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Volumn 180, Issue 13, 2010, Pages 2560-2570

Generating probabilistic Boolean networks from a prescribed stationary distribution

Author keywords

Boolean networks; Genetic networks; Inverse problem; Probabilistic Boolean networks; Stationary distribution

Indexed keywords

BOOLEAN NETWORK; BOOLEAN NETWORKS; CONJUGATE GRADIENT ALGORITHMS; CONSTRAINED LEAST SQUARES; DETERMINISTIC MODELS; ESTIMATION METHODS; GENE REGULATIONS; GENETIC NETWORKS; GENOMIC RESEARCH; ILL POSED; LEAST SQUARES PROBLEMS; LONG-RUN BEHAVIOR; NUMERICAL EXAMPLE; PROBABILISTIC BOOLEAN NETWORKS; REGULATORY INTERACTIONS; STATIONARY DISTRIBUTION; SYSTEM SYNTHESIS;

EID: 77950863180     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ins.2010.03.014     Document Type: Article
Times cited : (20)

References (39)
  • 1
    • 0036749170 scopus 로고    scopus 로고
    • Evolutionary modeling and inference of gene network
    • Ando S., Sakamoto E., and Iba H. Evolutionary modeling and inference of gene network. Information Sciences 145 2-4 (2002) 237-259
    • (2002) Information Sciences , vol.145 , Issue.2-4 , pp. 237-259
    • Ando, S.1    Sakamoto, E.2    Iba, H.3
  • 3
    • 62249092344 scopus 로고    scopus 로고
    • A chance to learn: on matching probabilities to optimize utilities
    • Burns K., and Demaree H. A chance to learn: on matching probabilities to optimize utilities. Information Sciences 179 11 (2009) 1599-1607
    • (2009) Information Sciences , vol.179 , Issue.11 , pp. 1599-1607
    • Burns, K.1    Demaree, H.2
  • 4
    • 0034714499 scopus 로고    scopus 로고
    • Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics
    • Celis J., Kruhøfferm M., Gromova I., Frederiksen C., Østergaard M., and Ørntoft T. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Letters 480 (2000) 2-16
    • (2000) FEBS Letters , vol.480 , pp. 2-16
    • Celis, J.1    Kruhøfferm, M.2    Gromova, I.3    Frederiksen, C.4    Østergaard, M.5    Ørntoft, T.6
  • 5
    • 33644618250 scopus 로고    scopus 로고
    • On construction of stochastic genetic networks based on gene expression sequences
    • Ching W., Fung E., Ng M., and Akutsu T. On construction of stochastic genetic networks based on gene expression sequences. International Journal of Neural Systems 15 (2005) 297-310
    • (2005) International Journal of Neural Systems , vol.15 , pp. 297-310
    • Ching, W.1    Fung, E.2    Ng, M.3    Akutsu, T.4
  • 6
    • 34547840185 scopus 로고    scopus 로고
    • An approximation method for solving the steady-state probability distributions of probabilistic Boolean networks
    • Ching W., Zhang S., Ng M., and Akutsu T. An approximation method for solving the steady-state probability distributions of probabilistic Boolean networks. Bioinformatics 23 (2007) 1511-1518
    • (2007) Bioinformatics , vol.23 , pp. 1511-1518
    • Ching, W.1    Zhang, S.2    Ng, M.3    Akutsu, T.4
  • 7
    • 62649169298 scopus 로고    scopus 로고
    • Optimal control policy for probabilistic Boolean networks with hard constraints
    • Ching W., Zhang S., Jiao Y., Akutsu T., and Wong A. Optimal control policy for probabilistic Boolean networks with hard constraints. IET Systems Biology 3 (2009) 90-99
    • (2009) IET Systems Biology , vol.3 , pp. 90-99
    • Ching, W.1    Zhang, S.2    Jiao, Y.3    Akutsu, T.4    Wong, A.5
  • 8
    • 77950865013 scopus 로고    scopus 로고
    • A genetic algorithm for optimal control of probabilistic Boolean networks
    • in: The Second International Symposium on Optimization and Systems Biology OSB 2008, Ding-Zhu Du, Xiang-Sun Zhang, Eds
    • W. Ching, H. Leung, N. Tsing, S. Zhang, A genetic algorithm for optimal control of probabilistic Boolean networks, in: The Second International Symposium on Optimization and Systems Biology (OSB 2008), in: Ding-Zhu Du, Xiang-Sun Zhang, (Eds.), Lecture Notes in Operations Research, vol. 9, 2008, pp. 29-35.
    • (2008) Lecture Notes in Operations Research , vol.9 , pp. 29-35
    • Ching, W.1    Leung, H.2    Tsing, N.3    Zhang, S.4
  • 10
    • 0038724486 scopus 로고    scopus 로고
    • External control in Markovian genetic regulatory networks
    • Datta A., Choudhary A., Bitter M., and Dougherty E. External control in Markovian genetic regulatory networks. Machine Learning 52 (2003) 169-191
    • (2003) Machine Learning , vol.52 , pp. 169-191
    • Datta, A.1    Choudhary, A.2    Bitter, M.3    Dougherty, E.4
  • 11
    • 2342444140 scopus 로고    scopus 로고
    • External control in Markovian genetic regulatory networks: the imperfect information case
    • Datta A., Choudhary A., Bitter M., and Dougherty E. External control in Markovian genetic regulatory networks: the imperfect information case. Bioinformatics 20 (2004) 924-930
    • (2004) Bioinformatics , vol.20 , pp. 924-930
    • Datta, A.1    Choudhary, A.2    Bitter, M.3    Dougherty, E.4
  • 12
    • 0036207347 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 9 (2002) 69-103
    • (2002) Journal of Computational Biology , vol.9 , pp. 69-103
    • de Jong, H.1
  • 13
    • 0034302007 scopus 로고    scopus 로고
    • Coefficient of determination in nonlinear signal processing
    • Dougherty E., Kim S., and Chen Y. Coefficient of determination in nonlinear signal processing. Signal Processing 80 (2000) 2219-2235
    • (2000) Signal Processing , vol.80 , pp. 2219-2235
    • Dougherty, E.1    Kim, S.2    Chen, Y.3
  • 15
    • 54149092914 scopus 로고    scopus 로고
    • Boolean delay equations: a simple way of looking at complex systems
    • Ghila M., Zaliapind I., and Coluzzib B. Boolean delay equations: a simple way of looking at complex systems. Physica D: Nonlinear Phenomena 237 23 (2008) 2967-2986
    • (2008) Physica D: Nonlinear Phenomena , vol.237 , Issue.23 , pp. 2967-2986
    • Ghila, M.1    Zaliapind, I.2    Coluzzib, B.3
  • 16
    • 0032809387 scopus 로고    scopus 로고
    • Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery
    • Huang S. Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. Journal of Molecular Medicine 77 (1999) 469-480
    • (1999) Journal of Molecular Medicine , vol.77 , pp. 469-480
    • Huang, S.1
  • 17
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed gene nets
    • Kauffman S. Metabolic stability and epigenesis in randomly constructed gene nets. Journal of Theoretical Biology 22 (1969) 437-467
    • (1969) Journal of Theoretical Biology , vol.22 , pp. 437-467
    • Kauffman, S.1
  • 18
    • 0014671878 scopus 로고
    • Homeostasis and differentiation in random genetic control networks
    • Kauffman S. Homeostasis and differentiation in random genetic control networks. Nature 224 (1969) 177-178
    • (1969) Nature , vol.224 , pp. 177-178
    • Kauffman, S.1
  • 20
    • 84958595689 scopus 로고    scopus 로고
    • Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data, Proc. 1st Computational Methods in Systems Biology*****
    • Kim S., Imoto S., and Miyano S. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data, Proc. 1st Computational Methods in Systems Biology*****. Lecture Notes in Computer Science 2602 (2003) 104-113
    • (2003) Lecture Notes in Computer Science , vol.2602 , pp. 104-113
    • Kim, S.1    Imoto, S.2    Miyano, S.3
  • 22
    • 0038047901 scopus 로고    scopus 로고
    • On learning gene regulatory networks under the Boolean network model
    • Lähdesmäki H., Shmulevich I., and Yli-Harja O. On learning gene regulatory networks under the Boolean network model. Machine Learning 52 (2003) 147-167
    • (2003) Machine Learning , vol.52 , pp. 147-167
    • Lähdesmäki, H.1    Shmulevich, I.2    Yli-Harja, O.3
  • 23
    • 38549107133 scopus 로고    scopus 로고
    • Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks
    • Li P., Zhang C., Perkins E.J., Gong P., and Deng Y. Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks. BMC Bioinformatics 8 Suppl. 7 (2007) S13
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 7
    • Li, P.1    Zhang, C.2    Perkins, E.J.3    Gong, P.4    Deng, Y.5
  • 24
    • 0036798717 scopus 로고    scopus 로고
    • Could correlation-based methods be used to derive genetic association networks?
    • Lindløf A., and Olsson B. Could correlation-based methods be used to derive genetic association networks?. Information Sciences 146 1-4 (2002) 103-113
    • (2002) Information Sciences , vol.146 , Issue.1-4 , pp. 103-113
    • Lindløf, A.1    Olsson, B.2
  • 26
    • 52949139054 scopus 로고    scopus 로고
    • Replacement strategies to preserve useful diversity in steady-state genetic algorithms
    • Lozano M., Herrera F., and Cano J. Replacement strategies to preserve useful diversity in steady-state genetic algorithms. Information Sciences 178 23 (2008) 4421-4433
    • (2008) Information Sciences , vol.178 , Issue.23 , pp. 4421-4433
    • Lozano, M.1    Herrera, F.2    Cano, J.3
  • 27
    • 27744569877 scopus 로고    scopus 로고
    • Generating Boolean networks with a prescribed attractor structure
    • Pal R., Ivanov I., Datta A., Bittner M., and Dougherty E. Generating Boolean networks with a prescribed attractor structure. Bioinformatics 21 (2005) 4021-4025
    • (2005) Bioinformatics , vol.21 , pp. 4021-4025
    • Pal, R.1    Ivanov, I.2    Datta, A.3    Bittner, M.4    Dougherty, E.5
  • 28
    • 16344368806 scopus 로고    scopus 로고
    • Intervention in context-sensitive probabilistic Boolean networks
    • Pal R., Datta A., Bittner M., and Dougherty E. Intervention in context-sensitive probabilistic Boolean networks. Bioinformatics 21 (2005) 1211-1218
    • (2005) Bioinformatics , vol.21 , pp. 1211-1218
    • Pal, R.1    Datta, A.2    Bittner, M.3    Dougherty, E.4
  • 29
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich I., Dougherty E., Kim S., and Zhang W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18 (2002) 261-274
    • (2002) Bioinformatics , vol.18 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.2    Kim, S.3    Zhang, W.4
  • 30
    • 0347164904 scopus 로고    scopus 로고
    • Control of stationary behavior in probabilistic Boolean networks by means of structural intervention
    • Shmulevich I., Dougherty E., Kim S., and Zhang W. Control of stationary behavior in probabilistic Boolean networks by means of structural intervention. Journal of Biological Systems 10 (2002) 431-445
    • (2002) Journal of Biological Systems , vol.10 , pp. 431-445
    • Shmulevich, I.1    Dougherty, E.2    Kim, S.3    Zhang, W.4
  • 31
    • 0345983657 scopus 로고    scopus 로고
    • From Boolean networks to probabilistic Boolean networks as models of genetic regulatory networks
    • Shmulevich I., Dougherty E., Kim S., and Zhang W. From Boolean networks to probabilistic Boolean networks as models of genetic regulatory networks. Proceedings of the IEEE 90 (2002) 1778-1792
    • (2002) Proceedings of the IEEE , vol.90 , pp. 1778-1792
    • Shmulevich, I.1    Dougherty, E.2    Kim, S.3    Zhang, W.4
  • 32
    • 0036772705 scopus 로고    scopus 로고
    • Gene perturbation and intervention in probabilistic Boolean networks
    • Shmulevich I., Dougherty E., and Zhang W. Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics 18 (2002) 1319-1331
    • (2002) Bioinformatics , vol.18 , pp. 1319-1331
    • Shmulevich, I.1    Dougherty, E.2    Zhang, W.3
  • 35
    • 0033725197 scopus 로고    scopus 로고
    • Mathematical modeling of gene network
    • Smolen P., Baxter D., and Byrne J. Mathematical modeling of gene network. Neuron 26 (2000) 567-580
    • (2000) Neuron , vol.26 , pp. 567-580
    • Smolen, P.1    Baxter, D.2    Byrne, J.3
  • 36
    • 56149118708 scopus 로고    scopus 로고
    • Degrees of conditional (in)dependence: a framework for approximate Bayesian networks and examples related to the rough set-based feature selection
    • Slezak D. Degrees of conditional (in)dependence: a framework for approximate Bayesian networks and examples related to the rough set-based feature selection. Information Sciences 179 3 (2009) 197-209
    • (2009) Information Sciences , vol.179 , Issue.3 , pp. 197-209
    • Slezak, D.1
  • 37
    • 63149128570 scopus 로고    scopus 로고
    • Particle swarm optimization with preference order ranking for multi-objective optimization
    • Wang Y., and Yang Y. Particle swarm optimization with preference order ranking for multi-objective optimization. Information Sciences 179 12 (2009) 1944-1959
    • (2009) Information Sciences , vol.179 , Issue.12 , pp. 1944-1959
    • Wang, Y.1    Yang, Y.2


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