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Volumn 802, Issue , 2012, Pages 185-197

Modeling gene regulation networks using ordinary differential equations

Author keywords

Dynamic system; Gene regulation network; Generalized profiling method; Spline smoothing; Systems biology; Time course gene expression

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; FUNGAL GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE; TIME;

EID: 84555190018     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-400-1_12     Document Type: Article
Times cited : (44)

References (21)
  • 2
    • 73449106062 scopus 로고    scopus 로고
    • Reconstructing transcriptional regulatory networks through genomics data
    • Sun N, Zhao H (2009) Reconstructing transcriptional regulatory networks through genomics data. Statistical Methods in Medical Research 18:595-617.
    • (2009) Statistical Methods in Medical Research , vol.18 , pp. 595-617
    • Sun, N.1    Zhao, H.2
  • 3
    • 0030797355 scopus 로고    scopus 로고
    • Robustness in simple biochemical networks
    • DOI 10.1038/43199
    • Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387:913-917. (Pubitemid 27289593)
    • (1997) Nature , vol.387 , Issue.6636 , pp. 913-917
    • Barkai, N.1    Leibler, S.2
  • 5
    • 36249019789 scopus 로고    scopus 로고
    • Dialogue on reverseengineering assessment and methods: The dream of high-throughput pathway inference
    • Stolovitzky G, Monroe D, Califano A (2007) Dialogue on reverseengineering assessment and methods: The dream of high-throughput pathway inference. Annals of the New York Academy of Sciences 1115:11-22.
    • (2007) Annals of the New York Academy of Sciences , vol.1115 , pp. 11-22
    • Stolovitzky, G.1    Monroe, D.2    Califano, A.3
  • 7
    • 77949644952 scopus 로고    scopus 로고
    • Towards a rigorous assessment of systems biology models: The dream3 challenges
    • Prill RJ, Marbach D, Saez-Rodriguez J et al (2010) Towards a rigorous assessment of systems biology models: the dream3 challenges. PLoS One 5:e9202.
    • (2010) PLoS One , vol.5
    • Prill, R.J.1    Marbach, D.2    Saez-Rodriguez, J.3
  • 8
    • 84860883861 scopus 로고    scopus 로고
    • Dialogue for Reverse Engineering Assessments and Methods (DREAM)
    • Dialogue for Reverse Engineering Assessments and Methods (DREAM), http://wiki.c2b2.columbia.edu/dream.
  • 9
    • 42349101913 scopus 로고    scopus 로고
    • Efficient local estimation for time-varying coefficients in deterministic dynamic models with applications to HIV-1 dynamics
    • Chen J, Wu H (2008) Efficient local estimation for time-varying coefficients in deterministic dynamic models with applications to HIV-1 dynamics. Journal of the American Statistical Association 103(481):369-383.
    • (2008) Journal of the American Statistical Association , vol.103 , Issue.481 , pp. 369-383
    • Chen, J.1    Wu, H.2
  • 10
    • 35648981518 scopus 로고    scopus 로고
    • Parameter estimation for differential equations: A generalized smoothing approach (with discussion)
    • Ramsay JO, Hooker G, Campbell D et al (2007) Parameter estimation for differential equations: a generalized smoothing approach (with discussion). Journal of the Royal Statistical Society, Series B 69:741-796.
    • (2007) Journal of the Royal Statistical Society, Series B , vol.69 , pp. 741-796
    • Ramsay, J.O.1    Hooker, G.2    Campbell, D.3
  • 11
    • 73949083888 scopus 로고    scopus 로고
    • Asymptotic efficiency and finite-sample properties of the generalized profiling estimation of parameters in ordinary differential equations
    • Qi X, Zhao H (2010) Asymptotic efficiency and finite-sample properties of the generalized profiling estimation of parameters in ordinary differential equations. The Annals of Statistics 38:435-481.
    • (2010) The Annals of Statistics , vol.38 , pp. 435-481
    • Qi, X.1    Zhao, H.2
  • 12
    • 36448970861 scopus 로고    scopus 로고
    • Inferring transcriptional regulatory networks from high-throughput data
    • DOI 10.1093/bioinformatics/btm465
    • Wang R, Wang Y, Zhang X et al (2007) Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics 23:3056-3064. (Pubitemid 350162871)
    • (2007) Bioinformatics , vol.23 , Issue.22 , pp. 3056-3064
    • Wang, R.-S.1    Wang, Y.2    Zhang, X.-S.3    Chen, L.4
  • 13
    • 34249856850 scopus 로고    scopus 로고
    • Bayesian model-based inference of transcription factor activity
    • Rogers S, Khanin R, Girolami M (2007) Bayesian model-based inference of transcription factor activity. BMC Bioinformatics 8:1-11.
    • (2007) BMC Bioinformatics , vol.8 , pp. 1-11
    • Rogers, S.1    Khanin, R.2    Girolami, M.3
  • 14
    • 49549105346 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gao P, Honkela A, Rattray M et al (2008) Genomic expression programs in the response of yeast cells to environmental changes. Bioinformatics 24:i70-i75.
    • (2008) Bioinformatics , vol.24
    • Gao, P.1    Honkela, A.2    Rattray, M.3
  • 15
    • 70449375094 scopus 로고    scopus 로고
    • Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics
    • Aijo T, Lahdesmaki H (2009) Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics. Bioinformatics 25:2937-2944.
    • (2009) Bioinformatics , vol.25 , pp. 2937-2944
    • Aijo, T.1    Lahdesmaki, H.2
  • 16
    • 65549161909 scopus 로고    scopus 로고
    • Gaussian process regression bootstrapping: Exploring the effects of uncertainty in time course data
    • Kirk PDW, Stumpf MPH (2009) Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinformatics 25:1300-1306.
    • (2009) Bioinformatics , vol.25 , pp. 1300-1306
    • Pdw, K.1    Mph, S.2
  • 17
    • 62549093118 scopus 로고    scopus 로고
    • Benchmarks for identification of ordinary differential equations from time series data
    • Gennemark P,Wedelin D (2009) Benchmarks for identification of ordinary differential equations from time series data. Bioinformatics 25:780-786.
    • (2009) Bioinformatics , vol.25 , pp. 780-786
    • Gennemark, P.1    Wedelin, D.2
  • 18
    • 84860883862 scopus 로고    scopus 로고
    • Matlab codes for estimating parameters in the ODE models
    • Matlab codes for estimating parameters in the ODE models, http://www.stat.sfu.ca/-cao/Research.html.
  • 19
    • 47049084462 scopus 로고    scopus 로고
    • Estimating dynamic models for gene regulation networks
    • DOI 10.1093/bioinformatics/btn246
    • Cao J, Zhao H (2008) Estimating dynamic models for gene regulation networks. Bioinformatics 24:1619-1624. (Pubitemid 351966161)
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1619-1624
    • Cao, J.1    Zhao, H.2
  • 20
    • 0004045887 scopus 로고    scopus 로고
    • Brooks/Cole, Pacific Grove, California, seventh edition
    • Burden RL, Douglas FJ (2000) Numerical Analysis. Brooks/Cole, Pacific Grove, California, seventh edition.
    • (2000) Numerical Analysis
    • Burden, R.L.1    Douglas, F.J.2
  • 21
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch AP, Spellman PT, Kao CM et al (2000) Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11:4241-4257.
    • (2000) Molecular Biology of the Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1    Spellman, P.T.2    Kao, C.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.