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Results: 1 to 20 of 68

1.

The effect of coupled stochastic processes in a two-state biochemical switch.

Graham GC, Lipan O.

J Biol Phys. 2011 Sep;37(4):441-62. doi: 10.1007/s10867-011-9226-8. Epub 2011 Jun 11.

PMID:
22942487
[PubMed]
Free PMC Article
2.

A probability generating function method for stochastic reaction networks.

Kim P, Lee CH.

J Chem Phys. 2012 Jun 21;136(23):234108. doi: 10.1063/1.4729374.

PMID:
22779582
[PubMed - indexed for MEDLINE]
3.

Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation.

Macnamara S, Bersani AM, Burrage K, Sidje RB.

J Chem Phys. 2008 Sep 7;129(9):095105. doi: 10.1063/1.2971036.

PMID:
19044893
[PubMed - indexed for MEDLINE]
4.

Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

Barik D, Paul MR, Baumann WT, Cao Y, Tyson JJ.

Biophys J. 2008 Oct;95(8):3563-74. doi: 10.1529/biophysj.108.129155. Epub 2008 Jul 11.

PMID:
18621809
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The Goldbeter-Koshland switch in the first-order region and its response to dynamic disorder.

Xing J, Chen J.

PLoS One. 2008 May 14;3(5):e2140. doi: 10.1371/journal.pone.0002140.

PMID:
18478088
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

How robust are switches in intracellular signaling cascades?

Blüthgen N, Herzel H.

J Theor Biol. 2003 Dec 7;225(3):293-300.

PMID:
14604583
[PubMed - indexed for MEDLINE]
7.

Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation.

Mélykúti B, Burrage K, Zygalakis KC.

J Chem Phys. 2010 Apr 28;132(16):164109. doi: 10.1063/1.3380661.

PMID:
20441260
[PubMed - indexed for MEDLINE]
8.

Stochastic quasi-steady state approximations for asymptotic solutions of the chemical master equation.

Alarcón T.

J Chem Phys. 2014 May 14;140(18):184109. doi: 10.1063/1.4874653.

PMID:
24832255
[PubMed - in process]
9.

Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks.

Munsky B, Khammash M.

IET Syst Biol. 2008 Sep;2(5):323-33. doi: 10.1049/iet-syb:20070082.

PMID:
19045827
[PubMed - indexed for MEDLINE]
10.

Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.

Ciliberto A, Capuani F, Tyson JJ.

PLoS Comput Biol. 2007 Mar 16;3(3):e45.

PMID:
17367203
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Sensing the heat stress by Mammalian cells.

Cates J, Graham GC, Omattage N, Pavesich E, Setliff I, Shaw J, Smith CL, Lipan O.

BMC Biophys. 2011 Aug 11;4:16. doi: 10.1186/2046-1682-4-16.

PMID:
21834999
[PubMed]
Free PMC Article
12.

Efficient parametric analysis of the chemical master equation through model order reduction.

Waldherr S, Haasdonk B.

BMC Syst Biol. 2012 Jul 2;6:81. doi: 10.1186/1752-0509-6-81.

PMID:
22748204
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

Salis H, Kaznessis YN.

J Chem Phys. 2005 Dec 1;123(21):214106.

PMID:
16356038
[PubMed - indexed for MEDLINE]
14.

Effects of input noise on a simple biochemical switch.

Hu B, Kessler DA, Rappel WJ, Levine H.

Phys Rev Lett. 2011 Sep 30;107(14):148101. Epub 2011 Sep 28.

PMID:
22107236
[PubMed - indexed for MEDLINE]
15.

Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch.

Morelli MJ, Allen RJ, Tănase-Nicola S, ten Wolde PR.

J Chem Phys. 2008 Jan 28;128(4):045105. doi: 10.1063/1.2821957. Erratum in: J Chem Phys. 2008 Apr 28;128(16):169901.

PMID:
18248012
[PubMed - indexed for MEDLINE]
16.

Stochastic analysis of a miRNA-protein toggle switch.

Giampieri E, Remondini D, de Oliveira L, Castellani G, Lió P.

Mol Biosyst. 2011 Oct;7(10):2796-803. doi: 10.1039/c1mb05086a. Epub 2011 Jun 30.

PMID:
21717010
[PubMed - indexed for MEDLINE]
17.

Zero-order ultrasensitivity: a study of criticality and fluctuations under the total quasi-steady state approximation in the linear noise regime.

Jithinraj PK, Roy U, Gopalakrishnan M.

J Theor Biol. 2014 Mar 7;344:1-11. doi: 10.1016/j.jtbi.2013.11.014. Epub 2013 Dec 3. Erratum in: J Theor Biol. 2014 Jun 7;350:111.

PMID:
24309434
[PubMed - indexed for MEDLINE]
18.

Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks.

Ribeiro AS.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Nov;76(5 Pt 1):051915. Epub 2007 Nov 20.

PMID:
18233695
[PubMed - indexed for MEDLINE]
19.

Stochastic modelling of the eukaryotic heat shock response.

Mizera A, Gambin B.

J Theor Biol. 2010 Aug 7;265(3):455-66. doi: 10.1016/j.jtbi.2010.04.029. Epub 2010 May 6.

PMID:
20438739
[PubMed - indexed for MEDLINE]
20.

Coupling oscillations and switches in genetic networks.

Gonze D.

Biosystems. 2010 Jan;99(1):60-9. doi: 10.1016/j.biosystems.2009.08.009. Epub 2009 Sep 6.

PMID:
19735694
[PubMed - indexed for MEDLINE]

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