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Volumn 53, Issue SPECIAL ISSUE, 2008, Pages 177-188

Sensitivity measures for oscillating systems: Application to mammalian circadian gene network

Author keywords

Biological clock; Phase response curve

Indexed keywords

BIOLOGICAL CLOCK; CELLULAR LEVELS; CIRCADIAN CLOCK; COMPLEX NETWORKS; EXTERNAL ENVIRONMENTS; GENE NETWORKS; OSCILLATING SYSTEMS; PARAMETRIC IMPULSE; PHASE RESPONSE CURVES; SALIENT FEATURES; SENSITIVITY TOOLS; STABLE LIMIT CYCLE; PHASE RESPONSE CURVE;

EID: 39849102205     PISSN: 00189286     EISSN: None     Source Type: Journal    
DOI: 10.1109/TAC.2007.911364     Document Type: Article
Times cited : (57)

References (42)
  • 1
    • 10444264607 scopus 로고    scopus 로고
    • Some new directions in control theory inspired by systems biology
    • Jun.
    • E. D. Sontag, "Some new directions in control theory inspired by systems biology," IET Syst. Biol., vol. 1, no. 1, pp. 9-18, Jun. 2004.
    • (2004) IET Syst. Biol. , vol.1 , Issue.1 , pp. 9-18
    • Sontag, E.D.1
  • 2
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • H. Kitano, "Systems biology: A brief overview," in Proc. Nat. Acad. Sci., 2002, vol.295, pp. 1662-1664.
    • (2002) Proc. Nat. Acad. Sci. , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 3
    • 33750628424 scopus 로고    scopus 로고
    • Systems interface biology
    • Oct.
    • F. J. Doyle, III and J. Stelling, "Systems interface biology," J. R. Soc. Interface, vol. 3, no. 10, pp. 603-616, Oct. 2006.
    • (2006) J. R. Soc. Interface , vol.3 , Issue.10 , pp. 603-616
    • Doyle III, F.J.1    Stelling, J.2
  • 4
    • 0036500834 scopus 로고    scopus 로고
    • Reverse engineering of biological complexity
    • M. Csete and J. Doyle, "Reverse engineering of biological complexity," Proc. Nat. Acad. Sci. USA, vol.295, pp. 1664-1669, 2002.
    • (2002) Proc. Nat. Acad. Sci. USA , vol.295 , pp. 1664-1669
    • Csete, M.1    Doyle, J.2
  • 5
  • 6
    • 0000188718 scopus 로고    scopus 로고
    • Highly optimized tolerance: Robustness and design in complex systems
    • Mar.
    • J. M. Carlson and J. Doyle, "Highly optimized tolerance: Robustness and design in complex systems," Phys. Rev. Lett., vol. 84, no. 11, pp. 2529-2532, Mar. 2000.
    • (2000) Phys. Rev. Lett. , vol.84 , Issue.11 , pp. 2529-2532
    • Carlson, J.M.1    Doyle, J.2
  • 7
    • 33747848852 scopus 로고    scopus 로고
    • Advanced methods and algorithms for biological networks analysis
    • Apr.
    • H. El-Samad, S. Prajna, A. Papachristodoulou, J. Doyle, and M. Khammash, "Advanced methods and algorithms for biological networks analysis," Proc. IEEE, vol. 94, no. 4, pp. 832-853, Apr. 2006.
    • (2006) Proc. IEEE , vol.94 , Issue.4 , pp. 832-853
    • El-Samad, H.1    Prajna, S.2    Papachristodoulou, A.3    Doyle, J.4    Khammash, M.5
  • 8
    • 7644238181 scopus 로고    scopus 로고
    • Biological robustness
    • Nov.
    • H. Kitano, "Biological robustness," Nat. Rev. Genet., vol. 5, no. 11, pp. 826-37, Nov. 2004.
    • (2004) Nat. Rev. Genet. , vol.5 , Issue.11 , pp. 826-837
    • Kitano, H.1
  • 9
    • 0036301511 scopus 로고    scopus 로고
    • Robustness as a measure of plausibility in models of biochemical networks
    • May
    • M. Morohashi, A. E. Winn, M. T. Borisuk, H. Bolouri, J. Doyle, and H. Kitano, "Robustness as a measure of plausibility in models of biochemical networks," J. Theor. Biol., vol. 216, no. 1, pp. 19-30, May 2002.
    • (2002) J. Theor. Biol. , vol.216 , Issue.1 , pp. 19-30
    • Morohashi, M.1    Winn, A.E.2    Borisuk, M.T.3    Bolouri, H.4    Doyle, J.5    Kitano, H.6
  • 10
    • 33747424764 scopus 로고    scopus 로고
    • Robustness analysis of biochemical network models
    • May
    • J. Kim, D. G. Bates, I. Postlethwaite, L. Ma, and P. A. Iglesias, "Robustness analysis of biochemical network models," IET Syst. Biol., vol. 153, no. 3, pp. 96-104, May 2006.
    • (2006) IET Syst. Biol. , vol.153 , Issue.3 , pp. 96-104
    • Kim, J.1    Bates, D.G.2    Postlethwaite, I.3    Ma, L.4    Iglesias, P.A.5
  • 11
    • 4444322221 scopus 로고    scopus 로고
    • Robustness properties of circadian clock architectures
    • Sep.
    • J. Stelling, E. D. Gilles, and F. J. Doyle, III, "Robustness properties of circadian clock architectures," Science, vol. 101, no. 36, pp. 13210-5, Sep. 2004.
    • (2004) Science , vol.101 , Issue.36 , pp. 13210-5
    • Stelling, J.1    Gilles, E.D.2    Doyle III, F.J.3
  • 12
    • 33846085492 scopus 로고    scopus 로고
    • A novel computational model of the circadian clock in arabidopsis that incorporates PRR7 and PRR9
    • M. N. Zeilinger, E. M. Farré, S. R. Taylor, S. A. Kay, and F. J. Doyle, III, "A novel computational model of the circadian clock in arabidopsis that incorporates PRR7 and PRR9," Mol. Syst. Biol., vol.2, p. 58, 2006.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 58
    • Zeilinger, M.N.1    Farré, E.M.2    Taylor, S.R.3    Kay, S.A.4    Doyle III, F.J.5
  • 13
    • 0032752042 scopus 로고    scopus 로고
    • Forty years of PRCs - What have we learned?
    • Nov.
    • C. H. Johnson, "Forty years of PRCs - What have we learned?," Chronobiol. Int., vol. 16, no. 6, pp. 711-43, Nov. 1999.
    • (1999) Chronobiol. Int. , vol.16 , Issue.6 , pp. 711-743
    • Johnson, C.H.1
  • 14
    • 33847264998 scopus 로고    scopus 로고
    • Quantitative performance metrics for robustness in circadian rhythms
    • Feb.
    • N. Bagheri, J. Stelling, and F. J. Doyle, III, "Quantitative performance metrics for robustness in circadian rhythms," Bioinformatics, vol. 23, no. 3, pp. 358-364, Feb. 2007.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 358-364
    • Bagheri, N.1    Stelling, J.2    Doyle III, F.J.3
  • 15
    • 0345826009 scopus 로고    scopus 로고
    • Temporal precision in the mammalian circadian system: A reliable clock from less reliable neurons
    • Feb.
    • E. D. Herzog, S. J. Aton, R. Numano, Y. Sakaki, and H. Tei, "Temporal precision in the mammalian circadian system: A reliable clock from less reliable neurons," J. Biol. Rhythm., vol. 19, no. 1, pp. 35-46, Feb. 2004.
    • (2004) J. Biol. Rhythm. , vol.19 , Issue.1 , pp. 35-46
    • Herzog, E.D.1    Aton, S.J.2    Numano, R.3    Sakaki, Y.4    Tei, H.5
  • 16
    • 1542351229 scopus 로고    scopus 로고
    • On the phase reduction and response dynamics of neural oscillator populations
    • Apr.
    • E. Brown, J. Moehlis, and P. Holmes, "On the phase reduction and response dynamics of neural oscillator populations," Neural Comput., vol. 16, no. 4, pp. 673-715, Apr. 2004.
    • (2004) Neural Comput. , vol.16 , Issue.4 , pp. 673-715
    • Brown, E.1    Moehlis, J.2    Holmes, P.3
  • 17
    • 0039592729 scopus 로고    scopus 로고
    • From Kuramoto to Crawford: Exploring the onset of synchronization in populations of coupled oscillators
    • S. H. Strogatz, "From Kuramoto to Crawford: Exploring the onset of synchronization in populations of coupled oscillators," Physica D, vol.143, pp. 1-20, 2000.
    • (2000) Physica D , vol.143 , pp. 1-20
    • Strogatz, S.H.1
  • 18
    • 0037194790 scopus 로고    scopus 로고
    • Coordination of circadian timing in mammals
    • Aug.
    • S. M. Reppert and D. R. Weaver, "Coordination of circadian timing in mammals," Nature, vol. 418, no. 6901, pp. 935-941, Aug. 2002.
    • (2002) Nature , vol.418 , Issue.6901 , pp. 935-941
    • Reppert, S.M.1    Weaver, D.R.2
  • 19
    • 12244277104 scopus 로고    scopus 로고
    • Modeling feedback loops of the mammalian circadian oscillator
    • Nov.
    • S. Becker-Weimann, J. Wolf, H. Herzel, and A. Kramer, "Modeling feedback loops of the mammalian circadian oscillator," Biophys. J., vol. 87, no. 5, pp. 3023-3034, Nov. 2004.
    • (2004) Biophys. J. , vol.87 , Issue.5 , pp. 3023-3034
    • Becker-Weimann, S.1    Wolf, J.2    Herzel, H.3    Kramer, A.4
  • 20
    • 12244297781 scopus 로고    scopus 로고
    • Entrainment in a model of the mammalian circadian oscillator
    • Feb.
    • F. Geier, S. Becker-Weimann, A. Kramer, and H. Herzel, "Entrainment in a model of the mammalian circadian oscillator," J. Biol. Rhythm., vol. 20, no. 1, pp. 83-93, Feb. 2005.
    • (2005) J. Biol. Rhythm. , vol.20 , Issue.1 , pp. 83-93
    • Geier, F.1    Becker-Weimann, S.2    Kramer, A.3    Herzel, H.4
  • 21
    • 0017198155 scopus 로고
    • A functional analysis of circadian pacemakers in nocturnal rodents. II. The variability of phase response curves
    • Oct.
    • S. Daan and C. S. Pittendrigh, "A functional analysis of circadian pacemakers in nocturnal rodents. II. The variability of phase response curves," J. Comp. Physiol., vol. 106, no. 3, pp. 253-266, Oct. 1976.
    • (1976) J. Comp. Physiol. , vol.106 , Issue.3 , pp. 253-266
    • Daan, S.1    Pittendrigh, C.S.2
  • 24
    • 0021502682 scopus 로고
    • Sensitivity analysis of oscillatory systems
    • M. Kramer, H. Rabitz, and J. Calo, "Sensitivity analysis of oscillatory systems," Appl. Math. Model., vol.8, pp. 328-340, 1984.
    • (1984) Appl. Math. Model. , vol.8 , pp. 328-340
    • Kramer, M.1    Rabitz, H.2    Calo, J.3
  • 25
    • 33645642280 scopus 로고    scopus 로고
    • Autonomously oscillating biochemical systems: Parametric sensitivity of extrema and period
    • Jun.
    • B. P. Ingalls, "Autonomously oscillating biochemical systems: Parametric sensitivity of extrema and period," IET Syst. Biol., vol. 1, no. 1, pp. 62-70, Jun. 2004.
    • (2004) IET Syst. Biol. , vol.1 , Issue.1 , pp. 62-703
    • Ingalls, B.P.1
  • 26
    • 15744389129 scopus 로고    scopus 로고
    • Sensitivity analysis of oscillatory (bio)chemical systems
    • D. E. Zak, J. Stelling, and F. J. Doyle, III, "Sensitivity analysis of oscillatory (bio)chemical systems," Comput. Chem. Eng., vol. 29, no. 3, pp. 663-673, 2005.
    • (2005) Comput. Chem. Eng. , vol.29 , Issue.3 , pp. 663-673
    • Zak, D.E.1    Stelling, J.2    Doyle III, F.J.3
  • 27
    • 33748465152 scopus 로고    scopus 로고
    • Isochron-based phase response analysis of circadian rhythms
    • Jun.
    • R. Gunawan and F. J. Doyle, III, "Isochron-based phase response analysis of circadian rhythms," Biophys. J., vol.91, pp. 2131-2141, Jun. 2006.
    • (2006) Biophys. J. , vol.91 , pp. 2131-2141
    • Gunawan, R.1    Doyle III, F.J.2
  • 31
    • 0016314153 scopus 로고
    • Isochrons and phaseless sets
    • Sep.
    • J. Guckenheimer, "Isochrons and phaseless sets," J. Math. Biol., vol. 1, no. 3, pp. 259-273, Sep. 1975.
    • (1975) J. Math. Biol. , vol.1 , Issue.3 , pp. 259-273
    • Guckenheimer, J.1
  • 32
    • 0032758081 scopus 로고    scopus 로고
    • A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM
    • Nov.
    • J. J. Tyson, C. I. Hong, C. D. Thron, and B. Novak, "A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM ," Biophys. J., vol. 77, no. 5, pp. 2411-7, Nov. 1999.
    • (1999) Biophys. J. , vol.77 , Issue.5 , pp. 2411-7
    • Tyson, J.J.1    Hong, C.I.2    Thron, C.D.3    Novak, B.4
  • 33
    • 0035047945 scopus 로고    scopus 로고
    • Molecular analysis of mammalian circadian rhythms
    • S. M. Reppert and D. R. Weaver, "Molecular analysis of mammalian circadian rhythms," Annu. Rev. Physiol., vol.63, pp. 647-676, 2001.
    • (2001) Annu. Rev. Physiol. , vol.63 , pp. 647-676
    • Reppert, S.M.1    Weaver, D.R.2
  • 34
    • 0038070188 scopus 로고    scopus 로고
    • Adjoint sensitivity analysis for differential-algebraic equations: The adjoint DAE system and its numerical solution
    • Y. Cao, S. Li, L. Petzold, and R. Serban, "Adjoint sensitivity analysis for differential-algebraic equations: The adjoint DAE system and its numerical solution," SIAM J. Sci. Comput., vol. 24, no. 3, pp. 1076-1089, 2003.
    • (2003) SIAM J. Sci. Comput. , vol.24 , Issue.3 , pp. 1076-1089
    • Cao, Y.1    Li, S.2    Petzold, L.3    Serban, R.4
  • 35
    • 77955154364 scopus 로고    scopus 로고
    • DAE software website [Online]. Available
    • DAE software website [Online]. Available: http://www.engineering.ucsb. edu/~cse
  • 36
    • 33748694309 scopus 로고    scopus 로고
    • Phase and period responses of the circadian system of mice (Mus musculus) to light stimuli of different duration
    • Oct.
    • M. Comas, D. G. M. Beersma, K. Spoelstra, and S. Daan, "Phase and period responses of the circadian system of mice (Mus musculus) to light stimuli of different duration," J. Biol. Rhythm., vol. 21, no. 5, pp. 362-372, Oct. 2006.
    • (2006) J. Biol. Rhythm. , vol.21 , Issue.5 , pp. 362-372
    • Comas, M.1    Beersma, D.G.M.2    Spoelstra, K.3    Daan, S.4
  • 37
    • 0014108715 scopus 로고
    • Biological rhythms and the behavior of populations of coupled oscillators
    • Jul.
    • A. T.Winfree, "Biological rhythms and the behavior of populations of coupled oscillators," J. Theor. Biol., vol. 16, no. 1, pp. 15-42, Jul. 1967.
    • (1967) J. Theor. Biol. , vol.16 , Issue.1 , pp. 15-42
    • Winfree, A.T.1
  • 38
    • 33747111430 scopus 로고    scopus 로고
    • Design principles underlying circadian clocks
    • Nov.
    • D. A. Rand, B. V. Shulgin, D. Salazar, and A. J. Millar, "Design principles underlying circadian clocks," J. R. Soc. Interface, vol. 1, no. 1, pp. 119-130, Nov. 2004.
    • (2004) J. R. Soc. Interface , vol.1 , Issue.1 , pp. 119-130
    • Rand, D.A.1    Shulgin, B.V.2    Salazar, D.3    Millar, A.J.4
  • 39
    • 30444453830 scopus 로고    scopus 로고
    • Uncovering the design principles of circadian clocks: Mathematical analysis of flexibility and evolutionary goals
    • Feb.
    • D. A. Rand, B. V. Shulgin, J. D. Salazar, and A. J. Millar, "Uncovering the design principles of circadian clocks: Mathematical analysis of flexibility and evolutionary goals," J. Theor. Biol., vol. 238, no. 3, pp. 616-635, Feb. 2006.
    • (2006) J. Theor. Biol. , vol.238 , Issue.3 , pp. 616-635
    • Rand, D.A.1    Shulgin, B.V.2    Salazar, J.D.3    Millar, A.J.4
  • 40
    • 0036037385 scopus 로고    scopus 로고
    • Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators
    • Jun.
    • H. R. Ueda, K. Hirose, and M. Iino, "Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators," J. Theor. Biol., vol. 216, no. 4, pp. 501-512, Jun. 2002.
    • (2002) J. Theor. Biol. , vol.216 , Issue.4 , pp. 501-512
    • Ueda, H.R.1    Hirose, K.2    Iino, M.3
  • 41
    • 34250367538 scopus 로고    scopus 로고
    • A molecular model for intercellular synchronization in the mammalian circadian clock
    • Mar.
    • T.-L. To, M. A. Henson, E. D. Herzog, and F. J. Doyle, III, "A molecular model for intercellular synchronization in the mammalian circadian clock," Biophys. J., vol.92, pp. 3792-3803, Mar. 2007.
    • (2007) Biophys. J. , vol.92 , pp. 3792-3803
    • To, T.-L.1    Henson, M.A.2    Herzog, E.D.3    Doyle III, F.J.4
  • 42
    • 33747440791 scopus 로고    scopus 로고
    • Amplitude of circadian oscillations entrained by 24-h light-dark cycles
    • Sep.
    • G. Kurosawa and A. Goldbeter, "Amplitude of circadian oscillations entrained by 24-h light-dark cycles," J. Theor. Biol., vol. 242, no. 2, pp. 478-488, Sep. 2006.
    • (2006) J. Theor. Biol. , vol.242 , Issue.2 , pp. 478-488
    • Kurosawa, G.1    Goldbeter, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.