-
1
-
-
0015502072
-
Transients and cooperativity: A slow transition model for relating transients and cooperative kinetics of enzymes
-
Ainslie GR, Shill JP, Neet KE. 1972. Transients and cooperativity: a slow transition model for relating transients and cooperative kinetics of enzymes. J. Biol. Chem. 247:7088-96
-
(1972)
J. Biol. Chem.
, vol.247
, pp. 7088-7096
-
-
Ainslie, G.R.1
Shill, J.P.2
Neet, K.E.3
-
2
-
-
38749098685
-
Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution
-
Ao P, Galas D, Hood L, Zhu X. 2008. Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med. Hypoth. 70:678-84
-
(2008)
Med. Hypoth.
, vol.70
, pp. 678-684
-
-
Ao, P.1
Galas, D.2
Hood, L.3
Zhu, X.4
-
3
-
-
37649018636
-
Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities
-
Artyomov MN, Das J, Kardar M, Chakraborty AK. 2007. Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc. Natl. Acad. Sci. USA 104:18958-63
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18958-18963
-
-
Artyomov, M.N.1
Das, J.2
Kardar, M.3
Chakraborty, A.K.4
-
6
-
-
0033855774
-
Fluctuations and quality of control in biological cells: Zero-order ultrasensitivity reinvestigated
-
Berg OG, Paulsson J, Ehrenberg M. 2000. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79:1228-36
-
(2000)
Biophys. J.
, vol.79
, pp. 1228-1236
-
-
Berg, O.G.1
Paulsson, J.2
Ehrenberg, M.3
-
7
-
-
0033638791
-
Fluctuations in repressor control: Thermodynamic constraints on stochastic focusing
-
Berg OG, Paulsson J, Ehrenberg M. 2000. Fluctuations in repressor control: thermodynamic constraints on stochastic focusing. Biophys. J. 79:2944-53
-
(2000)
Biophys. J.
, vol.79
, pp. 2944-2953
-
-
Berg, O.G.1
Paulsson, J.2
Ehrenberg, M.3
-
8
-
-
74049092279
-
Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinase
-
Bishop LM, Qian H. 2010. Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinase. Biophys. J. 98:1-11
-
(2010)
Biophys. J.
, vol.98
, pp. 1-11
-
-
Bishop, L.M.1
Qian, H.2
-
9
-
-
70350336588
-
Architecture-dependent noise discriminates functionally analogous differentiation circuits
-
Caǧatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Süel GM. 2009. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139:512-22
-
(2009)
Cell
, vol.139
, pp. 512-522
-
-
Caǧatay, T.1
Turcotte, M.2
Elowitz, M.B.3
Garcia-Ojalvo, J.4
Süel, G.M.5
-
10
-
-
78649871073
-
Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda
-
Cao Y, Lu H-M, Liang J. 2010. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proc. Natl. Acad. Sci. USA 107:18445-50
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 18445-18450
-
-
Cao, Y.1
Lu, H.-M.2
Liang, J.3
-
11
-
-
0023295224
-
Asymmetry and external noise-induced free energy transduction
-
Chen Y-D. 1987. Asymmetry and external noise-induced free energy transduction. Proc. Natl. Acad. Sci. USA 84:729-33
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 729-733
-
-
Chen, Y.-D.1
-
12
-
-
58249092059
-
Digital signaling and hysteresis characterize Ras activation in lymphoid cells
-
Das J, Ho M, Zikherman J, Govern C, Yang M, et al. 2009. Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136:337-51
-
(2009)
Cell
, vol.136
, pp. 337-351
-
-
Das, J.1
Ho, M.2
Zikherman, J.3
Govern, C.4
Yang, M.5
-
13
-
-
0000296912
-
Statistical fluctuations in autocatalytic reactions
-
Delbrück M. 1940. Statistical fluctuations in autocatalytic reactions. J. Chem. Phys. 8:120-24
-
(1940)
J. Chem. Phys.
, vol.8
, pp. 120-124
-
-
Delbrück, M.1
-
15
-
-
34249080596
-
Theoretical analysis of epigenetic cell memory by nucleosome modification
-
Dodd IB, Micheelsen MA, Sneppen K, Thon G. 2007. Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129:813-22
-
(2007)
Cell
, vol.129
, pp. 813-822
-
-
Dodd, I.B.1
Micheelsen, M.A.2
Sneppen, K.3
Thon, G.4
-
16
-
-
47649130574
-
Capturing cooperativity
-
Editorial.
-
Editorial. 2008. Capturing cooperativity. Nat. Chem. Biol. 4:433-47
-
(2008)
Nat. Chem. Biol.
, vol.4
, pp. 433-447
-
-
-
18
-
-
0032496358
-
The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
-
Ferrell JE, Machleder EM. 1998. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280:895-98
-
(1998)
Science
, vol.280
, pp. 895-898
-
-
Ferrell, J.E.1
MacHleder, E.M.2
-
19
-
-
0037605637
-
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible
-
Ferrell JE, Xiong W. 2001. Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible. Chaos 11:227-36
-
(2001)
Chaos
, vol.11
, pp. 227-236
-
-
Ferrell, J.E.1
Xiong, W.2
-
20
-
-
0000813480
-
Ratchet and pawl
-
Reading, MA: Addison-Wesley
-
Feynman RP, Leighton RB, Sands M. 1963. Ratchet and pawl. In The Feynman Lectures on Physics, Vol. 1, pp. 46-1-46-9. Reading, MA: Addison-Wesley
-
(1963)
The Feynman Lectures on Physics
, vol.1
, pp. 461-469
-
-
Feynman, R.P.1
Leighton, R.B.2
Sands, M.3
-
21
-
-
0014940726
-
Kinetic aspects of regulation of metabolic processes: The hysteretic enzyme concept
-
Frieden C. 1970. Kinetic aspects of regulation of metabolic processes: the hysteretic enzyme concept. J. Biol. Chem. 245:5788-99
-
(1970)
J. Biol. Chem.
, vol.245
, pp. 5788-5799
-
-
Frieden, C.1
-
23
-
-
70349931588
-
Thermodynamic limit of a nonequilibrium steady-state: Maxwell-type construction for a bistable biochemical system
-
Ge H, Qian H. 2009. Thermodynamic limit of a nonequilibrium steady-state: Maxwell-type construction for a bistable biochemical system. Phys. Rev. Lett. 103:148103
-
(2009)
Phys. Rev. Lett.
, vol.103
, pp. 148103
-
-
Ge, H.1
Qian, H.2
-
24
-
-
78649786267
-
Nonequilibrium phase transition in mesoscopic biochemical systems: From stochastic to nonlinear dynamics and beyond
-
Ge H, Qian H. 2011. Nonequilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond. J. R. Soc. Interf. 8:107-16
-
(2011)
J. R. Soc. Interf.
, vol.8
, pp. 107-116
-
-
Ge, H.1
Qian, H.2
-
25
-
-
46749104726
-
Sensitivity amplification in the phosphorylation-dephosphorylation cycle: Nonequi-librium steady states, chemical master equation and temporal cooperativity
-
Ge H, Qian M. 2008. Sensitivity amplification in the phosphorylation- dephosphorylation cycle: nonequi-librium steady states, chemical master equation and temporal cooperativity. J. Chem. Phys. 129:015104
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 015104
-
-
Ge, H.1
Qian, M.2
-
26
-
-
83255165435
-
Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics
-
Ge H, Qian M, Qian H. 2012. Stochastic theory of nonequilibrium steady states. Part II: applications in chemical biophysics. Phys. Rep. 510:87-118
-
(2012)
Phys. Rep.
, vol.510
, pp. 87-118
-
-
Ge, H.1
Qian, M.2
Qian, H.3
-
27
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
Gillespie DT. 2007. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58:35-55
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
28
-
-
0001424903
-
An amplified sensitivity arising from covalent modification in biological systems
-
Goldbeter A, Koshland DE. 1981. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA 78:6840-44
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 6840-6844
-
-
Goldbeter, A.1
Koshland, D.E.2
-
29
-
-
33750121794
-
Protein synthesis molecule by molecule
-
Golding I, Cox EC. 2006. Protein synthesis molecule by molecule. Genome Biol. 7:212-13
-
(2006)
Genome Biol.
, vol.7
, pp. 212-213
-
-
Golding, I.1
Cox, E.C.2
-
30
-
-
77949916347
-
Two-component signaling circuit structure and properties
-
Goulian M. 2010. Two-component signaling circuit structure and properties. Curr. Opin. Microbiol. 13:184-89
-
(2010)
Curr. Opin. Microbiol.
, vol.13
, pp. 184-189
-
-
Goulian, M.1
-
31
-
-
26844571282
-
Multisite protein phosphorylation makes a good threshold but can be a poor switch
-
Gunawardena J. 2005. Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proc. Natl. Acad. Sci. USA 102:14617-22
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 14617-14622
-
-
Gunawardena, J.1
-
35
-
-
0015698515
-
Relation between structure, cooperativity and spectra in a model of hemoglobin action
-
Hopfield JJ. 1973. Relation between structure, cooperativity and spectra in a model of hemoglobin action. J. Mol. Biol. 77:207-22
-
(1973)
J. Mol. Biol.
, vol.77
, pp. 207-222
-
-
Hopfield, J.J.1
-
36
-
-
0000359208
-
Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity
-
Hopfield JJ. 1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA 71:4135-39
-
(1974)
Proc. Natl. Acad. Sci. USA
, vol.71
, pp. 4135-4139
-
-
Hopfield, J.J.1
-
37
-
-
0019134996
-
The energy relay: A proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis
-
Hopfield JJ. 1980. The energy relay: a proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis. Proc. Natl. Acad. Sci. USA 77:5248-52
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 5248-5252
-
-
Hopfield, J.J.1
-
38
-
-
28844496741
-
Self-regulating gene: An exact solution
-
Hornos JEM, Schultz D, Innocentini GC, Wang J, Walczak AM, et al. 2005. Self-regulating gene: an exact solution. Phys. Rev. E. 72:051907
-
(2005)
Phys. Rev. E.
, vol.72
, pp. 051907
-
-
Hornos, J.E.M.1
Schultz, D.2
Innocentini, G.C.3
Wang, J.4
Walczak, A.M.5
-
39
-
-
0000481233
-
Noise-induced transitions: Theory, applications in physics, chemistry, and biology
-
Berlin: Springer-Verlag
-
Horsthemke W, Lefever R. 1984. Noise-Induced Transitions: Theory, Applications in Physics, Chemistry, and Biology. Springer Ser. Synergetics, Vol. 15. Berlin: Springer-Verlag
-
(1984)
Springer Ser. Synergetics
, vol.15
-
-
Horsthemke, W.1
Lefever, R.2
-
40
-
-
84861387553
-
The dynamics of zeroth-order ultrasensitivity: A critical phenomenon in cell biology
-
Huang Q, Qian H. 2011. The dynamics of zeroth-order ultrasensitivity: a critical phenomenon in cell biology. Discr. Cont. Dyn. Sys. S 4:1457-64
-
(2011)
Discr. Cont. Dyn. Sys. S
, vol.4
, pp. 1457-1464
-
-
Huang, Q.1
Qian, H.2
-
44
-
-
0035193294
-
Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
-
Kepler TB, Elston TC. 2001. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81:3116-36
-
(2001)
Biophys. J.
, vol.81
, pp. 3116-3136
-
-
Kepler, T.B.1
Elston, T.C.2
-
45
-
-
77249103975
-
Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses
-
Kierzek AM, Zhou L, Wanner BL. 2010. Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses. Mol. Biosyst. 6:531-42
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 531-542
-
-
Kierzek, A.M.1
Zhou, L.2
Wanner, B.L.3
-
46
-
-
33947304756
-
Substrate competition as a source of ultrasensitivity in the inactivation of Wee1
-
Kim SY, Ferrell JE. 2007. Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128:1133-45
-
(2007)
Cell
, vol.128
, pp. 1133-1145
-
-
Kim, S.Y.1
Ferrell, J.E.2
-
47
-
-
0019996706
-
Amplification and adaptation in regulatory and sensory systems
-
Koshland DE, Goldbeter A, Stock JB. 1982. Amplification and adaptation in regulatory and sensory systems. Science 217:220-25
-
(1982)
Science
, vol.217
, pp. 220-225
-
-
Koshland, D.E.1
Goldbeter, A.2
Stock, J.B.3
-
48
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland DE, Némethy G, Filmer D. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-85
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland, D.E.1
Némethy, G.2
Filmer, D.3
-
49
-
-
0034602686
-
The middle way
-
Laughlin RB, Pines D, Schmalian J, Stojković BP, Wolynes PG. 2000. The middle way. Proc. Natl. Acad. Sci. USA 97:32-37
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 32-37
-
-
Laughlin, R.B.1
Pines, D.2
Schmalian, J.3
Stojković, B.P.4
Wolynes, P.G.5
-
50
-
-
0036729047
-
Can a biologist fix a radio? Or, what i learned while studying apoptosis
-
Lazebnik Y. 2002. Can a biologist fix a radio? Or, what I learned while studying apoptosis. Cancer Cell 2:179-82
-
(2002)
Cancer Cell
, vol.2
, pp. 179-182
-
-
Lazebnik, Y.1
-
51
-
-
34547177356
-
Stochastic fluctuations in metabolic pathways
-
Levine E, Hwa T. 2007. Stochastic fluctuations in metabolic pathways. Proc. Natl. Acad. Sci. USA 104:9224-29
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 9224-9229
-
-
Levine, E.1
Hwa, T.2
-
52
-
-
0009100742
-
The symmetry of time in physics
-
Lewis GN. 1930. The symmetry of time in physics. Science 71:569-77
-
(1930)
Science
, vol.71
, pp. 569-577
-
-
Lewis, G.N.1
-
53
-
-
79960630264
-
Central dogma at the single-molecule level in living cells
-
Li G-W, Xie XS. 2011. Central dogma at the single-molecule level in living cells. Nature 475:308-15
-
(2011)
Nature
, vol.475
, pp. 308-315
-
-
Li, G.-W.1
Xie, X.S.2
-
54
-
-
75749152362
-
Computational cellular dynamics based on the chemical master equation: A challenge for understanding complexity (survey)
-
Liang J, Qian H. 2010. Computational cellular dynamics based on the chemical master equation: a challenge for understanding complexity (survey). J. Comput. Sci. Technol. 25:154-68
-
(2010)
J. Comput. Sci. Technol.
, vol.25
, pp. 154-168
-
-
Liang, J.1
Qian, H.2
-
55
-
-
0038637779
-
Perfect and near-perfect adaptation in a model of bacterial chemotaxis
-
Mello BA, Tu Y. 2003. Perfect and near-perfect adaptation in a model of bacterial chemotaxis. Biophys. J. 84:2943-56
-
(2003)
Biophys. J.
, vol.84
, pp. 2943-2956
-
-
Mello, B.A.1
Tu, Y.2
-
56
-
-
19344362210
-
The stability of a stochastic CaMKII switch: Dependence on the number of enzyme molecules and protein turnover
-
Miller P, Zhabotinsky AM, Lisman JE, Wang X-J. 2005. The stability of a stochastic CaMKII switch: dependence on the number of enzyme molecules and protein turnover. PLoS Biol. 3:e107
-
(2005)
PLoS Biol.
, vol.3
-
-
Miller, P.1
Zhabotinsky, A.M.2
Lisman, J.E.3
Wang, X.-J.4
-
57
-
-
33751265357
-
When does the Michaelis-Menten equation hold for fluctuating enzymes?
-
Min W, Gopich IV, English BP, Kou SC, Xie XS, Szabo A. 2006. When does the Michaelis-Menten equation hold for fluctuating enzymes? J. Phys. Chem. B 110:20093-97
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 20093-20097
-
-
Min, W.1
Gopich, I.V.2
English, B.P.3
Kou, S.C.4
Xie, X.S.5
Szabo, A.6
-
58
-
-
77951770226
-
Complex kinetics of fluctuating enzymes: Phase diagram characterization of a minimal kinetic scheme
-
Min W, Jiang L, Xie XS. 2010. Complex kinetics of fluctuating enzymes: phase diagram characterization of a minimal kinetic scheme. Chem. Asian J. 5:1129-38
-
(2010)
Chem. Asian J.
, vol.5
, pp. 1129-1138
-
-
Min, W.1
Jiang, L.2
Xie, X.S.3
-
59
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
Monod J, Wyman J, Changeux J-P. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.-P.3
-
61
-
-
0016793283
-
Kinetic amplification of enzyme discrimination
-
Ninio J. 1975. Kinetic amplification of enzyme discrimination. Biochimie 57:587-95
-
(1975)
Biochimie
, vol.57
, pp. 587-595
-
-
Ninio, J.1
-
63
-
-
20344389483
-
Models of stochastic gene expression
-
Paulsson J. 2005. Models of stochastic gene expression. Phys. Life Rev. 2:157-75
-
(2005)
Phys. Life Rev.
, vol.2
, pp. 157-175
-
-
Paulsson, J.1
-
64
-
-
0034691214
-
Stochastic focusing: Fluctuation-enhanced sensitivity of in-tracellular regulation
-
Paulsson J, Berg OG, Ehrenberg M. 2000. Stochastic focusing: fluctuation-enhanced sensitivity of in-tracellular regulation. Proc. Natl. Acad. Sci. USA 97:7148-53
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 7148-7153
-
-
Paulsson, J.1
Berg, O.G.2
Ehrenberg, M.3
-
65
-
-
0034608143
-
Random signal fluctuation can reduce random fluctuations in regulated components of chemical regulatory networks
-
Paulsson J, Ehrenberg M. 2000. Random signal fluctuation can reduce random fluctuations in regulated components of chemical regulatory networks. Phys. Rev. Lett. 84:5447-50
-
(2000)
Phys. Rev. Lett.
, vol.84
, pp. 5447-5450
-
-
Paulsson, J.1
Ehrenberg, M.2
-
66
-
-
0037187085
-
Equations for stochastic macromolecular mechanics of single proteins: Equilibrium fluctuations, transient kinetics and nonequilibrium steady-state
-
Qian H. 2002. Equations for stochastic macromolecular mechanics of single proteins: equilibrium fluctuations, transient kinetics and nonequilibrium steady-state. J. Phys. Chem. B 106:2065-73
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 2065-2073
-
-
Qian, H.1
-
67
-
-
0141560467
-
Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction
-
Qian H. 2003. Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction. Biophys. Chem. 105:585-93
-
(2003)
Biophys. Chem.
, vol.105
, pp. 585-593
-
-
Qian, H.1
-
68
-
-
33748094844
-
Reducing intrinsic biochemical noise in cells and its thermodynamic limit
-
Qian H. 2006. Reducing intrinsic biochemical noise in cells and its thermodynamic limit. J. Mol. Biol. 362:387-92
-
(2006)
J. Mol. Biol.
, vol.362
, pp. 387-392
-
-
Qian, H.1
-
69
-
-
33748107406
-
Phosphorylation energy hypothesis: Open chemical systems and their biological functions
-
Qian H. 2007. Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem. 58:113-42
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 113-142
-
-
Qian, H.1
-
70
-
-
46749083416
-
Cooperativity and specificity in enzyme kinetics: A single-molecule time-based perspective
-
Qian H. 2008. Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective. Biophys. J. 95:10-17
-
(2008)
Biophys. J.
, vol.95
, pp. 10-17
-
-
Qian, H.1
-
71
-
-
78649795390
-
Cellular biology in terms of stochastic nonlinear biochemical dynamics: Emergent properties, isogenetic variations and chemical system inheritability
-
Qian H. 2010. Cellular biology in terms of stochastic nonlinear biochemical dynamics: emergent properties, isogenetic variations and chemical system inheritability. J. Stat. Phys. 141:990-1013
-
(2010)
J. Stat. Phys.
, vol.141
, pp. 990-1013
-
-
Qian, H.1
-
72
-
-
78650154269
-
Cyclic conformational modification of an enzyme: Serial engagement, energy relay, hysteretic enzyme, and Fischer's hypothesis
-
Qian H. 2010. Cyclic conformational modification of an enzyme: serial engagement, energy relay, hysteretic enzyme, and Fischer's hypothesis. J. Phys. Chem. B 114:16105-11
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 16105-16111
-
-
Qian, H.1
-
73
-
-
79957877141
-
Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reactions systems-an analytical theory
-
Qian H. 2011. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reactions systems-an analytical theory. Nonlinearity 24:R19-49
-
(2011)
Nonlinearity
, vol.24
-
-
Qian, H.1
-
74
-
-
17244378347
-
Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
-
Qian H, Beard DA. 2005. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys. Chem. 114:213-20
-
(2005)
Biophys. Chem.
, vol.114
, pp. 213-220
-
-
Qian, H.1
Beard, D.A.2
-
75
-
-
77958514250
-
The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: Linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks
-
Qian H, Bishop LM. 2010. The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks. Int. J. Mol. Sci. 11:3472-500
-
(2010)
Int. J. Mol. Sci.
, vol.11
, pp. 3472-3500
-
-
Qian, H.1
Bishop, L.M.2
-
76
-
-
39749178412
-
Temporal cooperativity and sensitivity amplification in biological signal transduction
-
Qian H, Cooper JA. 2008. Temporal cooperativity and sensitivity amplification in biological signal transduction. Biochemistry 47:2211-20
-
(2008)
Biochemistry
, vol.47
, pp. 2211-2220
-
-
Qian, H.1
Cooper, J.A.2
-
77
-
-
1542327697
-
Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady states
-
Qian H, Elson EL. 2004. Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady states. Proc. Natl. Acad. Sci. USA 101:2828-33
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2828-2833
-
-
Qian, H.1
Elson, E.L.2
-
78
-
-
18144407314
-
Nonequilibrium thermodynamics and nonlinear kineticsin a cellular signaling switch
-
Qian H, Reluga TC. 2005. Nonequilibrium thermodynamics and nonlinear kineticsin a cellular signaling switch. Phys. Rev. Lett. 94:028101
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 028101
-
-
Qian, H.1
Reluga, T.C.2
-
79
-
-
0036679175
-
Concentration fluctuations in a mesoscopic oscillating chemical reaction system
-
Qian H, Saffarian S, Elson EL. 2002. Concentration fluctuations in a mesoscopic oscillating chemical reaction system. Proc. Natl. Acad. Sci. USA 99:10376-81
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 10376-10381
-
-
Qian, H.1
Saffarian, S.2
Elson, E.L.3
-
80
-
-
65249133487
-
Fluctuating enzyme and its biological functions: Positive cooperativity without multiple states
-
Qian H, Shi P-Z. 2009. Fluctuating enzyme and its biological functions: positive cooperativity without multiple states. J. Phys. Chem. B 113:2225-30
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2225-2230
-
-
Qian, H.1
Shi, P.-Z.2
-
81
-
-
68849093960
-
Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity
-
Qian H, Shi P-Z, Xing J. 2009. Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity. Phys. Chem. Chem. Phys. 11:4861-70
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 4861-4870
-
-
Qian, H.1
Shi, P.-Z.2
Xing, J.3
-
82
-
-
0023655481
-
Cooperative and allosteric enzymes: 20 years on
-
Ricard J, Cornish-Bowden A. 1987. Cooperative and allosteric enzymes: 20 years on. Eur. J. Biochem. 166:255-72
-
(1987)
Eur. J. Biochem.
, vol.166
, pp. 255-272
-
-
Ricard, J.1
Cornish-Bowden, A.2
-
83
-
-
0035778150
-
Fluorescence correlation spectroscopy: Theory and applications
-
New York: Springer
-
Rigler R, Elson EL, eds. 2001. Fluorescence Correlation Spectroscopy: Theory and Applications. Springer Ser. Chem. Phys., Vol. 65. New York: Springer
-
(2001)
Springer Ser. Chem. Phys.
, vol.65
-
-
Rigler, R.1
Elson, E.L.2
-
84
-
-
14044265753
-
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations
-
Samoilov M, Plyasunov S, Arkin AP. 2005. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc. Natl. Acad. Sci. USA 102:2310-15
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 2310-2315
-
-
Samoilov, M.1
Plyasunov, S.2
Arkin, A.P.3
-
85
-
-
33947476272
-
The factors affecting the stability of hydrogen-bonded polypeptide structures in solution
-
Schellman JA. 1958. The factors affecting the stability of hydrogen-bonded polypeptide structures in solution. J. Phys. Chem. 62:1485-94
-
(1958)
J. Phys. Chem.
, vol.62
, pp. 1485-1494
-
-
Schellman, J.A.1
-
87
-
-
49549120841
-
The stochastic nature of biochemical networks
-
Shahrezaei V, Swain PS. 2008. The stochastic nature of biochemical networks. Curr. Opin. Biotechnol. 19:369-74
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 369-374
-
-
Shahrezaei, V.1
Swain, P.S.2
-
88
-
-
0022429106
-
The or control system of bacteriophage lambda. A physical-chemical model for gene regulation
-
Shea MA, Ackers GK. 1985. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J. Mol. Biol. 181:211-30
-
(1985)
J. Mol. Biol.
, vol.181
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
89
-
-
79951795015
-
A perturbation analysis of rate theory of self-regulating genes and signaling networks
-
Shi P-Z, Qian H. 2011. A perturbation analysis of rate theory of self-regulating genes and signaling networks. J. Chem. Phys. 134:065104
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 065104
-
-
Shi, P.-Z.1
Qian, H.2
-
91
-
-
31144467483
-
The quantal theory of immunity
-
Smith KA. 2006. The quantal theory of immunity. Cell Res. 16:11-19
-
(2006)
Cell Res.
, vol.16
, pp. 11-19
-
-
Smith, K.A.1
-
94
-
-
57349131603
-
A genetic timer through noise-induced stabilization of an unstable state
-
Turcotte M, Garcia-Ojalvo J, Süel GM. 2008. A genetic timer through noise-induced stabilization of an unstable state. Proc. Natl. Acad. Sci. USA 105:15732-37
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 15732-15737
-
-
Turcotte, M.1
Garcia-Ojalvo, J.2
Süel, G.M.3
-
95
-
-
34250698472
-
A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox
-
Vellela M, Qian H. 2007. A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox. Bull. Math. Biol. 69:1727-46
-
(2007)
Bull. Math. Biol.
, vol.69
, pp. 1727-1746
-
-
Vellela, M.1
Qian, H.2
-
96
-
-
77749308573
-
On Poincaré-Hill cycle map of rotational random walk: Locating stochastic limit cycle in reversible Schnakenberg model
-
Vellela M, Qian H. 2010. On Poincaré-Hill cycle map of rotational random walk: locating stochastic limit cycle in reversible Schnakenberg model. Proc. R. Sci. A. 466:771-88
-
(2010)
Proc. R. Sci. A.
, vol.466
, pp. 771-788
-
-
Vellela, M.1
Qian, H.2
-
98
-
-
34347235771
-
From "simple" DNA-protein interactions to the macromolecular machines of gene expression
-
von Hippel PH. 2007. From "simple" DNA-protein interactions to the macromolecular machines of gene expression. Annu. Rev. Biophys. Biomol. Struct. 36:79-105
-
(2007)
Annu. Rev. Biophys. Biomol. Struct.
, vol.36
, pp. 79-105
-
-
Von Hippel, P.H.1
-
100
-
-
77952334362
-
Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network
-
Wang J, Li C, Wang E. 2010. Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network. Proc. Natl. Acad. Sci. USA 107:8195-200
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 8195-8200
-
-
Wang, J.1
Li, C.2
Wang, E.3
-
101
-
-
50449104011
-
Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations
-
Wang J, Xu L, Wang E. 2008. Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations. Proc. Natl. Acad. Sci. USA 105:12271-76
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 12271-12276
-
-
Wang, J.1
Xu, L.2
Wang, E.3
-
102
-
-
77957307520
-
Non-essential sites improve phosphorylation switch
-
Wang L, Nie Q, Enciso G. 2010. Non-essential sites improve phosphorylation switch. Biophys. J. 99:L41-43
-
(2010)
Biophys. J.
, vol.99
-
-
Wang, L.1
Nie, Q.2
Enciso, G.3
-
103
-
-
5044227742
-
The evolution of molecular biology into systems biology
-
Westerhoff HV, Palsson BO. 2004. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22:1249-52
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1249-1252
-
-
Westerhoff, H.V.1
Palsson, B.O.2
-
104
-
-
48249095613
-
Single-molecule approach to molecular biology in living bacterial cells
-
Xie XS, Choi PJ, Li G-W, Lee NK, Lia G. 2008. Single-molecule approach to molecular biology in living bacterial cells. Annu. Rev. Biophys. 37:417-44
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 417-444
-
-
Xie, X.S.1
Choi, P.J.2
Li, G.-W.3
Lee, N.K.4
Lia, G.5
-
105
-
-
0033523011
-
Single-molecule enzymology
-
Xie XS, Lu HP. 1999. Single-molecule enzymology. J. Biol. Chem. 274:15967-70
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 15967-15970
-
-
Xie, X.S.1
Lu, H.P.2
-
106
-
-
0345359924
-
A positive-feedback-based bistable 'memory module' that governs a cell fate decision
-
Xiong W, Ferrell JE. 2003. A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 426:460-65
-
(2003)
Nature
, vol.426
, pp. 460-465
-
-
Xiong, W.1
Ferrell, J.E.2
-
107
-
-
33645033645
-
Probing gene expression in live E. coli cells: One molecule at a time
-
Yu J, Xiao J, Ren X, Lao K, Xie XS. 2006. Probing gene expression in live E. coli cells: one molecule at a time. Science 311:1600-3
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
108
-
-
82455192486
-
Stochastic theory of nonequilibrium steady states and its applications. Part i
-
Zhang X-J, Qian H, Qian M. 2012. Stochastic theory of nonequilibrium steady states and its applications. Part I. Phys. Rep. 510:1-86
-
(2012)
Phys. Rep.
, vol.510
, pp. 1-86
-
-
Zhang, X.-J.1
Qian, H.2
Qian, M.3
-
109
-
-
79960629007
-
Role of fluctuations in ligand binding cooperativity of membrane receptors
-
Zhu L, Frenkel D, Bolhuis PG. 2011. Role of fluctuations in ligand binding cooperativity of membrane receptors. Phys. Rev. Lett. 106:168103
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 168103
-
-
Zhu, L.1
Frenkel, D.2
Bolhuis, P.G.3
-
110
-
-
0000668407
-
Theory of the phase transition between helix and random coil in polypeptide chains
-
Zimm BH, Bragg JK. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31:526-31
-
(1959)
J. Chem. Phys.
, vol.31
, pp. 526-531
-
-
Zimm, B.H.1
Bragg, J.K.2
|