-
2
-
-
33947230522
-
Functioning and robustness of a bacterial circadian clock
-
1847943 17353932 10.1038/msb4100128
-
Clodong S Dühring U Kronk L Wilde A Axmann I Herzel H Kollmann M Functioning and robustness of a bacterial circadian clock Mol Syst Biol 2007, 3:90 1847943 17353932 10.1038/msb4100128
-
(2007)
Mol Syst Biol
, vol.3
, pp. 90
-
-
Clodong, S.1
Dühring, U.2
Kronk, L.3
Wilde, A.4
Axmann, I.5
Herzel, H.6
Kollmann, M.7
-
3
-
-
34748871477
-
Regulation of gene expression by small non-coding RNAs: A quantitative view
-
2013925 17893699 10.1038/msb4100181
-
Shimoni Y Friedlander G Hetzroni G Niv G Altuvia S Biham O Margalit H Regulation of gene expression by small non-coding RNAs: A quantitative view Mol Syst Biol 2007, 3:138 2013925 17893699 10.1038/msb4100181
-
(2007)
Mol Syst Biol
, vol.3
, pp. 138
-
-
Shimoni, Y.1
Friedlander, G.2
Hetzroni, G.3
Niv, G.4
Altuvia, S.5
Biham, O.6
Margalit, H.7
-
4
-
-
34547646131
-
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos
-
1943426 17667953 10.1038/msb4100171
-
Calzone L Thieffry D Tyson JJ Novak B Dynamical modeling of syncytial mitotic cycles in Drosophila embryos Mol Syst Biol 2007, 3:131 1943426 17667953 10.1038/msb4100171
-
(2007)
Mol Syst Biol
, vol.3
, pp. 131
-
-
Calzone, L.1
Thieffry, D.2
Tyson, J.J.3
Novak, B.4
-
5
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
10.1016/0021-9991(76)90041-3
-
Gillespie DT A general method for numerically simulating the stochastic time evolution of coupled chemical reactions Journal of Computational Physics 1976, 22(4):403-434 10.1016/0021-9991(76)90041-3
-
(1976)
Journal of Computational Physics
, vol.22
, Issue.4
, pp. 403-434
-
-
Gillespie, D.T.1
-
6
-
-
0001144902
-
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
-
10.1021/jp993732q
-
Gibson M Bruck J Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels Journal of Physical Chemistry A 2000, 104(9):1876-1889 10.1021/jp993732q
-
(2000)
Journal of Physical Chemistry A
, vol.104
, Issue.9
, pp. 1876-1889
-
-
Gibson, M.1
Bruck, J.2
-
7
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
10.1063/1.1778376 15332951
-
Cao Y Li H Petzold L Efficient formulation of the stochastic simulation algorithm for chemically reacting systems J Chem Phys 2004, 121(9):4059-4067 10.1063/1.1778376 15332951
-
(2004)
J Chem Phys
, vol.121
, Issue.9
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
-
8
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
10.1063/1.1378322
-
Gillespie DT Approximate accelerated stochastic simulation of chemically reacting systems J Chem Phys 2001, 115:1716-1733 10.1063/1.1378322
-
(2001)
J Chem Phys
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
9
-
-
23944491675
-
Avoiding negative populations in explicit Poisson tau-leaping
-
10.1063/1.1992473 16108628
-
Cao Y Gillespie DT Petzold LR Avoiding negative populations in explicit Poisson tau-leaping J Chem Phys 2005, 123(5):054104 10.1063/1.1992473 16108628
-
(2005)
J Chem Phys
, vol.123
, Issue.5
, pp. 054104
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
10
-
-
31544465969
-
Efficient step size selection for the tau-leaping simulation method
-
10.1063/1.2159468 16460151
-
Cao Y Gillespie DT Petzold LR Efficient step size selection for the tau-leaping simulation method Journal of Chemical Physics 2006, 124;044109 10.1063/1.2159468 16460151
-
(2006)
Journal of Chemical Physics
, vol.124
, pp. 044109
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
11
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
10.1063/1.1505860
-
Haseltine EL Rawlings JB Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics The Journal of Chemical Physics 2002, 117:6959-6969 10.1063/1.1505860
-
(2002)
The Journal of Chemical Physics
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
12
-
-
2442438819
-
A multi-scaled approach for simulating chemical reaction systems
-
10.1016/j.pbiomolbio.2004.01.014 15142745
-
Burrage K Tian T Burrage P A multi-scaled approach for simulating chemical reaction systems Prog Biophys Mol Biol 2004, 85(2-3):217-234 10.1016/j.pbiomolbio.2004.01.014 15142745
-
(2004)
Prog Biophys Mol Biol
, vol.85
, Issue.2-3
, pp. 217-234
-
-
Burrage, K.1
Tian, T.2
Burrage, P.3
-
13
-
-
0347724159
-
Adaptive stochastic-deterministic chemical kinetic simulations
-
10.1093/bioinformatics/btg376 14693812
-
Vasudeva K Bhalla US Adaptive stochastic-deterministic chemical kinetic simulations Bioinformatics 2004, 20:78-84 10.1093/bioinformatics/btg376 14693812
-
(2004)
Bioinformatics
, vol.20
, pp. 78-84
-
-
Vasudeva, K.1
Bhalla, U.S.2
-
14
-
-
1342309249
-
Hybrid simulation of cellular behavior
-
10.1093/bioinformatics/btg409 14960457
-
Kiehl TR Mattheyses RM Simmons MK Hybrid simulation of cellular behavior Bioinformatics 2004, 20(3):316-322 10.1093/bioinformatics/btg409 14960457
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 316-322
-
-
Kiehl, T.R.1
Mattheyses, R.M.2
Simmons, M.K.3
-
15
-
-
22944451159
-
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
-
10.1063/1.1835951 15740306
-
Salis H Kaznessis Y Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions J Chem Phys 2005, 122(5):54103 10.1063/1.1835951 15740306
-
(2005)
J Chem Phys
, vol.122
, Issue.5
, pp. 54103
-
-
Salis, H.1
Kaznessis, Y.2
-
16
-
-
18144386494
-
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
-
10.1016/j.jcp.2004.12.014
-
Cao Y Gillespie D Petzold L Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems Journal of Computational Physics 2005, 206:395-411 10.1016/ j.jcp.2004.12.014
-
(2005)
Journal of Computational Physics
, vol.206
, pp. 395-411
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
17
-
-
33751113261
-
Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways
-
17279942
-
Chiam KH Tan CM Bhargava V Rajagopal G Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways Phys Rev E Stat Nonlin Soft Matter Phys 2006, 74(5 Pt 1);051910 17279942
-
(2006)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.74
, Issue.1 PART 1
, pp. 051910
-
-
Chiam, K.H.1
Tan, C.M.2
Bhargava, V.3
Rajagopal, G.4
-
18
-
-
33749989765
-
"partitioned leaping" approach for multiscale modeling of chemical reaction dynamics
-
10.1063/1.2354085 17042579
-
Harris LA Clancy P A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics J Chem Phys 2006, 125(14):144107 10.1063/1.2354085 17042579
-
(2006)
J Chem Phys
, vol.125
, Issue.4
, pp. 144107
-
-
Harris, L.A.1
Clancy, P.2
-
19
-
-
1542345686
-
Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
-
1303974 14990466
-
Puchalka J Kierzek AM Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks Biophys J 2004, 86(3):1357-1372 1303974 14990466
-
(2004)
Biophys J
, vol.86
, Issue.3
, pp. 1357-1372
-
-
Puchalka, J.1
Kierzek, A.M.2
-
20
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
10.1063/1.1545446
-
Rao CV Arkin AP Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm The Journal of Chemical Physics 2003, 118(11):4999-5010 10.1063/1.1545446
-
(2003)
The Journal of Chemical Physics
, vol.118
, Issue.11
, pp. 4999-5010
-
-
Rao, C.V.1
Arkin, A.P.2
-
21
-
-
18144386494
-
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
-
10.1016/j.jcp.2004.12.014
-
Cao Y Gillespie DT Petzold LR Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems Journal of Computational Physics 2004, 206:395-411 10.1016/ j.jcp.2004.12.014
-
(2004)
Journal of Computational Physics
, vol.206
, pp. 395-411
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
22
-
-
33645463036
-
An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks
-
10.1063/1.2131050 16356038
-
Salis H Kaznessis YN An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks J Chem Phys 2005, 123(21):214106 10.1063/ 1.2131050 16356038
-
(2005)
J Chem Phys
, vol.123
, Issue.21
, pp. 214106
-
-
Salis, H.1
Kaznessis, Y.N.2
-
23
-
-
22944480262
-
The slow-scale stochastic simulation algorithm
-
10.1063/1.1824902 15638651
-
Cao Y Gillespie DT Petzold LR The slow-scale stochastic simulation algorithm J Chem Phys 2005, 122:14116 10.1063/1.1824902 15638651
-
(2005)
J Chem Phys
, vol.122
, pp. 14116
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
24
-
-
18844402156
-
Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems
-
10.1063/1.1889434 15918689
-
Goutsias J Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems J Chem Phys 2005, 122(18):184102 10.1063/ 1.1889434 15918689
-
(2005)
J Chem Phys
, vol.122
, Issue.18
, pp. 184102
-
-
Goutsias, J.1
-
25
-
-
26944450876
-
Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm
-
10.1063/1.2046628 16238381
-
Samant A Vlachos DG Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm J Chem Phys 2005, 123(14):144114 10.1063/1.2046628 16238381
-
(2005)
J Chem Phys
, vol.123
, Issue.14
, pp. 144114
-
-
Samant, A.1
Vlachos, D.G.2
-
26
-
-
34347222210
-
A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks
-
1894989 17524148 10.1186/1471-2105-8-175
-
Samant A Ogunnaike BA Vlachos DG A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks BMC Bioinformatics 2007, 8:175 1894989 17524148 10.1186/1471-2105-8-175
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 175
-
-
Samant, A.1
Ogunnaike, B.A.2
Vlachos, D.G.3
-
27
-
-
33845368513
-
COPASI-a COmplex PAthway SImulator
-
10.1093/bioinformatics/btl485 17032683
-
Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U COPASI-a COmplex PAthway SImulator Bioinformatics 2006, 22(24):3067-3074 10.1093/bioinformatics/btl485 17032683
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
28
-
-
17644396339
-
Dizzy: Stochastic simulation of large-scale genetic regulatory networks
-
10.1142/S0219720005001132 15852513
-
Ramsey S Orrell D Bolouri H Dizzy: Stochastic simulation of large-scale genetic regulatory networks J Bioinform Comput Biol 2005, 3(2):415-436 10.1142/S0219720005001132 15852513
-
(2005)
J Bioinform Comput Biol
, vol.3
, Issue.2
, pp. 415-436
-
-
Ramsey, S.1
Orrell, D.2
Bolouri, H.3
-
29
-
-
33644872942
-
Tools for the SBML Community
-
10.1093/bioinformatics/btk042 16410323
-
Gillespie CS Wilkinson DJ Proctor CJ Shanley DP Boys RJ Kirkwood TBL Tools for the SBML Community Bioinformatics 2006, 22(5):628-629 10.1093/ bioinformatics/btk042 16410323
-
(2006)
Bioinformatics
, vol.22
, Issue.5
, pp. 628-629
-
-
Gillespie, C.S.1
Wilkinson, D.J.2
Proctor, C.J.3
Shanley, D.P.4
Boys, R.J.5
Kirkwood, T.B.L.6
-
30
-
-
0036204115
-
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
-
10.1093/bioinformatics/18.3.470 11934747
-
Kierzek AM STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm Bioinformatics 2002, 18(3):470-481 10.1093/ bioinformatics/18.3.470 11934747
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 470-481
-
-
Kierzek, A.M.1
-
31
-
-
38949164415
-
Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems
-
10.1021/bp070255h 17894470
-
Li H Cao Y Petzold L Gillespie D Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems Biotechnol Prog 2008, 24(1):56-61 10.1021/bp070255h 17894470
-
(2008)
Biotechnol Prog
, vol.24
, Issue.1
, pp. 56-61
-
-
Li, H.1
Cao, Y.2
Petzold, L.3
Gillespie, D.4
-
32
-
-
2942514591
-
Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks
-
408466 15113411 10.1186/1471-2105-5-24
-
Adalsteinsson D McMillen D Elston TC Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks BMC Bioinformatics 2004, 5:24 408466 15113411 10.1186/ 1471-2105-5-24
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 24
-
-
Adalsteinsson, D.1
McMillen, D.2
Elston, T.C.3
-
33
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
SBML Forum 10.1093/bioinformatics/btg015 12611808
-
Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H Arkin AP Bornstein BJ Bray D Cornish-Bowden A Cuellar AA Dronov S Gilles ED Ginkel M Gor V Goryanin II Hedley WJ Hodgman TC Hofmeyr JH Hunter PJ Juty NS Kasberger JL Kremling A Kummer U Novère NL Loew LM Lucio D Mendes P Minch E Mjolsness ED Nakayama Y Nelson MR Nielsen PF Sakurada T Schaff JC Shapiro BE Shimizu TS Spence HD Stelling J Takahashi K Tomita M Wagner J Wang J SBML Forum The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics 2003, 19(4):524-531 10.1093/bioinformatics/btg015 12611808
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Novère, N.L.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
more..
-
34
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
10.1016/S1478-5382(03)02370-9
-
Funahashi A Tanimura N Morohashi M Kitano H CellDesigner: A process diagram editor for gene-regulatory and biochemical networks BIOSILICO 2003, 1:159-162 10.1016/S1478-5382(03)02370-9
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Tanimura, N.2
Morohashi, M.3
Kitano, H.4
-
35
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
403769 14597658 10.1101/gr.1239303
-
Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13(11):2498-2504 403769 14597658 10.1101/gr.1239303
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
36
-
-
0035896577
-
The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
-
10.1074/jbc.M006264200 11062240
-
Kierzek AM Zaim J Zielenkiewicz P The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression J Biol Chem 2001, 276(11):8165-8172 10.1074/ jbc.M006264200 11062240
-
(2001)
J Biol Chem
, vol.276
, Issue.11
, pp. 8165-8172
-
-
Kierzek, A.M.1
Zaim, J.2
Zielenkiewicz, P.3
-
37
-
-
0017389047
-
Transcription and translation initiation frequencies of the Escherichia coli lac operon
-
10.1016/0022-2836(77)90279-0 409848
-
Kennell D Riezman H Transcription and translation initiation frequencies of the Escherichia coli lac operon J Mol Biol 1977, 114:1-21 10.1016/ 0022-2836(77)90279-0 409848
-
(1977)
J Mol Biol
, vol.114
, pp. 1-21
-
-
Kennell, D.1
Riezman, H.2
-
38
-
-
33644817463
-
Colored Petri net modeling and simulation of signal transduction pathways
-
10.1016/j.ymben.2005.10.001 16376130
-
Lee DY Zimmer R Lee SY Park S Colored Petri net modeling and simulation of signal transduction pathways Metab Eng 2006, 8(2):112-122 10.1016/ j.ymben.2005.10.001 16376130
-
(2006)
Metab Eng
, vol.8
, Issue.2
, pp. 112-122
-
-
Lee, D.Y.1
Zimmer, R.2
Lee, S.Y.3
Park, S.4
-
39
-
-
38349167535
-
The SBML Discrete Stochastic Models Test Suite
-
10.1093/bioinformatics/btm566 18025005
-
Evans TW Gillespie CS Wilkinson DJ The SBML Discrete Stochastic Models Test Suite Bioinformatics 2008, 24(2):285-286 10.1093/bioinformatics/ btm566 18025005
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 285-286
-
-
Evans, T.W.1
Gillespie, C.S.2
Wilkinson, D.J.3
|