메뉴 건너뛰기




Volumn 2, Issue 3, 2008, Pages 786-802

Parameter identification for stochastic hybrid systems using randomized optimization: A case study on subtilin production by Bacillus subtilis

Author keywords

Biochemical networks; Parameter identification; Randomized optimization; Stochastic hybrid models; Subtilin production

Indexed keywords

(001) PARAMETER; (MIN ,MAX ,+) FUNCTIONS; B. SUBTILIS; BACILLUS SUBTILIS (BS2); CASE STUDIES; ELSEVIER (CO); EXPERIMENTAL DATA; FITTING PARAMETERS; HYBRID MODEL (HM); IDENTIFIABILITY; MARKOV CHAIN MONTE CARLO (MCMC) APPROACH; PARAMETER IDENTIFICATIONS; PARAMETER VALUES; SIMULATED MODEL; SIMULATION-BASED; STOCHASTIC HYBRID SYSTEMS (SHS); SUBTILIN;

EID: 45249124485     PISSN: 1751570X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.nahs.2007.11.009     Document Type: Article
Times cited : (13)

References (28)
  • 1
    • 84944214361 scopus 로고    scopus 로고
    • Hybrid modeling and simulation of biological systems
    • Hybrid Systems: Computation and Control. Di Benedetto M., and Sangiovanni-Vincentelli A. (Eds), Springer-Verlag, Berlin
    • Alur R., Belta C., Ivancic F., Kumar V., Mintz M., Pappas G., Rubin H., Schug J., and Pappas G.J. Hybrid modeling and simulation of biological systems. In: Di Benedetto M., and Sangiovanni-Vincentelli A. (Eds). Hybrid Systems: Computation and Control. LNCS vol. 2034 (2001), Springer-Verlag, Berlin 19-32
    • (2001) LNCS , vol.2034 , pp. 19-32
    • Alur, R.1    Belta, C.2    Ivancic, F.3    Kumar, V.4    Mintz, M.5    Pappas, G.6    Rubin, H.7    Schug, J.8    Pappas, G.J.9
  • 2
    • 12344296412 scopus 로고    scopus 로고
    • Mathematical modeling of planar cell polarity to understand domineering nonautonomy
    • Amonlirdviman K., Khare N.A., Tree D.R.P., Chen W.-S., Axelrod J.D., and Tomlin C.J. Mathematical modeling of planar cell polarity to understand domineering nonautonomy. Science 307 5708 (2005) 423-426
    • (2005) Science , vol.307 , Issue.5708 , pp. 423-426
    • Amonlirdviman, K.1    Khare, N.A.2    Tree, D.R.P.3    Chen, W.-S.4    Axelrod, J.D.5    Tomlin, C.J.6
  • 3
    • 24344435117 scopus 로고    scopus 로고
    • Qualitative analysis and verification of hybrid models of genetic regulatory networks: Nutritional stress response in Escherichia coli
    • Hybrid Systems: Computation and Control. Thiele L., and Morari M. (Eds), Springer-Verlag, Berlin
    • Batt G., Ropers D., de Jong H., Geiselmann J., Page M., and Schneider D. Qualitative analysis and verification of hybrid models of genetic regulatory networks: Nutritional stress response in Escherichia coli. In: Thiele L., and Morari M. (Eds). Hybrid Systems: Computation and Control. LNCS vol. 3414 (2005), Springer-Verlag, Berlin 134-150
    • (2005) LNCS , vol.3414 , pp. 134-150
    • Batt, G.1    Ropers, D.2    de Jong, H.3    Geiselmann, J.4    Page, M.5    Schneider, D.6
  • 4
    • 39849106163 scopus 로고    scopus 로고
    • E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros, Subtilin production by Bacillus subtilis: Stochastic hybrid models and parameter identification, in: Systems Biology, IEEE Transactions on Circuits and Systems-I (special issue) (2008) (in press)
    • E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros, Subtilin production by Bacillus subtilis: Stochastic hybrid models and parameter identification, in: Systems Biology, IEEE Transactions on Circuits and Systems-I (special issue) (2008) (in press)
  • 6
    • 12244265093 scopus 로고    scopus 로고
    • DNA replication origins in the Schizosaccharomyces pombe genome
    • Dai J., Chuang R.Y., and Kelly T.J. DNA replication origins in the Schizosaccharomyces pombe genome. PNAS 102 102 (2005) 337-342
    • (2005) PNAS , vol.102 , Issue.102 , pp. 337-342
    • Dai, J.1    Chuang, R.Y.2    Kelly, T.J.3
  • 7
    • 0000816682 scopus 로고
    • Piecewise-deterministic Markov processes: A general class of non-diffusion stochastic models
    • Davis M.H.A. Piecewise-deterministic Markov processes: A general class of non-diffusion stochastic models. Journal of the Royal Statistical Society B 46 3 (1984) 353-388
    • (1984) Journal of the Royal Statistical Society B , vol.46 , Issue.3 , pp. 353-388
    • Davis, M.H.A.1
  • 8
    • 39549089902 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong H. Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology 79 (2002) 726-739
    • (2002) Journal of Computational Biology , vol.79 , pp. 726-739
    • de Jong, H.1
  • 9
    • 35248865758 scopus 로고    scopus 로고
    • Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach
    • Hybrid Systems: Computation and Control. Maler O., and Pnueli A. (Eds), Springer Verlag, Berlin
    • de Jong H., Gouze J.-L., Hernandez C., Page M., Sari T., and Geiselmann J. Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach. In: Maler O., and Pnueli A. (Eds). Hybrid Systems: Computation and Control. LNCS vol. 2623 (2003), Springer Verlag, Berlin 267-282
    • (2003) LNCS , vol.2623 , pp. 267-282
    • de Jong, H.1    Gouze, J.-L.2    Hernandez, C.3    Page, M.4    Sari, T.5    Geiselmann, J.6
  • 10
    • 0141567816 scopus 로고    scopus 로고
    • Marginal maximum a posteriori estimation using Markov chain Monte Carlo
    • Doucet A., Godsill S.J., and Robert C.P. Marginal maximum a posteriori estimation using Markov chain Monte Carlo. Statistics and Computing 12 (2002) 77-84
    • (2002) Statistics and Computing , vol.12 , pp. 77-84
    • Doucet, A.1    Godsill, S.J.2    Robert, C.P.3
  • 11
    • 33745796556 scopus 로고    scopus 로고
    • Reconstruction of switching thresholds in piecewise-affne models of genetic regulatory networks
    • Hybrid Systems: Computation and Control. Hespanha J., and Tiwari A. (Eds), Springer Verlag, Berlin
    • Drulhe S., Ferrari-Trecate G., de Jong H., and Viari A. Reconstruction of switching thresholds in piecewise-affne models of genetic regulatory networks. In: Hespanha J., and Tiwari A. (Eds). Hybrid Systems: Computation and Control. Lecture Notes in Computer Science vol. 3927 (2006), Springer Verlag, Berlin 184-199
    • (2006) Lecture Notes in Computer Science , vol.3927 , pp. 184-199
    • Drulhe, S.1    Ferrari-Trecate, G.2    de Jong, H.3    Viari, A.4
  • 13
    • 84944196766 scopus 로고    scopus 로고
    • Lateral inhibition through delta-notch signalling: A piecewise affine hybrid model
    • Hybrid Systems: Computation and Control. Di Benedetto M., and Sangiovanni-Vincentelli A. (Eds), Springer-Verlag, Berlin
    • Ghosh R., and Tomlin C. Lateral inhibition through delta-notch signalling: A piecewise affine hybrid model. In: Di Benedetto M., and Sangiovanni-Vincentelli A. (Eds). Hybrid Systems: Computation and Control. LNCS vol. 2034 (2001), Springer-Verlag, Berlin 232-246
    • (2001) LNCS , vol.2034 , pp. 232-246
    • Ghosh, R.1    Tomlin, C.2
  • 14
    • 77956890234 scopus 로고
    • Monte carlo sampling methods using markov chains and their applications
    • Hastings W.K. Monte carlo sampling methods using markov chains and their applications. Biometrika 57 (1970) 97-109
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 15
    • 27644447823 scopus 로고    scopus 로고
    • Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems
    • Hespanha J., and Singh A. Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems. International Journal on Robust Control 15 15 (2005) 669-689
    • (2005) International Journal on Robust Control , vol.15 , Issue.15 , pp. 669-689
    • Hespanha, J.1    Singh, A.2
  • 16
    • 35048839340 scopus 로고    scopus 로고
    • Modeling subtilin production in Bacillus subtilis using stochastic hybrid systems
    • Hybrid Systems: Computation and Control. Alur R., and Pappas G.J. (Eds), Springer-Verlag, Berlin
    • Hu J., Wu W.C., and Sastry S.S. Modeling subtilin production in Bacillus subtilis using stochastic hybrid systems. In: Alur R., and Pappas G.J. (Eds). Hybrid Systems: Computation and Control. LNCS vol. 2993 (2004), Springer-Verlag, Berlin 417-431
    • (2004) LNCS , vol.2993 , pp. 417-431
    • Hu, J.1    Wu, W.C.2    Sastry, S.S.3
  • 17
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: From theories to phenotypes
    • Kaern M., Elston T.C., Blake W.J., and Collins J.J. Stochasticity in gene expression: From theories to phenotypes. Nature Reviews Genetics 6 6 (2005) 451-464
    • (2005) Nature Reviews Genetics , vol.6 , Issue.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 18
    • 70349397825 scopus 로고    scopus 로고
    • Stochastic hybrid modeling of biochemical processes
    • Cassandras C.G., and Lygeros J. (Eds), CRC press
    • Kouretas P., Koutroumpas K., Lygeros J., and Lygerou Z. Stochastic hybrid modeling of biochemical processes. In: Cassandras C.G., and Lygeros J. (Eds). Stochastic Hybrid Systems vol. 9083 (2006), CRC press
    • (2006) Stochastic Hybrid Systems , vol.9083
    • Kouretas, P.1    Koutroumpas, K.2    Lygeros, J.3    Lygerou, Z.4
  • 24
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao C.V., Wolf D.M., and Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 6912 (2002) 231-237
    • (2002) Nature , vol.420 , Issue.6912 , pp. 231-237
    • Rao, C.V.1    Wolf, D.M.2    Arkin, A.P.3
  • 25
    • 0141642530 scopus 로고    scopus 로고
    • System identification with information theoretic criteria
    • Identification, Adaptation, Learning. Bittanti S., and Picci G. (Eds), Springer, Berlin
    • Stoorvogel A.A., and van Schuppen J.H. System identification with information theoretic criteria. In: Bittanti S., and Picci G. (Eds). Identification, Adaptation, Learning. NATO ASI F Series vol. 153 (1996), Springer, Berlin 289-338
    • (1996) NATO ASI F Series , vol.153 , pp. 289-338
    • Stoorvogel, A.A.1    van Schuppen, J.H.2
  • 26
    • 0037197850 scopus 로고    scopus 로고
    • Mechanisms of noise-resistance in genetic oscillators
    • Vilar J.M., Kueh H.Y., Barkai N., and Leibler S. Mechanisms of noise-resistance in genetic oscillators. PNAS 99 (2002) 5988-5992
    • (2002) PNAS , vol.99 , pp. 5988-5992
    • Vilar, J.M.1    Kueh, H.Y.2    Barkai, N.3    Leibler, S.4
  • 27
    • 14744282987 scopus 로고    scopus 로고
    • Diversity in times of adversity: Probabilistic strategies in microbial survival games
    • Wolf D., Vazirani V.V., and Arkin A.P. Diversity in times of adversity: Probabilistic strategies in microbial survival games. Journal of Theoretcial Biology 234 2 (2005) 227-253
    • (2005) Journal of Theoretcial Biology , vol.234 , Issue.2 , pp. 227-253
    • Wolf, D.1    Vazirani, V.V.2    Arkin, A.P.3
  • 28
    • 22744441386 scopus 로고    scopus 로고
    • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 tat fluctuations drive phenotypic diversity
    • Wu L., Burnett J.C., Toettcher J.E., Arkin A.P., and Schaffer D.V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 tat fluctuations drive phenotypic diversity. Cell 122 2 (2005) 169-182
    • (2005) Cell , vol.122 , Issue.2 , pp. 169-182
    • Wu, L.1    Burnett, J.C.2    Toettcher, J.E.3    Arkin, A.P.4    Schaffer, D.V.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.