메뉴 건너뛰기




Volumn 99, Issue , 2013, Pages 458-466

Reverse engineering of gene regulatory networks using flexible neural tree models

Author keywords

Flexible neural tree model; Gene regulatory network; Reverse engineering; Time series prediction

Indexed keywords

AKAIKE INFORMATION CRITERION; DATA SETS; DNA MICROARRAY TECHNOLOGY; FLEXIBLE NEURAL TREE MODEL; FLEXIBLE NEURAL TREES; GENE EXPRESSION DATA; GENE EXPRESSION LEVELS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; PREDICTION ACCURACY; REGULATORY ELEMENTS; TARGET GENES; TIME SERIES PREDICTION; TIME-SERIES DATA; VOTING STRATEGIES;

EID: 84867848934     PISSN: 09252312     EISSN: 18728286     Source Type: Journal    
DOI: 10.1016/j.neucom.2012.07.015     Document Type: Article
Times cited : (37)

References (36)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Control 1974, 19(6):716-723.
    • (1974) IEEE Trans. Autom. Control , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 2
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • T. Akutsu, S. Miyano, S. Kuhara, Identification of genetic networks from a small number of gene expression patterns under the Boolean network model, in: Pacific Symposium on Biocomputing, 1999, pp. 17-28.
    • (1999) in: Pacific Symposium on Biocomputing , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 4
    • 78751633682 scopus 로고    scopus 로고
    • Ensemble of Elman neural networks and support vector machines for reverse engineering of gene regulatory networks
    • Ao S.I., Palade V. Ensemble of Elman neural networks and support vector machines for reverse engineering of gene regulatory networks. Appl. Soft Comput. 2011, 11(2):1718-1726.
    • (2011) Appl. Soft Comput. , vol.11 , Issue.2 , pp. 1718-1726
    • Ao, S.I.1    Palade, V.2
  • 5
    • 84867871706 scopus 로고    scopus 로고
    • A new local search approach with execution time as an input parameter, Technical Report no. NOTTCS-TR-2002-3, School of Computer Science and Information Technology, University of Nottingham
    • E.K. Burke, Y. Bykov, J.P. Newall, S. Petrovic, A new local search approach with execution time as an input parameter, Technical Report no. NOTTCS-TR-2002-3, School of Computer Science and Information Technology, University of Nottingham, 2002.
    • (2002)
    • Burke, E.K.1    Bykov, Y.2    Newall, J.P.3    Petrovic, S.4
  • 6
    • 46249112705 scopus 로고    scopus 로고
    • Boolean network models of cellular regulation: prospects and limitations
    • Bornholdt S. Boolean network models of cellular regulation: prospects and limitations. J. R. Soc. Interf. 2008, 5(Suppl. 1):85-94.
    • (2008) J. R. Soc. Interf. , vol.5 , Issue.SUPPL. 1 , pp. 85-94
    • Bornholdt, S.1
  • 7
    • 77957695678 scopus 로고    scopus 로고
    • Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks
    • Chaitankar V., Ghosh P., Perkins E.J., Gong P., Zhang C. Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. BMC Bioinformatics 2010, 11(Suppl. 6):S19.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 6
    • Chaitankar, V.1    Ghosh, P.2    Perkins, E.J.3    Gong, P.4    Zhang, C.5
  • 8
    • 0031221187 scopus 로고    scopus 로고
    • Evolving computer programs without subtree crossover
    • Chellapilla K. Evolving computer programs without subtree crossover. IEEE Trans. Evol. Comput. 1997, 1:209-216.
    • (1997) IEEE Trans. Evol. Comput. , vol.1 , pp. 209-216
    • Chellapilla, K.1
  • 10
    • 21244438033 scopus 로고    scopus 로고
    • Time series forecasting using flexible neural tree model
    • Chen Y.H., Yang B., Dong J., Abraham A. Time series forecasting using flexible neural tree model. Inf. Sci. 2005, 174(3/4):219-235.
    • (2005) Inf. Sci. , vol.174 , Issue.3-4 , pp. 219-235
    • Chen, Y.H.1    Yang, B.2    Dong, J.3    Abraham, A.4
  • 11
    • 81155130791 scopus 로고    scopus 로고
    • Small-time scale network traffic prediction based on flexible neural tree
    • Chen Y.H., Yang B., Meng Q.F. Small-time scale network traffic prediction based on flexible neural tree. Appl. Soft Comput. 2012, 12:274-279.
    • (2012) Appl. Soft Comput. , vol.12 , pp. 274-279
    • Chen, Y.H.1    Yang, B.2    Meng, Q.F.3
  • 12
  • 13
    • 33845997779 scopus 로고    scopus 로고
    • Flexible neural trees ensemble for stock index modeling
    • Chen Y.H., Yang B., Abraham A. Flexible neural trees ensemble for stock index modeling. Neurocomputing 2007, 70:697-703.
    • (2007) Neurocomputing , vol.70 , pp. 697-703
    • Chen, Y.H.1    Yang, B.2    Abraham, A.3
  • 14
    • 77949372252 scopus 로고    scopus 로고
    • Inferring genetic interactions via a nonlinear model and an optimization algorithm
    • Chen C.M., Lee C., Chuang C.L., Wang C.C., Shieh G.S. Inferring genetic interactions via a nonlinear model and an optimization algorithm. BMC Syst. Biol. 2010, 4:16-26.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 16-26
    • Chen, C.M.1    Lee, C.2    Chuang, C.L.3    Wang, C.C.4    Shieh, G.S.5
  • 15
    • 33745616528 scopus 로고    scopus 로고
    • Identification of biochemical networks by S-tree based genetic programming
    • Cho K.H., Zhang B.T. Identification of biochemical networks by S-tree based genetic programming. Bioinformatics 2006, 22:1631-1640.
    • (2006) Bioinformatics , vol.22 , pp. 1631-1640
    • Cho, K.H.1    Zhang, B.T.2
  • 17
    • 20144387371 scopus 로고    scopus 로고
    • Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
    • Kimura S., Ide K., Kashihara A. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 2005, 21:1154-1163.
    • (2005) Bioinformatics , vol.21 , pp. 1154-1163
    • Kimura, S.1    Ide, K.2    Kashihara, A.3
  • 18
    • 0037461033 scopus 로고    scopus 로고
    • Dynamic modeling of genetic networks using genetic algorithm and S-system
    • Kikuchi S., Tominaga D., Arita M.K. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 2003, 19:643-650.
    • (2003) Bioinformatics , vol.19 , pp. 643-650
    • Kikuchi, S.1    Tominaga, D.2    Arita, M.K.3
  • 19
  • 20
    • 77955315182 scopus 로고    scopus 로고
    • A neural network based modeling and validation approach for identifying gene regulatory networks
    • Knott S., Mostafavi S., Mousavi P. A neural network based modeling and validation approach for identifying gene regulatory networks. Neurocomputing 2010, 73:2419-2429.
    • (2010) Neurocomputing , vol.73 , pp. 2419-2429
    • Knott, S.1    Mostafavi, S.2    Mousavi, P.3
  • 21
    • 0025999808 scopus 로고
    • Regulation of the yeast cyti gene encoding cytochrome cl by hap1 and hap2/3/4
    • Kschneider J., Guarente L. Regulation of the yeast cyti gene encoding cytochrome cl by hap1 and hap2/3/4. Mol. Cell. Biol. 1991, 11:4934-4942.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 4934-4942
    • Kschneider, J.1    Guarente, L.2
  • 22
    • 84867882429 scopus 로고    scopus 로고
    • Modeling Gene Expression Data using Dynamic Bayesian Network, Technical Report, Berkeley
    • K. Murphy, S. Mian, Modeling Gene Expression Data using Dynamic Bayesian Network, Technical Report, Berkeley, 1999.
    • (1999)
    • Murphy, K.1    Mian, S.2
  • 23
    • 34249010864 scopus 로고    scopus 로고
    • Gene networks reconstruction and time-series prediction from microarray data using recurrent neural fuzzy networks
    • Maraziotis I.A., Dragomir A., Bezerianosh A. Gene networks reconstruction and time-series prediction from microarray data using recurrent neural fuzzy networks. IET Syst. Biol. 2007, 1(1):41-50.
    • (2007) IET Syst. Biol. , vol.1 , Issue.1 , pp. 41-50
    • Maraziotis, I.A.1    Dragomir, A.2    Bezerianosh, A.3
  • 24
    • 33847348163 scopus 로고    scopus 로고
    • Causality and pathway search in microarray time series experiment
    • Mukhopadhyay N., Chatterjee S. Causality and pathway search in microarray time series experiment. Bioinformatics 2007, 23(4):442-449.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 442-449
    • Mukhopadhyay, N.1    Chatterjee, S.2
  • 25
    • 0001958391 scopus 로고
    • Study of a growth algorithm for a feedforward network
    • Nadal J.-P. Study of a growth algorithm for a feedforward network. Int. J. Neural Syst. 1989, 1:55-59.
    • (1989) Int. J. Neural Syst. , vol.1 , pp. 55-59
    • Nadal, J.-P.1
  • 26
    • 0346972456 scopus 로고    scopus 로고
    • A neuro-fuzzy approach for functional genomics data interpretation and analysis
    • Neagu D., Palade V. A neuro-fuzzy approach for functional genomics data interpretation and analysis. Neural Comput. Appl. 2003, 12:153-159.
    • (2003) Neural Comput. Appl. , vol.12 , pp. 153-159
    • Neagu, D.1    Palade, V.2
  • 28
    • 0036678794 scopus 로고    scopus 로고
    • Assigning number to the arrows. parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen M., Rosenberg R., Shraiman B.I., Allon U. Assigning number to the arrows. parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:10555-10560.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Allon, U.4
  • 29
    • 0035426475 scopus 로고    scopus 로고
    • Combining GP operators with SA search to evolve fuzzy rule based classifiers
    • Sánchez L., Cousob I., Corrales J.A. Combining GP operators with SA search to evolve fuzzy rule based classifiers. Inf. Sci. 2001, 136:175-191.
    • (2001) Inf. Sci. , vol.136 , pp. 175-191
    • Sánchez, L.1    Cousob, I.2    Corrales, J.A.3
  • 30
    • 0029185114 scopus 로고
    • Use of a quasi-Newton method in a feedforward neural network construction algorithm
    • Setiono R., Hui L.C.K. Use of a quasi-Newton method in a feedforward neural network construction algorithm. IEEE Trans. Neural Networks 1995, 6:273-277.
    • (1995) IEEE Trans. Neural Networks , vol.6 , pp. 273-277
    • Setiono, R.1    Hui, L.C.K.2
  • 31
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman P. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9:3273-3297.
    • (1998) Mol. Biol. Cell , vol.9 , pp. 3273-3297
    • Spellman, P.1
  • 32
    • 84870387877 scopus 로고    scopus 로고
    • Stages of gene regulatory network inference: the evolutionary algorithm role
    • in: Eisuke Kita (Ed.)
    • A. SÎrbu, H.J. Ruskin, M. Crane, Stages of gene regulatory network inference: the evolutionary algorithm role, in: Eisuke Kita (Ed.), Evolutionary Algorithms, InTech, 2011.
    • (2011) Evolutionary Algorithms, InTech
    • Sîrbu, A.1    Ruskin, H.J.2    Crane, M.3
  • 33
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks. integrating genetic perturbations with dynamical modeling
    • Tegner J., Yeung M., Hasty J., Collins J. Reverse engineering gene networks. integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. U.S.A. 2003, 100(10):5944-5949.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , Issue.10 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.2    Hasty, J.3    Collins, J.4
  • 34
    • 36248944068 scopus 로고    scopus 로고
    • Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization
    • Xu R., Wunsch I.I., Frank R.L. Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization. IEEE/ACM Trans. Comput. Biol. Bioinformatics 2007, 4:681-692.
    • (2007) IEEE/ACM Trans. Comput. Biol. Bioinformatics , vol.4 , pp. 681-692
    • Xu, R.1    Wunsch, I.I.2    Frank, R.L.3
  • 35
    • 0031143030 scopus 로고    scopus 로고
    • A new evolutionary system for evolving artificial neural networks
    • Yao X., Liu Y. A new evolutionary system for evolving artificial neural networks. IEEE Trans. Neural Networks 1997, 8:694-713.
    • (1997) IEEE Trans. Neural Networks , vol.8 , pp. 694-713
    • Yao, X.1    Liu, Y.2
  • 36
    • 0033362601 scopus 로고    scopus 로고
    • Evolving artificial neural networks
    • Yao X. Evolving artificial neural networks. Proc. IEEE 1999, 87:1423-1447.
    • (1999) Proc. IEEE , vol.87 , pp. 1423-1447
    • Yao, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.