-
1
-
-
0033593306
-
Molecular bases for circadian clocks
-
Dunlap JC, (1999) Molecular bases for circadian clocks. Cell 96: 271-290.
-
(1999)
Cell
, vol.96
, pp. 271-290
-
-
Dunlap, J.C.1
-
2
-
-
21344470923
-
Circadian rhythms from multiple oscillators: lessons from diverse organisms
-
Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, et al. (2005) Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet 6: 544-556.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 544-556
-
-
Bell-Pedersen, D.1
Cassone, V.M.2
Earnest, D.J.3
Golden, S.S.4
Hardin, P.E.5
-
3
-
-
56749160113
-
Design principles of biochemical oscillators
-
Novak B, Tyson JJ, (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9: 981-991.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, pp. 981-991
-
-
Novak, B.1
Tyson, J.J.2
-
4
-
-
0029094843
-
A model for circadian oscillations in the Drosophila period protein (PER)
-
Goldbeter A, (1995) A model for circadian oscillations in the Drosophila period protein (PER). Proc Biol Sci 261: 319-324.
-
(1995)
Proc Biol Sci
, vol.261
, pp. 319-324
-
-
Goldbeter, A.1
-
5
-
-
0031990984
-
A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins
-
Leloup JC, Goldbeter A, (1998) A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. J Biol Rhythms 13: 70-87.
-
(1998)
J Biol Rhythms
, vol.13
, pp. 70-87
-
-
Leloup, J.C.1
Goldbeter, A.2
-
6
-
-
0037795575
-
Toward a detailed computational model for the mammalian circadian clock
-
Leloup JC, Goldbeter A, (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100: 7051-7056.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 7051-7056
-
-
Leloup, J.C.1
Goldbeter, A.2
-
7
-
-
2142811057
-
Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK
-
Smolen P, Hardin PE, Lo BS, Baxter DA, Byrne JH, (2004) Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK. Biophys J 86: 2786-2802.
-
(2004)
Biophys J
, vol.86
, pp. 2786-2802
-
-
Smolen, P.1
Hardin, P.E.2
Lo, B.S.3
Baxter, D.A.4
Byrne, J.H.5
-
8
-
-
55849095134
-
Modeling the Drosophila melanogaster circadian oscillator via phase optimization
-
Bagheri N, Lawson MJ, Stelling J, Doyle FJ III, (2008) Modeling the Drosophila melanogaster circadian oscillator via phase optimization. J Biol Rhythms 23: 525-537.
-
(2008)
J Biol Rhythms
, vol.23
, pp. 525-537
-
-
Bagheri, N.1
Lawson, M.J.2
Stelling, J.3
Doyle III, F.J.4
-
9
-
-
67651115789
-
A model of the cell-autonomous mammalian circadian clock
-
Mirsky HP, Liu AC, Welsh DK, Kay SA, Doyle FJ III, (2009) A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci U S A 106: 11107-11112.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11107-11112
-
-
Mirsky, H.P.1
Liu, A.C.2
Welsh, D.K.3
Kay, S.A.4
Doyle III, F.J.5
-
10
-
-
0035449932
-
Modeling circadian oscillations with interlocking positive and negative feedback loops
-
Smolen P, Baxter DA, Byrne JH, (2001) Modeling circadian oscillations with interlocking positive and negative feedback loops. J Neurosci 21: 6644-6656.
-
(2001)
J Neurosci
, vol.21
, pp. 6644-6656
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
11
-
-
33847070037
-
Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops
-
Xie Z, Kulasiri D, (2007) Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops. J Theor Biol 245: 290-304.
-
(2007)
J Theor Biol
, vol.245
, pp. 290-304
-
-
Xie, Z.1
Kulasiri, D.2
-
12
-
-
0035927611
-
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm
-
Ueda HR, Hagiwara M, Kitano H, (2001) Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J Theor Biol 210: 401-406.
-
(2001)
J Theor Biol
, vol.210
, pp. 401-406
-
-
Ueda, H.R.1
Hagiwara, M.2
Kitano, H.3
-
13
-
-
0033828273
-
Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways
-
Alves R, Savageau MA, (2000) Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics 16: 534-547.
-
(2000)
Bioinformatics
, vol.16
, pp. 534-547
-
-
Alves, R.1
Savageau, M.A.2
-
14
-
-
42549157090
-
Mathematical identification of critical reactions in the interlocked feedback model
-
Kurata H, Tanaka T, Ohnishi F, (2007) Mathematical identification of critical reactions in the interlocked feedback model. PLoS ONE 2: e1103.
-
(2007)
PLoS ONE
, vol.2
-
-
Kurata, H.1
Tanaka, T.2
Ohnishi, F.3
-
16
-
-
74849130143
-
An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock
-
Xie Z, Kulasiri D, Samarasinghe S, Qian J, (2010) An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock. Biotechnol Bioeng 105: 250-259.
-
(2010)
Biotechnol Bioeng
, vol.105
, pp. 250-259
-
-
Xie, Z.1
Kulasiri, D.2
Samarasinghe, S.3
Qian, J.4
-
17
-
-
77951099999
-
Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks
-
Maeda K, Kurata H, (2009) Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks. IPSJ Transactions on Bioinformatics 2: 2-14.
-
(2009)
IPSJ Transactions on Bioinformatics
, vol.2
, pp. 2-14
-
-
Maeda, K.1
Kurata, H.2
-
18
-
-
0036500834
-
Reverse engineering of biological complexity
-
Csete ME, Doyle JC, (2002) Reverse engineering of biological complexity. Science 295: 1664-1669.
-
(2002)
Science
, vol.295
, pp. 1664-1669
-
-
Csete, M.E.1
Doyle, J.C.2
-
19
-
-
14544280668
-
Surviving heat shock: control strategies for robustness and performance
-
El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M, (2005) Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A 102: 2736-2741.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2736-2741
-
-
El-Samad, H.1
Kurata, H.2
Doyle, J.C.3
Gross, C.A.4
Khammash, M.5
-
20
-
-
33746639260
-
Module-based analysis of robustness tradeoffs in the heat shock response system
-
Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, et al. (2006) Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol 2: e59.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Kurata, H.1
El-Samad, H.2
Iwasaki, R.3
Ohtake, H.4
Doyle, J.C.5
-
21
-
-
0015231849
-
Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems
-
Savageau MA, (1971) Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229: 542-544.
-
(1971)
Nature
, vol.229
, pp. 542-544
-
-
Savageau, M.A.1
-
22
-
-
78650784246
-
Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks
-
Maeda K, Kurata H, (2011) Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks. J Theor Biol 272: 174-186.
-
(2011)
J Theor Biol
, vol.272
, pp. 174-186
-
-
Maeda, K.1
Kurata, H.2
-
23
-
-
0036302129
-
Comparative study of circadian clock models, in search of processes promoting oscillation
-
Kurosawa G, Mochizuki A, Iwasa Y, (2002) Comparative study of circadian clock models, in search of processes promoting oscillation. J Theor Biol 216: 193-208.
-
(2002)
J Theor Biol
, vol.216
, pp. 193-208
-
-
Kurosawa, G.1
Mochizuki, A.2
Iwasa, Y.3
-
24
-
-
0027382270
-
Thinking about genetic redundancy
-
Thomas JH, (1993) Thinking about genetic redundancy. Trends in Genetics 9: 395-399.
-
(1993)
Trends in Genetics
, vol.9
, pp. 395-399
-
-
Thomas, J.H.1
-
25
-
-
0030836756
-
Evolution of genetic redundancy
-
Nowak MA, Boerlijst MC, Cooke J, Smith JM, (1997) Evolution of genetic redundancy. Nature 388: 167-171.
-
(1997)
Nature
, vol.388
, pp. 167-171
-
-
Nowak, M.A.1
Boerlijst, M.C.2
Cooke, J.3
Smith, J.M.4
-
26
-
-
0031104842
-
Canalization: a molecular genetic perspective
-
Wilkins AS, (1997) Canalization: a molecular genetic perspective. BioEssays 19: 257-262.
-
(1997)
BioEssays
, vol.19
, pp. 257-262
-
-
Wilkins, A.S.1
-
27
-
-
0030986495
-
Evolutionary origins and maintenance of redundant gene expression during metazoan development
-
Cooke J, Nowak MA, Boerlijst M, Maynard-Smith J, (1997) Evolutionary origins and maintenance of redundant gene expression during metazoan development. Trends in genetics: TIG 13: 360-364.
-
(1997)
Trends in Genetics: TIG
, vol.13
, pp. 360-364
-
-
Cooke, J.1
Nowak, M.A.2
Boerlijst, M.3
Maynard-Smith, J.4
-
28
-
-
14344263352
-
Distributed robustness versus redundancy as causes of mutational robustness
-
Wagner A, (2005) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27: 176-188.
-
(2005)
Bioessays
, vol.27
, pp. 176-188
-
-
Wagner, A.1
-
29
-
-
0034288615
-
Entrainment Versus Chaos in a Model for a Circadian Oscillator Driven by Light-Dark Cycles
-
Gonze D, Goldbeter A, (2000) Entrainment Versus Chaos in a Model for a Circadian Oscillator Driven by Light-Dark Cycles. Journal of Statistical Physics 101: 649-663.
-
(2000)
Journal of Statistical Physics
, vol.101
, pp. 649-663
-
-
Gonze, D.1
Goldbeter, A.2
-
30
-
-
33747440791
-
Amplitude of circadian oscillations entrained by 24-h light-dark cycles
-
Kurosawa G, Goldbeter A, (2006) Amplitude of circadian oscillations entrained by 24-h light-dark cycles. J Theor Biol 242: 478-488.
-
(2006)
J Theor Biol
, vol.242
, pp. 478-488
-
-
Kurosawa, G.1
Goldbeter, A.2
-
31
-
-
0034161394
-
dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex
-
Bae K, Lee C, Hardin PE, Edery I, (2000) dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex. J Neurosci 20: 1746-1753.
-
(2000)
J Neurosci
, vol.20
, pp. 1746-1753
-
-
Bae, K.1
Lee, C.2
Hardin, P.E.3
Edery, I.4
-
32
-
-
0034640253
-
Interacting molecular loops in the mammalian circadian clock
-
Shearman LP, Sriram S, Weaver DR, Maywood ES, Chaves I, et al. (2000) Interacting molecular loops in the mammalian circadian clock. Science 288: 1013-1019.
-
(2000)
Science
, vol.288
, pp. 1013-1019
-
-
Shearman, L.P.1
Sriram, S.2
Weaver, D.R.3
Maywood, E.S.4
Chaves, I.5
-
33
-
-
0035047945
-
Molecular analysis of mammalian circadian rhythms
-
Reppert SM, Weaver DR, (2001) Molecular analysis of mammalian circadian rhythms. Annu Rev Physiol 63: 647-676.
-
(2001)
Annu Rev Physiol
, vol.63
, pp. 647-676
-
-
Reppert, S.M.1
Weaver, D.R.2
-
34
-
-
0032486432
-
Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim
-
Darlington TK, Wager-Smith K, Ceriani MF, Staknis D, Gekakis N, et al. (1998) Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim. Science 280: 1599-1603.
-
(1998)
Science
, vol.280
, pp. 1599-1603
-
-
Darlington, T.K.1
Wager-Smith, K.2
Ceriani, M.F.3
Staknis, D.4
Gekakis, N.5
-
35
-
-
17044451254
-
A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless
-
Allada R, White NE, So WV, Hall JC, Rosbash M, (1998) A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell 93: 791-804.
-
(1998)
Cell
, vol.93
, pp. 791-804
-
-
Allada, R.1
White, N.E.2
So, W.V.3
Hall, J.C.4
Rosbash, M.5
-
36
-
-
0032577450
-
CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless
-
Rutila JE, Suri V, Le M, So WV, Rosbash M, et al. (1998) CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell 93: 805-814.
-
(1998)
Cell
, vol.93
, pp. 805-814
-
-
Rutila, J.E.1
Suri, V.2
Le, M.3
So, W.V.4
Rosbash, M.5
-
37
-
-
0030989154
-
A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster
-
Hao H, Allen DL, Hardin PE, (1997) A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster. Mol Cell Biol 17: 3687-3693.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 3687-3693
-
-
Hao, H.1
Allen, D.L.2
Hardin, P.E.3
-
38
-
-
0028838668
-
Rhythmic expression of timeless: a basis for promoting circadian cycles in period gene autoregulation
-
Sehgal A, Rothenfluh-Hilfiker A, Hunter-Ensor M, Chen Y, Myers MP, et al. (1995) Rhythmic expression of timeless: a basis for promoting circadian cycles in period gene autoregulation. Science 270: 808-810.
-
(1995)
Science
, vol.270
, pp. 808-810
-
-
Sehgal, A.1
Rothenfluh-Hilfiker, A.2
Hunter-Ensor, M.3
Chen, Y.4
Myers, M.P.5
-
39
-
-
0032191902
-
The Drosophila CLOCK protein undergoes daily rhythms in abundance, phosphorylation, and interactions with the PER-TIM complex
-
Lee C, Bae K, Edery I, (1998) The Drosophila CLOCK protein undergoes daily rhythms in abundance, phosphorylation, and interactions with the PER-TIM complex. Neuron 21: 857-867.
-
(1998)
Neuron
, vol.21
, pp. 857-867
-
-
Lee, C.1
Bae, K.2
Edery, I.3
-
40
-
-
0029965130
-
Regulation of the Drosophila protein timeless suggests a mechanism for resetting the circadian clock by light
-
Hunter-Ensor M, Ousley A, Sehgal A, (1996) Regulation of the Drosophila protein timeless suggests a mechanism for resetting the circadian clock by light. Cell 84: 677-685.
-
(1996)
Cell
, vol.84
, pp. 677-685
-
-
Hunter-Ensor, M.1
Ousley, A.2
Sehgal, A.3
-
41
-
-
0029989521
-
Light-induced degradation of TIMELESS and entrainment of the Drosophila circadian clock
-
Myers MP, Wager-Smith K, Rothenfluh-Hilfiker A, Young MW, (1996) Light-induced degradation of TIMELESS and entrainment of the Drosophila circadian clock. Science 271: 1736-1740.
-
(1996)
Science
, vol.271
, pp. 1736-1740
-
-
Myers, M.P.1
Wager-Smith, K.2
Rothenfluh-Hilfiker, A.3
Young, M.W.4
-
42
-
-
0029979174
-
A light-entrainment mechanism for the Drosophila circadian clock
-
Zeng H, Qian Z, Myers MP, Rosbash M, (1996) A light-entrainment mechanism for the Drosophila circadian clock. Nature 380: 129-135.
-
(1996)
Nature
, vol.380
, pp. 129-135
-
-
Zeng, H.1
Qian, Z.2
Myers, M.P.3
Rosbash, M.4
-
43
-
-
0033665572
-
Extending the method of mathematically controlled comparison to include numerical comparisons
-
Alves R, Savageau MA, (2000) Extending the method of mathematically controlled comparison to include numerical comparisons. Bioinformatics 16: 786-798.
-
(2000)
Bioinformatics
, vol.16
, pp. 786-798
-
-
Alves, R.1
Savageau, M.A.2
-
45
-
-
84937657473
-
The Synthesis of Minimum Sensitivity Networks
-
Schoeffler J, (1964) The Synthesis of Minimum Sensitivity Networks. IEEE Transactions on Circuit Theory 11: 271-276.
-
(1964)
IEEE Transactions on Circuit Theory
, vol.11
, pp. 271-276
-
-
Schoeffler, J.1
-
46
-
-
36749043657
-
Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
-
Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, et al. (2007) Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 35: e134.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kurata, H.1
Inoue, K.2
Maeda, K.3
Masaki, K.4
Shimokawa, Y.5
-
47
-
-
17844397967
-
CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models
-
Kurata H, Masaki K, Sumida Y, Iwasaki R, (2005) CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res 15: 590-600.
-
(2005)
Genome Res
, vol.15
, pp. 590-600
-
-
Kurata, H.1
Masaki, K.2
Sumida, Y.3
Iwasaki, R.4
-
48
-
-
0242380634
-
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
-
Kurata H, Matoba N, Shimizu N, (2003) CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res 31: 4071-4084.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 4071-4084
-
-
Kurata, H.1
Matoba, N.2
Shimizu, N.3
|