymüller, U.5
  • 12
    • 40149110264 scopus 로고    scopus 로고
    • Parameter estimate of signal transduction pathways
    • Arisi I, Cattaneo A, Rosato V (2006) Parameter estimate of signal transduction pathways. BMC Neurosci 7(Suppl 1): S6.
    • (2006) BMC Neurosci , vol.7 , Issue.SUPPL. 1
    • Arisi, I.1    Cattaneo, A.2    Rosato, V.3
  • 13
    • 0242574982 scopus 로고    scopus 로고
    • Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
    • Moles CG, Mendes, P, Banga JR (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    Mendes, P.2    Banga, J.R.3
  • 14
    • 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
  • 15
    • 33845875759 scopus 로고    scopus 로고
    • Simulated maximum likelihood method for estimating kinetic rates in gene expression
    • Tian T, Xu S, Gao J, Burrage K (2006) Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics 23(1): 84-91.
    • (2006) Bioinformatics , vol.23 , Issue.1 , pp. 84-91
    • Tian, T.1    Xu, S.2    Gao, J.3    Burrage, K.4
  • 16
    • 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(2): 155-164.
    • (2005) Biosystems , vol.80 , Issue.2 , pp. 155-164
    • Sugimoto, M.1    Kikuchi, S.2    Tomita, M.3
  • 17
    • 33751418323 scopus 로고    scopus 로고
    • a simplified method for power-law modeling of metabolic pathways from time-course data and steady-state flux profiles
    • Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M (2006) a simplified method for power-law modeling of metabolic pathways from time-course data and steady-state flux profiles. Theory Biology Med Model 3: 24.
    • (2006) Theory Biology Med Model , vol.3 , pp. 24
    • Kitayama, T.1    Kinoshita, A.2    Sugimoto, M.3    Nakayama, Y.4    Tomita, M.5
  • 18
    • 33749340654 scopus 로고    scopus 로고
    • Parameter estimation in biochemical systems models with alternating regression
    • Chou IC, Martens H, Voit EO (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    Martens, H.2    Voit, E.O.3
  • 19
    • 36549012683 scopus 로고    scopus 로고
    • Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
    • Quach M, Brunel N, d'Alché-Buc F (2007) Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. Bioinformatics 23(23): 3209-3216.
    • (2007) Bioinformatics , vol.23 , Issue.23 , pp. 3209-3216
    • Quach, M.1    Brunel, N.2    d'Alché-Buc, F.3
  • 20
    • 0028409736 scopus 로고
    • Adaptive model architecture and extended Kalman-Bucy filters
    • Costa PJ (1994) Adaptive model architecture and extended Kalman-Bucy filters. IEEE Trans. Aerospace Electron System 30: 525-533.
    • (1994) IEEE Trans. Aerospace Electron System , vol.30 , pp. 525-533
    • Costa, P.J.1
  • 21
    • 84899008192 scopus 로고    scopus 로고
    • Learning nonlinear dynamical systems using an EM algorithm
    • NIPS'98, 431-437
    • Ghahramani Z, Roweis S (1999) Learning nonlinear dynamical systems using an EM algorithm. Neural Information Processing Systems 11 (NIPS'98): 431-437.
    • (1999) Neural Information Processing Systems , vol.11
    • Ghahramani, Z.1    Roweis, S.2
  • 22
    • 84889830739 scopus 로고    scopus 로고
    • Simon D (2006) optimal state estimation-Kalman, H∞, and nonlinear approaches. New Jersey: A John Wiley & Sons, Inc. Hoboken. 552 p.
    • Simon D (2006) optimal state estimation-Kalman, H∞, and nonlinear approaches. New Jersey: A John Wiley & Sons, Inc. Hoboken. 552 p.
  • 23
    • 21244437999 scopus 로고    scopus 로고
    • Unscented filtering and nonlinear estimation
    • Julier SJ, Uhlmann JK (2004) Unscented filtering and nonlinear estimation. Proceedings of the IEEE 92: 401-422.
    • (2004) Proceedings of the IEEE , vol.92 , pp. 401-422
    • Julier, S.J.1    Uhlmann, J.K.2
  • 25
    • 0001460136 scopus 로고    scopus 로고
    • On sequential Monte Carlo sampling methods for Bayesian filtering
    • Doucet A, Godsill S, Andrieu C (2000) On sequential Monte Carlo sampling methods for Bayesian filtering. Statistics and Computing 10: 197-208.
    • (2000) Statistics and Computing , vol.10 , pp. 197-208
    • Doucet, A.1    Godsill, S.2    Andrieu, C.3
  • 26
    • 34547583106 scopus 로고    scopus 로고
    • Bayesian estimation via sequential Monte Carlo sampling - Constrained dynamic systems
    • Lang L, Chen W, Bakshi BR, Goel PK, Ungarala S (2007) Bayesian estimation via sequential Monte Carlo sampling - Constrained dynamic systems. Automatica 3: 1615-1622.
    • (2007) Automatica , vol.3 , pp. 1615-1622
    • Lang, L.1    Chen, W.2    Bakshi, B.R.3    Goel, P.K.4    Ungarala, S.5
  • 27
    • 30344486983 scopus 로고    scopus 로고
    • Recursive Monte Carlo filters: Algorithms and theoretical analysis
    • Künsch HR (2005) Recursive Monte Carlo filters: algorithms and theoretical analysis. Annals of Statistics 33: 1983-2021.
    • (2005) Annals of Statistics , vol.33 , pp. 1983-2021
    • Künsch, H.R.1
  • 28
    • 33846939958 scopus 로고    scopus 로고
    • Sequential Monte Carlo without Likelihoods
    • Sisson SA, Fan Y, Tanaka MM (2007) Sequential Monte Carlo without Likelihoods. Proc Natl Acad Sci 104: 1760-1765.
    • (2007) Proc Natl Acad Sci , vol.104 , pp. 1760-1765
    • Sisson, S.A.1    Fan, Y.2    Tanaka, M.M.3
  • 31
    • 33750845118 scopus 로고    scopus 로고
    • TGF-â concentration dependence of Smad phosphorylation kinetics: A systems perspective
    • Clarke DC, Betterton MD, Liu X (2006) TGF-â concentration dependence of Smad phosphorylation kinetics: a systems perspective. IEEE Systems Biology 153: 412-424.
    • (2006) IEEE Systems Biology , vol.153 , pp. 412-424
    • Clarke, D.C.1    Betterton, M.D.2    Liu, X.3
  • 32
    • 41449088987 scopus 로고    scopus 로고
    • â2-Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real Time cAMP Dynamics
    • ViolinD, DiPilato LM, Yildirim N, Elston TC, Zhang J, et al. (2008) â2-Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real Time cAMP Dynamics. J Biol Chem 283: 2949-2961.
    • (2008) J Biol Chem , vol.283 , pp. 2949-2961
    • Violin, D.1    DiPilato, L.M.2    Yildirim, N.3    Elston, T.C.4    Zhang, J.5
  • 34
    • 0037138370 scopus 로고    scopus 로고
    • Signaling through the JAK/STAT pathway, recent advances and future Challenges
    • Kisseleva T, Bhattacharya S, Braunstein J, Schindler CW (2002) Signaling through the JAK/STAT pathway, recent advances and future Challenges. Gene 285: 1-24.
    • (2002) Gene , vol.285 , pp. 1-24
    • Kisseleva, T.1    Bhattacharya, S.2    Braunstein, J.3    Schindler, C.W.4
  • 35
    • 0034667593 scopus 로고    scopus 로고
    • Meaningful relationships: The regulation of the Ras/Raf/ MEK/ ERK pathway by protein interaction
    • Kolch W (2000) Meaningful relationships: the regulation of the Ras/Raf/ MEK/ ERK pathway by protein interaction. Biochem J 351: 289-305.
    • (2000) Biochem J , vol.351 , pp. 289-305
    • Kolch, W.1
  • 36
    • 0004237102 scopus 로고    scopus 로고
    • Third edition. New Jersey: Prentice Hall, Upper Saddle River
    • Ogata K (1998) System Dynamics. Third edition. New Jersey: Prentice Hall, Upper Saddle River.
    • (1998) System Dynamics
    • Ogata, K.1
  • 37
    • 42949164125 scopus 로고    scopus 로고
    • Formulating genome-scale kinetic models in the post-genome era
    • Jamshidi N, Palsson BØ (2008) Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology 4: 171.
    • (2008) Molecular Systems Biology , vol.4 , pp. 171
    • Jamshidi, N.1    Palsson, B.2
  • 39
    • 10944253539 scopus 로고    scopus 로고
    • Estimation of parameters in a linear state space model using a Rao-Blackwellised particle filter
    • Li P, Goodall R, Kadirkamanathan V (2004) Estimation of parameters in a linear state space model using a Rao-Blackwellised particle filter. IEE Proc Control Theory Appl 151: 727-738.
    • (2004) IEE Proc Control Theory Appl , vol.151 , pp. 727-738
    • Li, P.1    Goodall, R.2    Kadirkamanathan, V.3
  • 40
    • 1542329124 scopus 로고    scopus 로고
    • Polynomial extended kalman filtering for discrete-time nonlinear stochastic systems
    • Maui, Hawii, USA, December
    • Germani A, Manes C, Palumbo P (2003) Polynomial extended kalman filtering for discrete-time nonlinear stochastic systems. Proceedings of the 42nd IEEE Conference on Decision and Control Maui, Hawii, USA, December 2003 1: 886-891.
    • (2003) Proceedings of the 42nd IEEE Conference on Decision and Control , vol.1 , pp. 886-891
    • Germani, A.1    Manes, C.2    Palumbo, P.3
  • 43
    • 37649031765 scopus 로고    scopus 로고
    • Estimation of parameters and unobserved components for nonlinear systems from noisy time series
    • Sitz A, Schwarz U, Kurths J, Voss HU (2002) Estimation of parameters and unobserved components for nonlinear systems from noisy time series. Physical Review E 66: 016210.
    • (2002) Physical Review E , vol.66 , pp. 016210
    • Sitz, A.1    Schwarz, U.2    Kurths, J.3    Voss, H.U.4
  • 44
    • 41349094363 scopus 로고    scopus 로고
    • Freedom of expression Introduction to special issue
    • Riddihough G, Purnell BA, Travis J (2008) Freedom of expression Introduction to special issue. Science 319(5871): 1781.
    • (2008) Science , vol.319 , Issue.5871 , pp. 1781
    • Riddihough, G.1    Purnell, B.A.2    Travis, J.3
  • 45
    • 14844307159 scopus 로고    scopus 로고
    • Inferring quantitative models of regulatory networks from expression data
    • Nachman I, Regev A, Friedman N (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 (Suppl. 1): 248-256.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1 , pp. 248-256
    • Nachman, I.1    Regev, A.2    Friedman, N.3
  • 46
    • 0018435192 scopus 로고
    • asymptotic behavior of the extended Kalman filter as a parameter estimator for linear systems
    • Ljung L. (1979) asymptotic behavior of the extended Kalman filter as a parameter estimator for linear systems. IEEE Trans on Automatic Control AC-2: 36-50.
    • (1979) IEEE Trans on Automatic Control , vol.AC-2 , pp. 36-50
    • Ljung, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.