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Volumn 53, Issue 11, 2006, Pages 2444-2450

Designing gene regulatory networks with specified functions

Author keywords

Bistable switches; Cyclic; Feedback networks; Gene regulatory networks; Hybrid; Modules; Oscillators; Positive

Indexed keywords

RECURRENT NEURAL NETWORKS; SYSTEMS ANALYSIS; SYSTEMS SCIENCE;

EID: 34548411346     PISSN: 10577122     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCSI.2006.883880     Document Type: Article
Times cited : (24)

References (34)
  • 1
    • 1242274449 scopus 로고    scopus 로고
    • "Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems"
    • D. Angeli, J. Ferrell, and E. Sontag, "Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems," Proc. Natl. Acad. Sci., vol. 101, pp. 1822-1827, 2004.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 1822-1827
    • Angeli, D.1    Ferrell, J.2    Sontag, E.3
  • 2
    • 0242334021 scopus 로고    scopus 로고
    • "Monotone control systems"
    • Dec
    • D. Angeli and E. Sontag, "Monotone control systems," IEEE Trans. Autom. Contr., vol. 48, no. 12, pp. 1684-1698, Dec. 2003.
    • (2003) IEEE Trans. Autom. Contr. , vol.48 , Issue.12 , pp. 1684-1698
    • Angeli, D.1    Sontag, E.2
  • 3
    • 0035822634 scopus 로고    scopus 로고
    • "Bistability in the JNK cascade"
    • C. P. Bagowski and J. E. Ferrell, "Bistability in the JNK cascade," Current Biol., vol. 11, pp. 1176-1182, 2001.
    • (2001) Current Biol. , vol.11 , pp. 1176-1182
    • Bagowski, C.P.1    Ferrell, J.E.2
  • 4
    • 0034688220 scopus 로고    scopus 로고
    • "Biological rhythms: Circadian clocks limited by noise"
    • N. Barbai and S. Leibler, "Biological rhythms: Circadian clocks limited by noise," Nature, vol. 403, pp. 267-268, 2000.
    • (2000) Nature , vol.403 , pp. 267-268
    • Barbai, N.1    Leibler, S.2
  • 5
    • 17144456808 scopus 로고    scopus 로고
    • "Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion"
    • A. Becskei, B. Seraphin, and L. Serrano, "Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion," EMBO J., vol. 20, pp. 2528-2535, 2001.
    • (2001) EMBO J. , vol.20 , pp. 2528-2535
    • Becskei, A.1    Seraphin, B.2    Serrano, L.3
  • 6
    • 0037047611 scopus 로고    scopus 로고
    • "MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network"
    • U. S. Bhalla, P. T. Ram, and R. Iyengar, "MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network," Science, vol. 297, pp. 1018-1023, 2002.
    • (2002) Science , vol.297 , pp. 1018-1023
    • Bhalla, U.S.1    Ram, P.T.2    Iyengar, R.3
  • 7
    • 0036576340 scopus 로고    scopus 로고
    • "Stability of genetic regulatory networks with time delay"
    • May
    • L. Chen and K. Aihara, "Stability of genetic regulatory networks with time delay," IEEE Trans. Circuits Syst. I, Fundam. Theory Appl., vol. 49, no. 5, pp. 602-608, May 2002.
    • (2002) IEEE Trans. Circuits Syst. I, Fundam. Theory Appl. , vol.49 , Issue.5 , pp. 602-608
    • Chen, L.1    Aihara, K.2
  • 8
    • 0036803078 scopus 로고    scopus 로고
    • "A model of periodic oscillation for genetic regulatory systems"
    • Nov
    • L. Chen and K. Aihara, "A model of periodic oscillation for genetic regulatory systems," IEEE Trans. Circuits Syst. I, Fundam. Theory Appl., vol. 49, no. 11, pp. 1429-1436, Nov. 2002.
    • (2002) IEEE Trans. Circuits Syst. I, Fundam. Theory Appl. , vol.49 , Issue.11 , pp. 1429-1436
    • Chen, L.1    Aihara, K.2
  • 9
    • 20744444887 scopus 로고    scopus 로고
    • "Noise-induced cooperative behaviors in a multi-cell system"
    • L. Chen, R. Wang, and T. Zhou, "Noise-induced cooperative behaviors in a multi-cell system," Bioinformatics, vol. 21, pp. 2722-2729, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 2722-2729
    • Chen, L.1    Wang, R.2    Zhou, T.3
  • 10
    • 0033593306 scopus 로고    scopus 로고
    • "Molecular bases for circadian clocks"
    • J. C. Dunlap, "Molecular bases for circadian clocks," Cell, vol. 96, pp. 271-290, 1999.
    • (1999) Cell , vol.96 , pp. 271-290
    • Dunlap, J.C.1
  • 11
    • 0034688173 scopus 로고    scopus 로고
    • "A synthetic oscillatory network of transcriptional regulators"
    • M. B. Elowitz and S. Leibler, "A synthetic oscillatory network of transcriptional regulators," Nature, vol. 403, pp. 335-338, 2000.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 12
    • 0037119587 scopus 로고    scopus 로고
    • "Stochastic gene expression in a single cell"
    • M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, "Stochastic gene expression in a single cell," Science, vol. 297, pp. 1183-1186, 2002.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 13
    • 0347635508 scopus 로고    scopus 로고
    • "Design of genetic networks with specfied functions by evolution in silico"
    • P. François and V. Hakim, "Design of genetic networks with specfied functions by evolution in silico," Proc. Natl. Acad. Sci., vol. 101, pp. 580-585, 2004.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 580-585
    • François, P.1    Hakim, V.2
  • 14
    • 0034688174 scopus 로고    scopus 로고
    • "Construction of a genetic toggle switch in Escherichia Coli"
    • T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a genetic toggle switch in Escherichia Coli," Nature, vol. 403, pp. 339-342, 2000.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 15
    • 0029094843 scopus 로고
    • "A model for circadian oscillations in the Drosophila period protein (PER)"
    • A. Goldbeter, "A model for circadian oscillations in the Drosophila period protein (PER)," Proc. R. Soc. Lond. B, vol. 261, pp. 319-324, 1995.
    • (1995) Proc. R. Soc. Lond. B , vol.261 , pp. 319-324
    • Goldbeter, A.1
  • 16
    • 0037154231 scopus 로고    scopus 로고
    • "Robustness of circadian rhythms with respect to molecular noise"
    • A. Goldbeter, "Robustness of circadian rhythms with respect to molecular noise," Proc. Natl. Acad. Sci., vol. 99, pp. 673-678, 2002.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 673-678
    • Goldbeter, A.1
  • 17
    • 0013823048 scopus 로고
    • "Oscillatory behavior in enzymatic control process"
    • B. C. Goodwin, "Oscillatory behavior in enzymatic control process," Adv. Enzyme Regua., vol. 3, pp. 425-438, 1965.
    • (1965) Adv. Enzyme Regua. , vol.3 , pp. 425-438
    • Goodwin, B.C.1
  • 18
    • 0037041888 scopus 로고    scopus 로고
    • "Synthetic gene network for entraining and amplifying cellular oscillations"
    • 148101
    • J. Hasty, M. Dolnik, V. Rottschäfer, and J. J. Collins, "Synthetic gene network for entraining and amplifying cellular oscillations," Phys. Rev. Lett., vol. 88, pp. 1-4, 2002, 148101.
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 1-4
    • Hasty, J.1    Dolnik, M.2    Rottschäfer, V.3    Collins, J.J.4
  • 19
    • 0006092502 scopus 로고    scopus 로고
    • "Designer gene networks: Towards fundamental cellular control"
    • J. Hasty, F. Isaacs, M. Dolnik, D. McMillen, and J. J. Colins, "Designer gene networks: Towards fundamental cellular control," Chaos, vol. 11, pp. 207-220, 2001.
    • (2001) Chaos , vol.11 , pp. 207-220
    • Hasty, J.1    Isaacs, F.2    Dolnik, M.3    McMillen, D.4    Colins, J.J.5
  • 20
    • 0036207347 scopus 로고    scopus 로고
    • "Modeling and simulation of genetic regulatory systems: A literature review"
    • H. Jong, "Modeling and simulation of genetic regulatory systems: A literature review," J. Comput. Biol., vol. 9, pp. 67-103, 2002.
    • (2002) J. Comput. Biol. , vol.9 , pp. 67-103
    • Jong, H.1
  • 21
    • 0345549531 scopus 로고    scopus 로고
    • "Modelling genetic switches with positive feedback loops"
    • T. Kobayashi, L. Chen, and K. Aihara, "Modelling genetic switches with positive feedback loops," J. Theor. Biol., vol. 221, pp. 379-399, 2003.
    • (2003) J. Theor. Biol. , vol.221 , pp. 379-399
    • Kobayashi, T.1    Chen, L.2    Aihara, K.3
  • 22
    • 0030102662 scopus 로고    scopus 로고
    • "Systems of differential delay equations: Floquet multipliers and discrete Lyapunov functions"
    • J. Mallet-Paret and G. R. Sell, "Systems of differential delay equations: Floquet multipliers and discrete Lyapunov functions," J. Diff. Eq., vol. 125, pp. 385-440, 1996.
    • (1996) J. Diff. Eq. , vol.125 , pp. 385-440
    • Mallet-Paret, J.1    Sell, G.R.2
  • 23
    • 0030102885 scopus 로고    scopus 로고
    • "The Poincaré-Bendixson theorem for monotone cyclic feedback systems with delay"
    • J. Mallet-Paret and G. R. Sell, "The Poincaré-Bendixson theorem for monotone cyclic feedback systems with delay," J. Diff. Eq., vol. 125, pp. 441-489, 1996.
    • (1996) J. Diff. Eq. , vol.125 , pp. 441-489
    • Mallet-Paret, J.1    Sell, G.R.2
  • 24
    • 0037154293 scopus 로고    scopus 로고
    • "Synchronizing genetic relaxation oscillators by intercell signaling"
    • D. McMillen, N. Kopell, J. Hasty, and J. J. Collins, "Synchronizing genetic relaxation oscillators by intercell signaling," Proc. Natl. Acad. Sci., vol. 99, pp. 679-684, 2002.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 679-684
    • McMillen, D.1    Kopell, N.2    Hasty, J.3    Collins, J.J.4
  • 25
    • 1442354192 scopus 로고    scopus 로고
    • "Multistability in the lactose utilization network of Escherichia coli"
    • E. M. Ozbudak, M. Thattai, H. N. Lim, B. Shraiman, and A. V. Oudenaardeb, "Multistability in the lactose utilization network of Escherichia coli," Nature, vol. 427, pp. 737-740, 2004.
    • (2004) Nature , vol.427 , pp. 737-740
    • Ozbudak, E.M.1    Thattai, M.2    Lim, H.N.3    Shraiman, B.4    Oudenaardeb, A.V.5
  • 26
    • 0001220918 scopus 로고
    • "Periodic tridiagonal competitive and cooperative systems of differential equations"
    • H. Smith, "Periodic tridiagonal competitive and cooperative systems of differential equations," SIAM J. Math. Anal., vol. 22, pp. 1102-1109, 1991.
    • (1991) SIAM J. Math. Anal. , vol.22 , pp. 1102-1109
    • Smith, H.1
  • 27
    • 0003726932 scopus 로고
    • Monotone Dynamical Systems: An Introduction to the Theory of Competitive and Cooperative Systems
    • Providence, RI: American Mathematical Society
    • H. Smith, Monotone Dynamical Systems: An Introduction to the Theory of Competitive and Cooperative Systems. Providence, RI: American Mathematical Society, 1995.
    • (1995)
    • Smith, H.1
  • 28
    • 0036790975 scopus 로고    scopus 로고
    • "Intrinsic and extrinsic contributions to stochasticity in gene expression"
    • P. S. Swain, M. B. Elowitz, and E. D. Siggia, "Intrinsic and extrinsic contributions to stochasticity in gene expression," Proc. Natl. Acad. Sci., vol. 99, pp. 12795-12800, 2002.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 29
    • 13744253986 scopus 로고    scopus 로고
    • "Modelling periodic oscillation of biological systems with multiple timescale networks"
    • R. Wang, T. Zhou, Z. Jing, and L. Chen, "Modelling periodic oscillation of biological systems with multiple timescale networks," Syst. Biol., vol. 1, pp. 71-84, 2004.
    • (2004) Syst. Biol. , vol.1 , pp. 71-84
    • Wang, R.1    Zhou, T.2    Jing, Z.3    Chen, L.4
  • 30
    • 13744262451 scopus 로고    scopus 로고
    • "Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems"
    • R. Wang, Z. Jing, and L. Chen, "Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems," Bull. Math. Biol., vol. 67, pp. 339-367, 2005.
    • (2005) Bull. Math. Biol. , vol.67 , pp. 339-367
    • Wang, R.1    Jing, Z.2    Chen, L.3
  • 31
    • 33747410211 scopus 로고    scopus 로고
    • "Construction of genetic oscillators with interlocked feedback networks"
    • 10.1016/j.jtbi.2006.03.015
    • R. Wang, L. Chen, and K. Aihara, "Construction of genetic oscillators with interlocked feedback networks," J. Theor. Biol., vol. 242, pp. 454-463, 2006, 10.1016/j.jtbi.2006.03.015.
    • (2006) J. Theor. Biol. , vol.242 , pp. 454-463
    • Wang, R.1    Chen, L.2    Aihara, K.3
  • 32
    • 33747889656 scopus 로고    scopus 로고
    • "Synchronizing a multicellular system by external input: An artificial control strategy"
    • 10.1093/bioinformatics/btl182
    • R. Wang, L. Chen, and K. Aihara, "Synchronizing a multicellular system by external input: An artificial control strategy," Bioinformatics, vol. 22, pp. 1775-1781, 2006, 10.1093/bioinformatics/btl182.
    • (2006) Bioinformatics , vol.22 , pp. 1775-1781
    • Wang, R.1    Chen, L.2    Aihara, K.3
  • 33
    • 0345359924 scopus 로고    scopus 로고
    • "A positive-feedback-based bistable memory module that governs a cell fate decision"
    • W. Xiong and J. E. Ferrell, Jr., "A positive-feedback-based bistable memory module that governs a cell fate decision," Nature, vol. 426, pp. 460-465, 2003.
    • (2003) Nature , vol.426 , pp. 460-465
    • Xiong, W.1    Ferrell Jr., J.E.2
  • 34
    • 28844491402 scopus 로고    scopus 로고
    • "Molecular communication through stochastic synchronization induced by extracellular fluctuations"
    • 178103
    • T. Zhou, L. Chen, and K. Aihara, "Molecular communication through stochastic synchronization induced by extracellular fluctuations," Phys. Rev. Lett., vol. 95, 178103, pp. 1-4, 2005.
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 1-4
    • Zhou, T.1    Chen, L.2    Aihara, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.