-
1
-
-
16344387146
-
Stochastic simulations of the origins and implications of long-tailed distributions in gene expression
-
Krishna S, Banerjee B, Ramakrishnan TV, Shivashankar GV: Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. Proc Natl Acad Sci U S A 2005, 102:4771-4776.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 4771-4776
-
-
Krishna, S.1
Banerjee, B.2
Ramakrishnan, T.V.3
Shivashankar, G.V.4
-
2
-
-
15544388848
-
Noise propagation in gene networks
-
Pedraza JM, van Oudenaarden A: Noise propagation in gene networks. Science 2005, 307:1965-1969.
-
(2005)
Science
, vol.307
, pp. 1965-1969
-
-
Pedraza, J.M.1
van Oudenaarden, A.2
-
3
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lamda infected Escherichia coli cells
-
Arkin AP, McAdams HH: Stochastic kinetic analysis of developmental pathway bifurcation in phage lamda infected Escherichia coli cells. Genetics 1998, 149:1633-1648.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.P.1
McAdams, H.H.2
-
4
-
-
15744378289
-
Numerical simulation of stochastic gene circuits
-
Salis H, Kaznessis Y: Numerical simulation of stochastic gene circuits. Comput Chem Eng 2005, 29:577-588.
-
(2005)
Comput Chem Eng
, vol.29
, pp. 577-588
-
-
Salis, H.1
Kaznessis, Y.2
-
5
-
-
0142106505
-
Analysis of Noise in Quorum Sensing
-
Cox CD, Peterson GD, Allen MS, Lancaster JM, McCollum JM, Austin D, Yan L, Sayler GS, Simpsons ML: Analysis of Noise in Quorum Sensing. OMICS 2003, 7:317-334.
-
(2003)
OMICS
, vol.7
, pp. 317-334
-
-
Cox, C.D.1
Peterson, G.D.2
Allen, M.S.3
Lancaster, J.M.4
McCollum, J.M.5
Austin, D.6
Yan, L.7
Sayler, G.S.8
Simpsons, M.L.9
-
6
-
-
27844563625
-
Model-Driven Designs of an Oscillating Gene Network
-
Tuttle L, Salis H, Tomshine J, Kaznessis YN: Model-Driven Designs of an Oscillating Gene Network. Biophys J 2005, 89:3873-3883.
-
(2005)
Biophys J
, vol.89
, pp. 3873-3883
-
-
Tuttle, L.1
Salis, H.2
Tomshine, J.3
Kaznessis, Y.N.4
-
7
-
-
14044265753
-
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations
-
Samoilov M, Plyasunov S, Arkin AP: Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A 2005, 102:2310-2315.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2310-2315
-
-
Samoilov, M.1
Plyasunov, S.2
Arkin, A.P.3
-
8
-
-
18744361871
-
Enhancement of cellular memory by reducing stochastic transitions
-
Acar M, Becskei A, van Oudenaarden A: Enhancement of cellular memory by reducing stochastic transitions. Nature 2005, 435:228-232.
-
(2005)
Nature
, vol.435
, pp. 228-232
-
-
Acar, M.1
Becskei, A.2
van Oudenaarden, A.3
-
9
-
-
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: Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 2005, 122:169-182.
-
(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
-
10
-
-
27944488416
-
Internal noise stochastic resonance for intracellular calcium oscillations in a cell system
-
Li H, Hou Z, Xin H: Internal noise stochastic resonance for intracellular calcium oscillations in a cell system. Phys Rev E 2005, 71:061916.
-
(2005)
Phys Rev E
, vol.71
, pp. 061916
-
-
Li, H.1
Hou, Z.2
Xin, H.3
-
11
-
-
22144498043
-
Sensitivity analysis of discrete stochastic systems
-
Gunawan F, Cao Y, Petzold L, Doyle FJ 3rd: Sensitivity analysis of discrete stochastic systems. Biophys J 2005, 88:2530-2540.
-
(2005)
Biophys J
, vol.88
, pp. 2530-2540
-
-
Gunawan, F.1
Cao, Y.2
Petzold, L.3
Doyle III, F.J.4
-
12
-
-
0017030517
-
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
-
Gillespie DT: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J Comput Phys 1976, 22:403-434.
-
(1976)
J Comput Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
13
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson MA, Bruck J: Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 2000, 104:1876-1889.
-
(2000)
J Phys Chem A
, vol.104
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
14
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
Cao Y, Li H, Petzold L: Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys 2004, 121:4059-4067.
-
(2004)
J Chem Phys
, vol.121
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
-
15
-
-
0030211187
-
Stochastic simulation of Coupled Reaction-Diffusion Processes
-
Stundzia AB, Lumsden CJ: Stochastic simulation of Coupled Reaction-Diffusion Processes. J Comput Phys 1996, 127:196-207.
-
(1996)
J Comput Phys
, vol.127
, pp. 196-207
-
-
Stundzia, A.B.1
Lumsden, C.J.2
-
16
-
-
84886765565
-
NetCDF Portable Scientific Data Format
-
NetCDF Portable Scientific Data Format [http://my.uni data.ucar.edu/ content/software/netcdf/index.html]
-
-
-
-
17
-
-
32644484370
-
A review of multiscale analysis: Examples from systems biology, materials engineering, and other fluid-surface interacting systems
-
Vlachos DG: A review of multiscale analysis: Examples from systems biology, materials engineering, and other fluid-surface interacting systems. Adv Chem Eng 2005, 30:1-61.
-
(2005)
Adv Chem Eng
, vol.30
, pp. 1-61
-
-
Vlachos, D.G.1
-
18
-
-
27844576653
-
Multi-scale Models for Gene Network Engineering
-
Kaznessis Y: Multi-scale Models for Gene Network Engineering. Chem Eng Sci 2006, 61:940-953.
-
(2006)
Chem Eng Sci
, vol.61
, pp. 940-953
-
-
Kaznessis, Y.1
-
19
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Haseltine EL, Rawlings JB: Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 2002, 117:6959-6969.
-
(2002)
J Chem Phys
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
20
-
-
0347724159
-
Adaptive stochastic-deterministic chemical kinetic simulations
-
Vasudeva K, Bhalla US: Adaptive stochastic-deterministic chemical kinetic simulations. Bioinformatics 2004, 20:78-84.
-
(2004)
Bioinformatics
, vol.20
, pp. 78-84
-
-
Vasudeva, K.1
Bhalla, U.S.2
-
21
-
-
1542345686
-
Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of biochemical reaction networks
-
Puchalka J, Kierzek AM: Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of biochemical reaction networks. Biophys J 2004, 86:1357-1372.
-
(2004)
Biophys J
, vol.86
, pp. 1357-1372
-
-
Puchalka, J.1
Kierzek, A.M.2
-
22
-
-
17644396339
-
Dizzy: Stochastic simulation of large-scale genetic regulatory networks
-
Ramsey S, Orrell D, Bolouri H: Dizzy: stochastic simulation of large-scale genetic regulatory networks. J Bioinform Comput Biol 2005, 3:415-436.
-
(2005)
J Bioinform Comput Biol
, vol.3
, pp. 415-436
-
-
Ramsey, S.1
Orrell, D.2
Bolouri, H.3
-
23
-
-
2942514591
-
Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks
-
Adalsteinsson D, McMillen D, Elston TC: Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 2004, 5:24.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 24
-
-
Adalsteinsson, D.1
McMillen, D.2
Elston, T.C.3
-
24
-
-
14844328879
-
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: Analysis of simple networks
-
Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomas-Oliveira I, Serrano L: SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. IEE Systems Biology 2004, 1:129-38.
-
(2004)
IEE Systems Biology
, vol.1
, pp. 129-138
-
-
Ander, M.1
Beltrao, P.2
Di Ventura, B.3
Ferkinghoff-Borg, J.4
Foglierini, M.5
Kaplan, A.6
Lemerle, C.7
Tomas-Oliveira, I.8
Serrano, L.9
-
25
-
-
84886757415
-
COPASI: Complex Pathway Simulator
-
Mendes P, Kummer U: COPASI: Complex Pathway Simulator. http://www.copasi.org
-
-
-
Mendes, P.1
Kummer, U.2
-
26
-
-
22944451159
-
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
-
Salis H, Kaznessis Y: Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J Chem Phys 2005, 122:054103.
-
(2005)
J Chem Phys
, vol.122
, pp. 054103
-
-
Salis, H.1
Kaznessis, Y.2
-
27
-
-
0034225547
-
The chemical Langevin equation
-
Gillespie DT: The chemical Langevin equation. J Chem Phys 2000, 113:297-306.
-
(2000)
J Chem Phys
, vol.113
, pp. 297-306
-
-
Gillespie, D.T.1
-
29
-
-
0031258411
-
Variable step size control in the numerical solution to stochastic differential equations
-
Gaines JG, Lyons TJ: Variable step size control in the numerical solution to stochastic differential equations. SIAM J Appl Math 1997, 57:1455-1484.
-
(1997)
SIAM J Appl Math
, vol.57
, pp. 1455-1484
-
-
Gaines, J.G.1
Lyons, T.J.2
-
30
-
-
0242708960
-
An adaptive timestepping algorithm for stochastic differential equations
-
Lamba H: An adaptive timestepping algorithm for stochastic differential equations. J Comput Appl Math 2003, 161:417-430.
-
(2003)
J Comput Appl Math
, vol.161
, pp. 417-430
-
-
Lamba, H.1
-
31
-
-
0035903016
-
Advanced computing. NSF launches teragrid for academic research
-
Mervis J: Advanced computing. NSF launches teragrid for academic research. Science 2001, 293:1235-1237.
-
(2001)
Science
, vol.293
, pp. 1235-1237
-
-
Mervis, J.1
-
32
-
-
0742293840
-
MPICH-G2: A Grid-Enabled Implementation of the Message Passing Interface
-
Karonis N, Toonen B, Foster I: MPICH-G2: A Grid-Enabled Implementation of the Message Passing Interface. J Parallel Distrib Comput 2003, 63:551-563.
-
(2003)
J Parallel Distrib Comput
, vol.63
, pp. 551-563
-
-
Karonis, N.1
Toonen, B.2
Foster, I.3
-
33
-
-
84886763625
-
MexCDF, SNC Tools, and the NetCDF Toolbox
-
Evans John: MexCDF, SNC Tools, and the NetCDF Toolbox. [http://mexcdf.sourceforge.net].
-
-
-
Evans, J.1
-
34
-
-
0036846553
-
Alternative designs for a genetic switch: Analysis of switching times using the piecewise power-law representation
-
Savageau MA: Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. Math Biosci 2002, 180:237-253.
-
(2002)
Math Biosci
, vol.180
, pp. 237-253
-
-
Savageau, M.A.1
-
35
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Rao CV, Arkin AP: Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J Chem Phys 2003, 118:4999-5010.
-
(2003)
J Chem Phys
, vol.118
, pp. 4999-5010
-
-
Rao, C.V.1
Arkin, A.P.2
-
36
-
-
33645463036
-
An equation-free probabilistic steady state approximation: Dynamic application to stochastic simulation of biochemical networks
-
Salis H, Kaznessis Y: An equation-free probabilistic steady state approximation: Dynamic application to stochastic simulation of biochemical networks. J Chem Phys 2005, 123:214106.
-
(2005)
J Chem Phys
, vol.123
, pp. 214106
-
-
Salis, H.1
Kaznessis, Y.2
-
37
-
-
26944450876
-
Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm
-
Samant A, Vlachos DG: Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm. J Chem Phys 2005, 123:144114.
-
(2005)
J Chem Phys
, vol.123
, pp. 144114
-
-
Samant, A.1
Vlachos, D.G.2
-
38
-
-
27744516835
-
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
-
Weinan E, Liu D, Vanden-Eijnden E: Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J Chem Phys 2005, 123:194107.
-
(2005)
J Chem Phys
, vol.123
, pp. 194107
-
-
Weinan, E.1
Liu, D.2
Vanden-Eijnden, E.3
|