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Volumn 52, Issue , 2014, Pages 18-24

Construction of a Boolean model of gene and protein regulatory network with memory

Author keywords

Algebraic form; Construction from attractors; Decay time; Least in degree model; Semi tensor product

Indexed keywords

ALGEBRA; ALGORITHMS; GENES; PROTEINS;

EID: 84892648137     PISSN: 08936080     EISSN: 18792782     Source Type: Journal    
DOI: 10.1016/j.neunet.2013.12.008     Document Type: Article
Times cited : (9)

References (34)
  • 1
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • Akutsu T., Miyano S., Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacific symposium on biocomputing, vol. 4 1999, 17-28.
    • (1999) Pacific symposium on biocomputing, vol. 4 , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 2
    • 84872178752 scopus 로고    scopus 로고
    • A new approach for global controllability of higher order Boolean control network
    • Chen H., Sun J. A new approach for global controllability of higher order Boolean control network. Neural Networks 2013, 39:12-17.
    • (2013) Neural Networks , vol.39 , pp. 12-17
    • Chen, H.1    Sun, J.2
  • 3
    • 67349272281 scopus 로고    scopus 로고
    • Controllability and observability of Boolean control networks
    • Cheng D., Qi H. Controllability and observability of Boolean control networks. Automatica 2009, 45(7):1659-1667.
    • (2009) Automatica , vol.45 , Issue.7 , pp. 1659-1667
    • Cheng, D.1    Qi, H.2
  • 4
    • 77957702887 scopus 로고    scopus 로고
    • A linear representation of dynamics of Boolean networks
    • Cheng D., Qi H. A linear representation of dynamics of Boolean networks. IEEE Transactions on Automatic Control 2010, 55(10):2251-2258.
    • (2010) IEEE Transactions on Automatic Control , vol.55 , Issue.10 , pp. 2251-2258
    • Cheng, D.1    Qi, H.2
  • 6
    • 79953822247 scopus 로고    scopus 로고
    • Model construction of Boolean network via observed data
    • Cheng D., Qi H., Li Z. Model construction of Boolean network via observed data. IEEE Transactions on Neural Networks 2011, 22(4):525-536.
    • (2011) IEEE Transactions on Neural Networks , vol.22 , Issue.4 , pp. 525-536
    • Cheng, D.1    Qi, H.2    Li, Z.3
  • 7
    • 0021375732 scopus 로고
    • Boolean difference equations, i: formulation and dynamic behavior
    • Dee D., Ghil M. Boolean difference equations, i: formulation and dynamic behavior. SIAM Journal on Applied Mathematics 1984, 44:111-126.
    • (1984) SIAM Journal on Applied Mathematics , vol.44 , pp. 111-126
    • Dee, D.1    Ghil, M.2
  • 8
    • 50549088838 scopus 로고    scopus 로고
    • Synchronous versus asynchronous modeling of gene regulatory networks
    • Garg A., Di Cara A., Xenarios I., Mendoza L., De Micheli G. Synchronous versus asynchronous modeling of gene regulatory networks. BMC Bioinformatics 2008, 24(17):1917-1925.
    • (2008) BMC Bioinformatics , vol.24 , Issue.17 , pp. 1917-1925
    • Garg, A.1    Di Cara, A.2    Xenarios, I.3    Mendoza, L.4    De Micheli, G.5
  • 9
    • 34547480306 scopus 로고    scopus 로고
    • An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments
    • Springer
    • Garg A., Xenarios I., Mendoza L., DeMicheli G. An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments. Research in computational molecular biology 2007, 62-76. Springer.
    • (2007) Research in computational molecular biology , pp. 62-76
    • Garg, A.1    Xenarios, I.2    Mendoza, L.3    DeMicheli, G.4
  • 10
    • 0015296342 scopus 로고
    • Co-operative components, spatial localization and oscillatory cellular dynamics
    • Glass L., Kauffman S.A. Co-operative components, spatial localization and oscillatory cellular dynamics. Journal of Theoretical Biology 1972, 34:219-237.
    • (1972) Journal of Theoretical Biology , vol.34 , pp. 219-237
    • Glass, L.1    Kauffman, S.A.2
  • 13
    • 0005126318 scopus 로고    scopus 로고
    • Time out of joint: attractors in asynchronous random Boolean networks
    • MIT Press, Cambridge
    • Harvey I., Bossomaier T. Time out of joint: attractors in asynchronous random Boolean networks. 4-th European conference on artificial life 1997, 67-75. MIT Press, Cambridge.
    • (1997) 4-th European conference on artificial life , pp. 67-75
    • Harvey, I.1    Bossomaier, T.2
  • 14
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman S. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 1969, 22(3):437-467.
    • (1969) Journal of Theoretical Biology , vol.22 , Issue.3 , pp. 437-467
    • Kauffman, S.1
  • 17
    • 28844465824 scopus 로고    scopus 로고
    • Stable and unstable attractors in Boolean networks
    • 055101(4)
    • Klemm K., Bornholdt S. Stable and unstable attractors in Boolean networks. Physical Review E 2005, 72(5):055101(4).
    • (2005) Physical Review E , vol.72 , Issue.5
    • Klemm, K.1    Bornholdt, S.2
  • 18
    • 3042799574 scopus 로고    scopus 로고
    • A computational algebra approach to the reverse engineering of gene regulatory networks
    • Laubenbacher R., Stigler B. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology 2004, 229(4):523-537.
    • (2004) Journal of Theoretical Biology , vol.229 , Issue.4 , pp. 523-537
    • Laubenbacher, R.1    Stigler, B.2
  • 19
    • 84865424011 scopus 로고    scopus 로고
    • Controllability and optimal control of a temporal Boolean network
    • Li F., Sun J. Controllability and optimal control of a temporal Boolean network. Neural Networks 2012, 34:10-17.
    • (2012) Neural Networks , vol.34 , pp. 10-17
    • Li, F.1    Sun, J.2
  • 20
    • 84864282274 scopus 로고    scopus 로고
    • Controllability of higher order boolean control networks
    • Li F., Sun J. Controllability of higher order boolean control networks. Applied Mathematics and Computation 2012, 219:158-169.
    • (2012) Applied Mathematics and Computation , vol.219 , pp. 158-169
    • Li, F.1    Sun, J.2
  • 21
    • 84862808523 scopus 로고    scopus 로고
    • Existence and number of fixed points of Boolean transformations via the semi-tensor product method
    • Li H., Wang Y., Liu Z. Existence and number of fixed points of Boolean transformations via the semi-tensor product method. Applied Mathematics Letters 2012, 25(8):1142-1147.
    • (2012) Applied Mathematics Letters , vol.25 , Issue.8 , pp. 1142-1147
    • Li, H.1    Wang, Y.2    Liu, Z.3
  • 22
    • 27744569877 scopus 로고    scopus 로고
    • Generating Boolean networks with a prescribed attractor structure
    • Pal R., Ivanov I., Datta A., Bittner M., Dougherty E. Generating Boolean networks with a prescribed attractor structure. BMC Bioinformatics 2005, 21(21):4021-4025.
    • (2005) BMC Bioinformatics , vol.21 , Issue.21 , pp. 4021-4025
    • Pal, R.1    Ivanov, I.2    Datta, A.3    Bittner, M.4    Dougherty, E.5
  • 23
    • 79951757406 scopus 로고    scopus 로고
    • State reduction for network intervention in probabilistic Boolean networks
    • Qian X., Ghaffari N., Ivanov I., Dougherty E. State reduction for network intervention in probabilistic Boolean networks. BMC Bioinformatics 2010, 26(24):3098-3104.
    • (2010) BMC Bioinformatics , vol.26 , Issue.24 , pp. 3098-3104
    • Qian, X.1    Ghaffari, N.2    Ivanov, I.3    Dougherty, E.4
  • 24
    • 77953671724 scopus 로고    scopus 로고
    • On the dynamics of random boolean networks subject to noise: attractors, ergodic sets and cell types
    • Serra R., Villani M., Barbieri A., Kauffman S., Colacci A. On the dynamics of random boolean networks subject to noise: attractors, ergodic sets and cell types. Journal of Theoretical Biology 2010, 265:185-193.
    • (2010) Journal of Theoretical Biology , vol.265 , pp. 185-193
    • Serra, R.1    Villani, M.2    Barbieri, A.3    Kauffman, S.4    Colacci, A.5
  • 25
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich I., Dougherty E., Kim S., Zhang W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. BMC Bioinformatics 2002, 18(2):261-274.
    • (2002) BMC Bioinformatics , vol.18 , Issue.2 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.2    Kim, S.3    Zhang, W.4
  • 27
    • 3343006617 scopus 로고    scopus 로고
    • Scaling in ordered and critical random Boolean networks
    • Socolar J., Kauffman S. Scaling in ordered and critical random Boolean networks. Physical Review Letters 2003, 90:068702.
    • (2003) Physical Review Letters , vol.90 , pp. 068702
    • Socolar, J.1    Kauffman, S.2
  • 28
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • Thomas R. Boolean formalization of genetic control circuits. Journal of Theoretical Biology 1973, 42:563-585.
    • (1973) Journal of Theoretical Biology , vol.42 , pp. 563-585
    • Thomas, R.1
  • 29
    • 0025948178 scopus 로고
    • Regulatory networks seen as asynchronous automata: a logical description
    • Thomas R. Regulatory networks seen as asynchronous automata: a logical description. Journal of Theoretical Biology 1991, 153:1-23.
    • (1991) Journal of Theoretical Biology , vol.153 , pp. 1-23
    • Thomas, R.1
  • 30
    • 79952783472 scopus 로고    scopus 로고
    • A dynamical model of genetic networks for cell differentiation
    • Villani M., Barbieri A., Serra R. A dynamical model of genetic networks for cell differentiation. PloS one 2011, 6:e17703.
    • (2011) PloS one , vol.6
    • Villani, M.1    Barbieri, A.2    Serra, R.3
  • 31
    • 84861889741 scopus 로고    scopus 로고
    • Evaluation of attractors and basins of asynchronous random Boolean networks
    • 056105(6)
    • Yang M., Chu T. Evaluation of attractors and basins of asynchronous random Boolean networks. Physical Review E 2012, 85(5):056105(6).
    • (2012) Physical Review E , vol.85 , Issue.5
    • Yang, M.1    Chu, T.2
  • 32
    • 77950863180 scopus 로고    scopus 로고
    • Generating probabilistic boolean networks from a prescribed stationary distribution
    • Zhang S., Ching W., Chen X., Tsing N. Generating probabilistic boolean networks from a prescribed stationary distribution. Information Sciences 2010, 180:2560-2570.
    • (2010) Information Sciences , vol.180 , pp. 2560-2570
    • Zhang, S.1    Ching, W.2    Chen, X.3    Tsing, N.4
  • 33
    • 28244441861 scopus 로고    scopus 로고
    • A remark on "scalar equations for synchronous Boolean networks with biological applications" by C. Farrow, J. Heidel, J. Maloney, and J. Rogers
    • Zhao Q. A remark on "scalar equations for synchronous Boolean networks with biological applications" by C. Farrow, J. Heidel, J. Maloney, and J. Rogers. IEEE Transactions on Neural Networks 2005, 16:1715-1716.
    • (2005) IEEE Transactions on Neural Networks , vol.16 , pp. 1715-1716
    • Zhao, Q.1
  • 34
    • 84880907533 scopus 로고    scopus 로고
    • Aggregation algorithm towards large-scale Boolean network analysis
    • Zhao Y., Kim J., Filippone M. Aggregation algorithm towards large-scale Boolean network analysis. IEEE Transactions on Automatic Control 2013, 58:1976-1985.
    • (2013) IEEE Transactions on Automatic Control , vol.58 , pp. 1976-1985
    • Zhao, Y.1    Kim, J.2    Filippone, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.