-
2
-
-
58149269561
-
Modelling reaction kinetics inside cells
-
Grima R, Schnell S, (2008) Modelling reaction kinetics inside cells. Essays in Biochemistry 45: 41.
-
(2008)
Essays in Biochemistry
, vol.45
, pp. 41
-
-
Grima, R.1
Schnell, S.2
-
3
-
-
77956520011
-
Functional roles for noise in genetic circuits
-
Eldar A, Elowitz MB, (2010) Functional roles for noise in genetic circuits. Nature 467: 167-173.
-
(2010)
Nature
, vol.467
, pp. 167-173
-
-
Eldar, A.1
Elowitz, M.B.2
-
4
-
-
29244454300
-
Greens-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space
-
van Zon J, Ten Wolde P, (2005) Greens-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space. The Journal of Chemical Physics 123: 234910.
-
(2005)
The Journal of Chemical Physics
, vol.123
, pp. 234910
-
-
van Zon, J.1
Ten Wolde, P.2
-
6
-
-
55149086309
-
Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
-
Kerr R, Bartol T, Kaminsky B, Dittrich M, Chang J, et al. (2008) Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM Journal on Scientific Computing 30: 3126.
-
(2008)
SIAM Journal on Scientific Computing
, vol.30
, pp. 3126
-
-
Kerr, R.1
Bartol, T.2
Kaminsky, B.3
Dittrich, M.4
Chang, J.5
-
7
-
-
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, et al. (2004) Smartcell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Systems biology 1: 129.
-
(2004)
Systems Biology
, vol.1
, pp. 129
-
-
Ander, M.1
Beltrao, P.2
Di Ventura, B.3
Ferkinghoff-Borg, J.4
Foglierini, M.5
-
8
-
-
20844432892
-
Stochastic reaction-diffusion simulation with MesoRD
-
Hattne J, Fange D, Elf J, (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21: 2923-2924.
-
(2005)
Bioinformatics
, vol.21
, pp. 2923-2924
-
-
Hattne, J.1
Fange, D.2
Elf, J.3
-
12
-
-
72049096926
-
A diffusional bimolecular propensity function
-
Gillespie D, (2009) A diffusional bimolecular propensity function. The Journal of Chemical Physics 131: 164109.
-
(2009)
The Journal of Chemical Physics
, vol.131
, pp. 164109
-
-
Gillespie, D.1
-
13
-
-
33751347484
-
The finite state projection algorithm for the solution of the chemical master equation
-
Munsky B, Khammash M, (2006) The finite state projection algorithm for the solution of the chemical master equation. The Journal of Chemical Physics 124: 044104.
-
(2006)
The Journal of Chemical Physics
, vol.124
, pp. 044104
-
-
Munsky, B.1
Khammash, M.2
-
14
-
-
84872489251
-
-
Accessed: 10 Feb
-
Cmepy v0.3 documentation. Accessed: 10 Feb http://fcostin.github.com/cmepy/. (2012).
-
(2012)
Cmepy v0.3 documentation
-
-
-
15
-
-
58849107628
-
Moment-closure approximations for mass-action models
-
Gillespie C, (2009) Moment-closure approximations for mass-action models. Systems Biology, IET 3: 52-58.
-
(2009)
Systems Biology, IET
, vol.3
, pp. 52-58
-
-
Gillespie, C.1
-
17
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (sbml) project
-
Hucka M, Finney A, Bornstein B, Keating S, Shapiro B, et al. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the systems biology markup language (sbml) project. Systems Biology 1: 41-53.
-
(2004)
Systems Biology
, vol.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.3
Keating, S.4
Shapiro, B.5
-
18
-
-
65649138437
-
Computational modeling of biochemical networks using copasi
-
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, et al. (2009) Computational modeling of biochemical networks using copasi. Methods in Molecular Biology 500: 17-59.
-
(2009)
Methods in Molecular Biology
, vol.500
, pp. 17-59
-
-
Mendes, P.1
Hoops, S.2
Sahle, S.3
Gauges, R.4
Dada, J.5
-
19
-
-
47949099328
-
Celldesigner 3.5: a versatile modeling tool for biochemical networks
-
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, et al. (2008) Celldesigner 3.5: a versatile modeling tool for biochemical networks. Proceedings of the IEEE 96: 1254-1265.
-
(2008)
Proceedings of the IEEE
, vol.96
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
-
20
-
-
33947623106
-
Sbmleditor: effective creation of models in the systems biology markup language (sbml)
-
Nicolas R, Donizelli M, Le Novere N, (2007) Sbmleditor: effective creation of models in the systems biology markup language (sbml). BMC Bioinformatics 8: 79.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 79
-
-
Nicolas, R.1
Donizelli, M.2
Le Novere, N.3
-
21
-
-
33644872942
-
Tools for the sbml community
-
Gillespie C, Wilkinson D, Proctor C, Shanley D, Boys R, et al. (2006) Tools for the sbml community. Bioinformatics 22: 628-629.
-
(2006)
Bioinformatics
, vol.22
, pp. 628-629
-
-
Gillespie, C.1
Wilkinson, D.2
Proctor, C.3
Shanley, D.4
Boys, R.5
-
22
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, et al. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4: 92.
-
(2010)
BMC Systems Biology
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
-
23
-
-
44949114109
-
Modeling and simulating chemical reactions
-
Higham D, (2008) Modeling and simulating chemical reactions. SIAM Review, Education Section 50: 347-368.
-
(2008)
SIAM Review, Education Section
, vol.50
, pp. 347-368
-
-
Higham, D.1
-
25
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D, (1977) Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81: 2340-2361.
-
(1977)
The Journal of Physical Chemistry
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.1
-
27
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
Cao Y, Li H, Petzold L, (2004) Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. The Journal of Chemical Physics 121: 4059.
-
(2004)
The Journal of Chemical Physics
, vol.121
, pp. 4059
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
-
28
-
-
0001601301
-
Stochastic approach to chemical kinetics
-
McQuarrie D, (1967) Stochastic approach to chemical kinetics. Journal of Applied Probability 4: 413-478.
-
(1967)
Journal of Applied Probability
, vol.4
, pp. 413-478
-
-
McQuarrie, D.1
-
29
-
-
0242490781
-
Fast evaluation of uctuations in biochemical networks with the linear noise approximation
-
Elf J, Ehrenberg M, (2003) Fast evaluation of uctuations in biochemical networks with the linear noise approximation. Genome Research 13: 2475-2484.
-
(2003)
Genome Research
, vol.13
, pp. 2475-2484
-
-
Elf, J.1
Ehrenberg, M.2
-
30
-
-
27244445075
-
The linear noise approximation for molecular uctuations within cells
-
Hayot F, Jayaprakash C, (2004) The linear noise approximation for molecular uctuations within cells. Physical Biology 1: 205.
-
(2004)
Physical Biology
, vol.1
, pp. 205
-
-
Hayot, F.1
Jayaprakash, C.2
-
31
-
-
77956247381
-
An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions
-
Grima R, (2010) An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions. The Journal of Chemical Physics 133: 035101.
-
(2010)
The Journal of Chemical Physics
, vol.133
, pp. 035101
-
-
Grima, R.1
-
32
-
-
66649109136
-
Noise-induced breakdown of the Michaelis-Menten equation in steady-state conditions
-
Grima R, (2009) Noise-induced breakdown of the Michaelis-Menten equation in steady-state conditions. Physical Review Letters 102: 218103.
-
(2009)
Physical Review Letters
, vol.102
, pp. 218103
-
-
Grima, R.1
-
33
-
-
70749122475
-
Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments
-
Grima R, (2009) Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments. BMC Systems Biology 3: 101.
-
(2009)
BMC Systems Biology
, vol.3
, pp. 101
-
-
Grima, R.1
-
34
-
-
78650646338
-
Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models
-
Thomas P, Straube A, Grima R, (2010) Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models. The Journal of Chemical Physics 133: 195101.
-
(2010)
The Journal of Chemical Physics
, vol.133
, pp. 195101
-
-
Thomas, P.1
Straube, A.2
Grima, R.3
-
35
-
-
84860127314
-
Discreteness-induced concentration inversion in mesoscopic chemical systems
-
Ramaswamy R, Gonzalez-Segredo N, Sbalzarini IF, Grima R, (2012) Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications 3: 779.
-
(2012)
Nature Communications
, vol.3
, pp. 779
-
-
Ramaswamy, R.1
Gonzalez-Segredo, N.2
Sbalzarini, I.F.3
Grima, R.4
-
36
-
-
0004161838
-
-
Cambridge University Press, 3rd Edition
-
Press W, Teukolsky S, Vetterling W, Flannery B, (2007) Numerical recipes: the art of scientific computing. Cambridge University Press, 3rd edition.
-
(2007)
Numerical recipes: The art of scientific computing
-
-
Press, W.1
Teukolsky, S.2
Vetterling, W.3
Flannery, B.4
-
39
-
-
0033564235
-
Sigmoidal kinetic model for two co-operative substrate-binding sites in a cytochrome p450 3a4 active site: an example of the metabolism of diazepam and its derivatives
-
Shou M, Mei Q, Ettore Jr M, Dai R, Baillie T, et al. (1999) Sigmoidal kinetic model for two co-operative substrate-binding sites in a cytochrome p450 3a4 active site: an example of the metabolism of diazepam and its derivatives. Biochemical Journal 340: 845.
-
(1999)
Biochemical Journal
, vol.340
, pp. 845
-
-
Shou, M.1
Mei, Q.2
Ettore Jr, M.3
Dai, R.4
Baillie, T.5
-
40
-
-
33745725676
-
Circadian rhythms and molecular noise
-
Gonze D, Goldbeter A, (2006) Circadian rhythms and molecular noise. Chaos 16: 26110.
-
(2006)
Chaos
, vol.16
, pp. 26110
-
-
Gonze, D.1
Goldbeter, A.2
-
41
-
-
70349559073
-
Mesoscopic statistical properties of multistep enzyme-mediated reactions
-
De Ronde W, Daniels B, Mugler A, Sinitsyn N, Nemenman I, (2009) Mesoscopic statistical properties of multistep enzyme-mediated reactions. Systems Biology, IET 3: 429-437.
-
(2009)
Systems Biology, IET
, vol.3
, pp. 429-437
-
-
de Ronde, W.1
Daniels, B.2
Mugler, A.3
Sinitsyn, N.4
Nemenman, I.5
-
42
-
-
78649240043
-
Elucidating cytochrome c release from mitochondria: Insights from an in silico three-dimensional model
-
Tam Z, Cai Y, Gunawan R, (2010) Elucidating cytochrome c release from mitochondria: Insights from an in silico three-dimensional model. Biophysical Journal 99: 3155-3163.
-
(2010)
Biophysical Journal
, vol.99
, pp. 3155-3163
-
-
Tam, Z.1
Cai, Y.2
Gunawan, R.3
-
43
-
-
66349087046
-
The challenge of lipid rafts
-
Pike L, (2009) The challenge of lipid rafts. Journal of Lipid Research 50: S323-S328.
-
(2009)
Journal of Lipid Research
, vol.50
-
-
Pike, L.1
-
44
-
-
0018240834
-
Malate dehydrogenase of the cytosol. A kinetic investigation of the reaction mechanism and a comparison with lactate dehydrogenase
-
Lodola A, Shore J, Parker D, Holbrook J, (1978) Malate dehydrogenase of the cytosol. A kinetic investigation of the reaction mechanism and a comparison with lactate dehydrogenase. Biochemical Journal 175: 987.
-
(1978)
Biochemical Journal
, vol.175
, pp. 987
-
-
Lodola, A.1
Shore, J.2
Parker, D.3
Holbrook, J.4
-
45
-
-
0033991590
-
Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area
-
Luby-Phelps K, (1999) Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. International Review of Cytology 192: 189-221.
-
(1999)
International Review of Cytology
, vol.192
, pp. 189-221
-
-
Luby-Phelps, K.1
-
46
-
-
0036201594
-
Atypical kinetic profiles in drug metabolism reactions
-
Hutzler J, Tracy T, (2002) Atypical kinetic profiles in drug metabolism reactions. Drug metabolism and disposition 30: 355-362.
-
(2002)
Drug Metabolism and Disposition
, vol.30
, pp. 355-362
-
-
Hutzler, J.1
Tracy, T.2
-
47
-
-
79958097953
-
The moderately efficient enzyme: evolutionary and physico-chemical trends shaping enzyme parameters
-
Bar-Even A, Noor E, Savir Y, Liebermeister W, Davidi D, et al. (2011) The moderately efficient enzyme: evolutionary and physico-chemical trends shaping enzyme parameters. Biochemistry 50: 4402.
-
(2011)
Biochemistry
, vol.50
, pp. 4402
-
-
Bar-Even, A.1
Noor, E.2
Savir, Y.3
Liebermeister, W.4
Davidi, D.5
-
48
-
-
34249937560
-
Amplified biochemical oscillations in cellular systems
-
McKane A, Nagy J, Newman T, Stefanini M, (2007) Amplified biochemical oscillations in cellular systems. Journal of Statistical Physics 128: 165-191.
-
(2007)
Journal of Statistical Physics
, vol.128
, pp. 165-191
-
-
McKane, A.1
Nagy, J.2
Newman, T.3
Stefanini, M.4
-
49
-
-
33644877313
-
Optimal observability of sustained stochastic competitive inhibition oscillations at organellar volumes
-
Davis K, Roussel M, (2006) Optimal observability of sustained stochastic competitive inhibition oscillations at organellar volumes. FEBS Journal 273: 84-95.
-
(2006)
FEBS Journal
, vol.273
, pp. 84-95
-
-
Davis, K.1
Roussel, M.2
-
50
-
-
0028258994
-
Negative feedback defining a circadian clock: autoregulation of the clock gene frequency
-
Aronson B, Johnson K, Loros J, Dunlap J, (1994) Negative feedback defining a circadian clock: autoregulation of the clock gene frequency. Science 263: 1578.
-
(1994)
Science
, vol.263
, pp. 1578
-
-
Aronson, B.1
Johnson, K.2
Loros, J.3
Dunlap, J.4
-
51
-
-
0037079015
-
Computational approaches to cellular rhythms
-
Goldbeter A, (2002) Computational approaches to cellular rhythms. Nature 420: 238-245.
-
(2002)
Nature
, vol.420
, pp. 238-245
-
-
Goldbeter, A.1
-
52
-
-
33644625748
-
Feedback repression is required for mammalian circadian clock function
-
Sato T, Yamada R, Ukai H, Baggs J, Miraglia L, et al. (2006) Feedback repression is required for mammalian circadian clock function. Nature Genetics 38: 312-319.
-
(2006)
Nature Genetics
, vol.38
, pp. 312-319
-
-
Sato, T.1
Yamada, R.2
Ukai, H.3
Baggs, J.4
Miraglia, L.5
-
56
-
-
0032473361
-
Nuclear localization is required for function of the essential clock protein FRQ
-
Luo C, Loros J, Dunlap J, (1998) Nuclear localization is required for function of the essential clock protein FRQ. The EMBO Journal 17: 1228-1235.
-
(1998)
The EMBO Journal
, vol.17
, pp. 1228-1235
-
-
Luo, C.1
Loros, J.2
Dunlap, J.3
-
57
-
-
33646540711
-
Predicting stochastic gene expression dynamics in single cells
-
Mettetal J, Muzzey D, Pedraza J, Ozbudak E, van Oudenaarden A, (2006) Predicting stochastic gene expression dynamics in single cells. Proceedings of the National Academy of Sciences of the United States of America 103: 7304.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 7304
-
-
Mettetal, J.1
Muzzey, D.2
Pedraza, J.3
Ozbudak, E.4
van Oudenaarden, A.5
-
58
-
-
84859746253
-
Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems
-
Ramaswamy R, Sbalzarini I, (2011) Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Scientific Reports 1.
-
(2011)
Scientific Reports 1
-
-
Ramaswamy, R.1
Sbalzarini, I.2
-
59
-
-
80052396994
-
How accurate are the nonlinear chemical fokker-planck and chemical langevin equations?
-
Grima R, Thomas P, Straube A, (2011) How accurate are the nonlinear chemical fokker-planck and chemical langevin equations? The Journal of Chemical Physics 135: 084103.
-
(2011)
The Journal of Chemical Physics
, vol.135
, pp. 084103
-
-
Grima, R.1
Thomas, P.2
Straube, A.3
-
60
-
-
11144311974
-
Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression
-
Welsh D, Yoo S, Liu A, Takahashi J, Kay S, (2004) Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Current Biology 14: 2289-2295.
-
(2004)
Current Biology
, vol.14
, pp. 2289-2295
-
-
Welsh, D.1
Yoo, S.2
Liu, A.3
Takahashi, J.4
Kay, S.5
-
61
-
-
15244359622
-
Modelling genetic networks with noisy and varied experimental data: the circadian clock in arabidopsis thaliana
-
Locke J, Millar A, Turner M, (2005) Modelling genetic networks with noisy and varied experimental data: the circadian clock in arabidopsis thaliana. Journal of Theoretical Biology 234: 383-393.
-
(2005)
Journal of Theoretical Biology
, vol.234
, pp. 383-393
-
-
Locke, J.1
Millar, A.2
Turner, M.3
-
62
-
-
40749162829
-
Libsbml: an api library for sbml
-
Bornstein B, Keating S, Jouraku A, Hucka M, (2008) Libsbml: an api library for sbml. Bioinformatics 24: 880.
-
(2008)
Bioinformatics
, vol.24
, pp. 880
-
-
Bornstein, B.1
Keating, S.2
Jouraku, A.3
Hucka, M.4
-
63
-
-
0036155651
-
Introduction to the ginac framework for symbolic computation within the c++ programming language
-
Bauer C, Frink A, Kreckel R, (2002) Introduction to the ginac framework for symbolic computation within the c++ programming language. Journal of Symbolic Computation 33: 1-12.
-
(2002)
Journal of Symbolic Computation
, vol.33
, pp. 1-12
-
-
Bauer, C.1
Frink, A.2
Kreckel, R.3
-
64
-
-
33745631242
-
The sbml ode solver library: a native api for symbolic and fast numerical analysis of reaction networks
-
Machné R, Finney A, Müller S, Lu J, Widder S, et al. (2006) The sbml ode solver library: a native api for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22: 1406.
-
(2006)
Bioinformatics
, vol.22
, pp. 1406
-
-
Machné, R.1
Finney, A.2
Müller, S.3
Lu, J.4
Widder, S.5
-
69
-
-
0004072686
-
-
Pearson/Addison Wesley
-
Aho A, Lam M, Sethi R, Ullman J, (2007) Compilers: principles, techniques, and tools. Pearson/Addison Wesley.
-
(2007)
Compilers: Principles, techniques, and tools
-
-
Aho, A.1
Lam, M.2
Sethi, R.3
Ullman, J.4
-
71
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Rao C, Arkin A, (2003) Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. The Journal of Chemical Physics 118: 4999.
-
(2003)
The Journal of Chemical Physics
, vol.118
, pp. 4999
-
-
Rao, C.1
Arkin, A.2
-
72
-
-
2942514591
-
Biochemical network stochastic simulator (BioNetS): software for stochastic modeling of biochemical networks
-
Adalsteinsson D, McMillen D, Elston T, (2004) Biochemical network stochastic simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5: 24.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 24
-
-
Adalsteinsson, D.1
McMillen, D.2
Elston, T.3
-
73
-
-
69949152143
-
Cain: Stochastic simulations for chemical kinetics
-
Mauch S, (2009) Cain: Stochastic simulations for chemical kinetics. http://cain. sourceforge. net.
-
(2009)
-
-
Mauch, S.1
-
75
-
-
77949521942
-
Cellmc - a multiplatform model compiler for the cell broadband engine and x86
-
Caulfield E, Hellander A, (2010) Cellmc - a multiplatform model compiler for the cell broadband engine and x86. Bioinformatics 26: 426-428.
-
(2010)
Bioinformatics
, vol.26
, pp. 426-428
-
-
Caulfield, E.1
Hellander, A.2
-
78
-
-
80051950768
-
Stochkit2: software for discrete stochastic simulation of biochemical systems with events
-
Sanft K, Wu S, Roh M, Fu J, Lim R, et al. (2011) Stochkit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics 27: 2457-2458.
-
(2011)
Bioinformatics
, vol.27
, pp. 2457-2458
-
-
Sanft, K.1
Wu, S.2
Roh, M.3
Fu, J.4
Lim, R.5
-
79
-
-
84872486121
-
-
Accessed: 10 Feb
-
StochPy user guide v0.1. Accessed: 10 Feb http://stompy.sourceforge.net/html/userguide.html. (2012)
-
(2012)
StochPy user guide v0.1
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