-
2
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected E. coli cells
-
Arkin AP, Ross J, McAdams HH. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected E. coli cells. Genetics 149:163 3-48
-
(1998)
Genetics
, vol.149
, Issue.163
, pp. 3-48
-
-
Arkin, A.P.1
Ross, J.2
McAdams, H.H.3
-
5
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
Raser JM, O'Shea EK. 2004. Control of stochasticity in eukaryotic gene expression. Science 304:1811-14
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
6
-
-
22744441386
-
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
-
Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. 2005. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122:169-82
-
(2005)
Cell
, vol.122
, pp. 169-182
-
-
Weinberger, L.S.1
Burnett, J.C.2
Toettcher, J.E.3
Arkin, A.P.4
Schaffer, D.V.5
-
7
-
-
14044265753
-
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced testability with oscillations
-
Samoilov M, Plyasunov S, Arkin AP. 2005. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced testability 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
-
8
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie DT. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22:403-34
-
(1976)
J. Comput. Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
9
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-61
-
(1977)
J. Phys. Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
10
-
-
44049109914
-
A rigorous derivation of the chemical master equation
-
Gillespie DT. 1992. A rigorous derivation of the chemical master equation. Pbysica A 188:404-25
-
(1992)
Pbysica A
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
12
-
-
0001601301
-
Stochastic approach to chemical kinetics
-
McQuarrie D. 1967. Stochastic approach to chemical kinetics. J. Appl. Probab. 4:413-78
-
(1967)
J. Appl. Probab
, vol.4
, pp. 413-478
-
-
McQuarrie, D.1
-
14
-
-
0007463735
-
Stochastic analysis of an oscillating chemical reaction
-
Nakanishi T. 1972. Stochastic analysis of an oscillating chemical reaction. J. Phys. Soc. Japan 32:1313-22
-
(1972)
J. Phys. Soc. Japan
, vol.32
, pp. 1313-1322
-
-
Nakanishi, T.1
-
15
-
-
34249942982
-
Simulation of first-order chemical reaction as a stochastic process on a digital computer
-
Sole M, Horsak I. 1972. Simulation of first-order chemical reaction as a stochastic process on a digital computer. Collect. Czech. Chem. Commun. 37:2994-3000
-
(1972)
Collect. Czech. Chem. Commun
, vol.37
, pp. 2994-3000
-
-
Sole, M.1
Horsak, I.2
-
16
-
-
34249932367
-
Simulation study of a stochastic model of reversible first-order reaction equilibrium
-
Horsak I, Sole M. 1973. Simulation study of a stochastic model of reversible first-order reaction equilibrium. Collect. Czech. Chem. Commun. 38:2200-3
-
(1973)
Collect. Czech. Chem. Commun
, vol.38
, pp. 2200-2203
-
-
Horsak, I.1
Sole, M.2
-
18
-
-
34249941142
-
Simulation study of a stochastic models of higher order reactions
-
Horsak I, Sole M. 1975. Simulation study of a stochastic models of higher order reactions. Collect. Czech. Chem. Commun. 40:321-25
-
(1975)
Collect. Czech. Chem. Commun
, vol.40
, pp. 321-325
-
-
Horsak, I.1
Sole, M.2
-
19
-
-
0042651432
-
Time dependent fluctuation in a nonlinear chemical system
-
Nakanishi T. 1976. Time dependent fluctuation in a nonlinear chemical system. J. Phys. Soc. Japan 40:1232-39
-
(1976)
J. Phys. Soc. Japan
, vol.40
, pp. 1232-1239
-
-
Nakanishi, T.1
-
20
-
-
0001144902
-
Exact stochastic simulation of chemical systems with many species and many channels
-
Gibson MA, Bruck J. 2000. Exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. 105:1876-89
-
(2000)
J. Phys. Chem
, vol.105
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
21
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
Cao Y, Li H, Petzold LR. 2004. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J. Chem. Phys. 121:4059-67
-
(2004)
J. Chem. Phys
, vol.121
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.R.3
-
22
-
-
14844289958
-
Automatic generation of cellular reaction networks with Moleculizer 1.0
-
Lok L, Brent R. 2005. Automatic generation of cellular reaction networks with Moleculizer 1.0. Nat. Biotech. 23:131-36
-
(2005)
Nat. Biotech
, vol.23
, pp. 131-136
-
-
Lok, L.1
Brent, R.2
-
23
-
-
31344458755
-
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
-
McCollum JM, Peterson GD, Cox CD, Simpson ML, Samatova NF. 2006. The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Comput. Bio. Chem. 30:39-49
-
(2006)
Comput. Bio. Chem
, vol.30
, pp. 39-49
-
-
McCollum, J.M.1
Peterson, G.D.2
Cox, C.D.3
Simpson, M.L.4
Samatova, N.F.5
-
24
-
-
34249941257
-
-
Deleted in proof
-
Deleted in proof
-
-
-
-
25
-
-
0034225547
-
The chemical Langevin equation
-
Gillespie DT. 2000. The chemical Langevin equation. J. Chem. Phys. 113:297-306
-
(2000)
J. Chem. Phys
, vol.113
, pp. 297-306
-
-
Gillespie, D.T.1
-
26
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
33
-
Gillespie DT. 2001. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115:1716-33
-
(1716)
J. Chem. Phys
, vol.115
-
-
Gillespie, D.T.1
-
27
-
-
0030516386
-
The multivariate Langevin and Fokker-Planck equations
-
Gillespie DT. 1996. The multivariate Langevin and Fokker-Planck equations. Am. J. Phys. 64:1246-57
-
(1996)
Am. J. Phys
, vol.64
, pp. 1246-1257
-
-
Gillespie, D.T.1
-
28
-
-
0037162152
-
The chemical Langevin and Fokker-Planck equations for the reversible isomerization reaction
-
Gillespie DT. 2002. The chemical Langevin and Fokker-Planck equations for the reversible isomerization reaction. J. Phys. Chem. A 106:5063-71
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 5063-5071
-
-
Gillespie, D.T.1
-
29
-
-
31544478933
-
Stochastic chemical kinetics
-
ed. S Yip, pp, Dordrecht: Springer
-
Gillespie DT. 2005. Stochastic chemical kinetics. In Handbook of Materials Modeling, ed. S Yip, pp. 1735-52. Dordrecht: Springer
-
(2005)
Handbook of Materials Modeling
, pp. 1735-1752
-
-
Gillespie, D.T.1
-
31
-
-
0242425970
-
Improved leap-size selection for accelerated stochastic simulation
-
Gillespie DT, Petzold LR. 2003. Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 119:8229-34
-
(2003)
J. Chem. Phys
, vol.119
, pp. 8229-8234
-
-
Gillespie, D.T.1
Petzold, L.R.2
-
32
-
-
31544465969
-
Efficient stepsize selection for the tau-leaping simulation method
-
Cao Y, Gillespie DT, Petzold LR. 2006. Efficient stepsize selection for the tau-leaping simulation method. J. Chem. Phys. 124:044109
-
(2006)
J. Chem. Phys
, vol.124
, pp. 044109
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
33
-
-
3142543968
-
Binomial leap methods for simulating stochastic chemical kinetics
-
3
-
3. Tian T, Burrage K. 2004. Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121:10356-64
-
(2004)
J. Chem. Phys
, vol.121
, pp. 10356-10364
-
-
Tian, T.1
Burrage, K.2
-
34
-
-
22944469465
-
Binomial distribution based τ-leap accelerated stochastic simulation
-
Chatterjee A, Vlachos D, Katsoulakis M. 2005. Binomial distribution based τ-leap accelerated stochastic simulation. J. Chem. Phys. 122:024112
-
(2005)
J. Chem. Phys
, vol.122
, pp. 024112
-
-
Chatterjee, A.1
Vlachos, D.2
Katsoulakis, M.3
-
35
-
-
23944491675
-
Avoiding negative populations in explicit Poisson tau-leaping
-
Cao Y, Gillespie DT, Petzold LR. 2005. Avoiding negative populations in explicit Poisson tau-leaping. J. Chem. Phys. 123:054104
-
(2005)
J. Chem. Phys
, vol.123
, pp. 054104
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
37
-
-
0942279178
-
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
-
Rathinam M, Petzold LR, Cao Y, Gillespie DT. 2003. Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J. Chem. Phys. 119:12784-94
-
(2003)
J. Chem. Phys
, vol.119
, pp. 12784-12794
-
-
Rathinam, M.1
Petzold, L.R.2
Cao, Y.3
Gillespie, D.T.4
-
38
-
-
34249936476
-
Trapezoidal tau-leaping formula for the stochastic simulation of chemically reacting systems
-
Cao Y, Petzold LR. 2005. Trapezoidal tau-leaping formula for the stochastic simulation of chemically reacting systems. Proc. Found. Syst. EM. Eng. (FOSBE 2005), pp. 149-52
-
(2005)
Proc. Found. Syst. EM. Eng. (FOSBE 2005)
, pp. 149-152
-
-
Cao, Y.1
Petzold, L.R.2
-
40
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Maschine EL, Rawlings JB. 2002. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 117:6959-69
-
(2002)
J. Chem. Phys
, vol.117
, pp. 6959-6969
-
-
Maschine, E.L.1
Rawlings, J.B.2
-
41
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Rao C, Arkin AP. 2003. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J. Chem. Phys. 118:4999-5010
-
(2003)
J. Chem. Phys
, vol.118
, pp. 4999-5010
-
-
Rao, C.1
Arkin, A.P.2
-
42
-
-
22944480262
-
The slow-scale stochastic simulation algorithm
-
Cao Y, Gillespie DT, Petzold LR. 2005. The slow-scale stochastic simulation algorithm. J. Chem. Phys. 122:014116
-
(2005)
J. Chem. Phys
, vol.122
, pp. 014116
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
43
-
-
18144386494
-
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
-
Cao Y, Gillespie DT, Petzold LR. 2005. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems. J. Comput. Phys. 206:395-411
-
(2005)
J. Comput. Phys
, vol.206
, pp. 395-411
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
44
-
-
26944450876
-
Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm
-
Samant A, Vlachos DG. 2005. Overcoming stiffness in stochastic simulation stemming from partial equilibrium: a multiscale Monte Carlo algorithm. J. Chem. Phys. 123:144114
-
(2005)
J. Chem. Phys
, vol.123
, pp. 144114
-
-
Samant, A.1
Vlachos, D.G.2
-
45
-
-
33846185710
-
Accelerated stochastic simulation of the stiff enzyme-substrate reaction
-
Cao Y, Gillespie DT, Petzold LR. 2005. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. J. Chem. Phys. 123:144917
-
(2005)
J. Chem. Phys
, vol.123
, pp. 144917
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
46
-
-
33751349145
-
On the origins of approximations for stochastic chemical kinetics
-
Haseltine EL, Rawlings JB. 2005. On the origins of approximations for stochastic chemical kinetics. J. Chem. Phys. 123:164115
-
(2005)
J. Chem. Phys
, vol.123
, pp. 164115
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
47
-
-
27744516835
-
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
-
Weinan E, Liu D, Vanden-Eijnden E. 2005. Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J. Chem. Phys. 123:194107
-
(2005)
J. Chem. Phys
, vol.123
, pp. 194107
-
-
Weinan, E.1
Liu, D.2
Vanden-Eijnden, E.3
-
48
-
-
33645463036
-
Equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks
-
Salis H, Kaznessis Y. 2005. Equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks. J. Chem. Phys. 123:214106
-
(2005)
J. Chem. Phys
, vol.123
, pp. 214106
-
-
Salis, H.1
Kaznessis, Y.2
|