메뉴 건너뛰기




Volumn 8, Issue 4, 2010, Pages 661-677

Inference of genetic networks using LPMs: Assessment of confidence values of regulations

Author keywords

bootstrap; gene expression; Genetic network inference

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 77955580243     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720010004859     Document Type: Article
Times cited : (8)

References (36)
  • 1
    • 0033737840 scopus 로고    scopus 로고
    • Inferring qualitative relations in genetic networks and metabolic pathways
    • Akutsu T, Miyano S, Kuhara S, Inferring qualitative relations in genetic networks and metabolic pathways, Bioinformatics 16:727-734, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 727-734
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 2
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From co-expression clustering to reverse engineering
    • D'haeseleer P, Liang S, Somogyi R, Genetic network inference: From co-expression clustering to reverse engineering, Bioinformatics 16:707-726, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 6
    • 0036372453 scopus 로고    scopus 로고
    • Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression
    • Imoto S, Goto T, Miyano S, Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression, Proc Pacific Symposium on Biocomputing 7:175-186, 2002.
    • (2002) Proc Pacific Symposium on Biocomputing , vol.7 , pp. 175-186
    • Imoto, S.1    Goto, T.2    Miyano, S.3
  • 8
    • 12344259602 scopus 로고    scopus 로고
    • Advances to Bayesian Network inference for generating causal networks from observational biological data
    • Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED, Advances to Bayesian Network inference for generating causal networks from observational biological data, Bioinformatics 20:3594-3603, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 3594-3603
    • Yu, J.1    Smith, V.A.2    Wang, P.P.3    Hartemink, A.J.4    Jarvis, E.D.5
  • 9
    • 34548388925 scopus 로고    scopus 로고
    • Inference of gene networks from temporal gene expression profiles
    • Bansal M, di Bernardo D, Inference of gene networks from temporal gene expression profiles, IET Syst Biol 5:306-312, 2007.
    • (2007) IET Syst Biol , vol.5 , pp. 306-312
    • Bansal, M.1    Di Bernardo, D.2
  • 10
    • 33745616528 scopus 로고    scopus 로고
    • Identification of biochemical networks by S-tree based genetic programming
    • Cho DY, Cho KH, Zhang BT, Identification of biochemical networks by S-tree based genetic programming, Bioinformatics 22:1631-1640, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 1631-1640
    • Cho, D.Y.1    Cho, K.H.2    Zhang, B.T.3
  • 11
    • 33749340654 scopus 로고    scopus 로고
    • Parameter estimation in biochemical systems models with alternating regression
    • Chou IC, Martens H, Voit EO, Parameter estimation in biochemical systems models with alternating regression, Theor Biol Med Model 3:25, 2006.
    • (2006) Theor Biol Med Model , vol.3 , pp. 25
    • Chou, I.C.1    Martens, H.2    Voit, E.O.3
  • 12
    • 65649102679 scopus 로고    scopus 로고
    • Recent developments in parameter estimation and structure identification of biochemical and genomic systems
    • Chou IC, Voit EO, Recent developments in parameter estimation and structure identification of biochemical and genomic systems, Math Biosci 219:57-83, 2009.
    • (2009) Math Biosci , vol.219 , pp. 57-83
    • Chou, I.C.1    Voit, E.O.2
  • 13
    • 33847314052 scopus 로고    scopus 로고
    • Parameter estimation using simulated annealing for S-system models of biochemical networks
    • Gonzalez OR, Küper C, Jung K, Naval Jr PC, Mendoza E, Parameter estimation using simulated annealing for S-system models of biochemical networks, Bioinformatics 23:480-486, 2007.
    • (2007) Bioinformatics , vol.23 , pp. 480-486
    • Gonzalez, O.R.1    Küper, C.2    Jung, K.3    Naval Jr., P.C.4    Mendoza, E.5
  • 14
    • 0037461033 scopus 로고    scopus 로고
    • Dynamic modeling of genetic networks using genetic algorithm and S-system
    • Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M, Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics 19:643-650, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 643-650
    • Kikuchi, S.1    Tominaga, D.2    Arita, M.3    Takahashi, K.4    Tomita, M.5
  • 17
    • 41949109225 scopus 로고    scopus 로고
    • Inference of biochemical network models in S-system using multiobjective optimization approach
    • Liu PK, Wang FS, Inference of biochemical network models in S-system using multiobjective optimization approach, Bioinformatics 24:1085-1092, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 1085-1092
    • Liu, P.K.1    Wang, F.S.2
  • 18
    • 16344385431 scopus 로고    scopus 로고
    • Evolutionary optimization with data collocation for reverse engineering of biological networks
    • Tsai KY, Wang FS, Evolutionary optimization with data collocation for reverse engineering of biological networks, Bioinformatics 21:1180-1188, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 1180-1188
    • Tsai, K.Y.1    Wang, F.S.2
  • 20
    • 4444351989 scopus 로고    scopus 로고
    • Decoupling dynamical systems for pathway identification from metabolic profiles
    • Voit EO, Almeida J, Decoupling dynamical systems for pathway identification from metabolic profiles, Bioinformatics 20:1670-1681, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 1670-1681
    • Voit, E.O.1    Almeida, J.2
  • 21
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • Yeung MKS, Tegńer J, Collins JJ, Reverse engineering gene networks using singular value decomposition and robust regression, Proc Natl Acad Sci USA 99:6163-6168, 2002.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6163-6168
    • Mks, Y.1    Tegńer, J.2    Collins, J.J.3
  • 22
    • 63549084899 scopus 로고    scopus 로고
    • Genetic network inference as a series of discrimination tasks
    • Kimura S, Nakayama S, Hatakeyama M, Genetic network inference as a series of discrimination tasks, Bioinformatics 25:918-925, 2009.
    • (2009) Bioinformatics , vol.25 , pp. 918-925
    • Kimura, S.1    Nakayama, S.2    Hatakeyama, M.3
  • 24
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the Jackknife
    • Efron B, Bootstrap methods: Another look at the Jackknife, Ann Stat 7:1-26, 1979.
    • (1979) Ann Stat , vol.7 , pp. 1-26
    • Efron, B.1
  • 25
    • 84936916896 scopus 로고
    • Robust locally weight regression and smoothing scatterplots
    • Cleveland WS, Robust locally weight regression and smoothing scatterplots, J Am Stat Assoc 79:829-836, 1979.
    • (1979) J Am Stat Assoc , vol.79 , pp. 829-836
    • Cleveland, W.S.1
  • 27
    • 0000561116 scopus 로고
    • On the implementation of a primal-dual interior point method
    • Mehrotra S, On the implementation of a primal-dual interior point method, SIAM J Optimization 2:575-601, 1992.
    • (1992) SIAM J Optimization , vol.2 , pp. 575-601
    • Mehrotra, S.1
  • 28
    • 70449437208 scopus 로고    scopus 로고
    • Inference of genetic networks using linear programming machines: Application of a priori knowledge
    • Atlanta, USA
    • Kimura S, Shiraishi Y, Hatakeyama M, Inference of genetic networks using linear programming machines: Application of a priori knowledge, Proc 2009 Int Joint Conf Neural Networks, Atlanta, USA, 1617-1624, 2009.
    • (2009) Proc 2009 Int Joint Conf Neural Networks , pp. 1617-1624
    • Kimura, S.1    Shiraishi, Y.2    Hatakeyama, M.3
  • 30
    • 0034513411 scopus 로고    scopus 로고
    • The SOS response: Recent insights into umuDC-dependent mutagenesis and DNA damage tolerance
    • Sutton MD, Smith BT, Godoy VG, Walker GC, The SOS response: Recent insights into umuDC-dependent mutagenesis and DNA damage tolerance, Ann Rev Genet 34:479-497, 2000.
    • (2000) Ann Rev Genet , vol.34 , pp. 479-497
    • Sutton, M.D.1    Smith, B.T.2    Godoy, V.G.3    Walker, G.C.4
  • 31
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen M, Rosenberg R, Shraiman BI, Alon U, Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics, Proc Natl Acad Sci USA 99:10555-10560, 2002.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Alon, U.4
  • 32
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • Gardner TS, di Bernardo D, Lorenz D, Collins JJ, Inferring genetic networks and identifying compound mode of action via expression profiling, Science 301:102-105, 2003.
    • (2003) Science , vol.301 , pp. 102-105
    • Gardner, T.S.1    Di Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 33
    • 49849100049 scopus 로고    scopus 로고
    • Method for inferring and extracting reliable genetic interactions from time-series profile of gene expression
    • Nakatsui M, Ueda T, Maki Y, Ono I, Okamoto M, Method for inferring and extracting reliable genetic interactions from time-series profile of gene expression, Math Biosci 215:105-114, 2008.
    • (2008) Math Biosci , vol.215 , pp. 105-114
    • Nakatsui, M.1    Ueda, T.2    Maki, Y.3    Ono, I.4    Okamoto, M.5
  • 34
    • 26444446584 scopus 로고    scopus 로고
    • Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data
    • Paris, France
    • Imoto S, Higuchi T, Kim SY, Jeong E, Miyano S, Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data, Proc 2nd Comput Methods Syst Biol, Paris, France, 149-160, 2004.
    • (2004) Proc 2nd Comput Methods Syst Biol , pp. 149-160
    • Imoto, S.1    Higuchi, T.2    Kim, S.Y.3    Jeong, E.4    Miyano, S.5
  • 35
    • 0036191190 scopus 로고    scopus 로고
    • Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
    • Toh H, Horimoto K, Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling, Bioinformatics 18:287-297, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 287-297
    • Toh, H.1    Horimoto, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.