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Results: 1 to 20 of 31

1.

Validity conditions for stochastic chemical kinetics in diffusion-limited systems.

Gillespie DT, Petzold LR, Seitaridou E.

J Chem Phys. 2014 Feb 7;140(5):054111. doi: 10.1063/1.4863990.

PMID:
24511926
[PubMed - in process]
2.

A neuropeptide speeds circadian entrainment by reducing intercellular synchrony.

An S, Harang R, Meeker K, Granados-Fuentes D, Tsai CA, Mazuski C, Kim J, Doyle FJ 3rd, Petzold LR, Herzog ED.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):E4355-61. doi: 10.1073/pnas.1307088110. Epub 2013 Oct 28.

PMID:
24167276
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Perspective: Stochastic algorithms for chemical kinetics.

Gillespie DT, Hellander A, Petzold LR.

J Chem Phys. 2013 May 7;138(17):170901. doi: 10.1063/1.4801941.

PMID:
23656106
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Linear noise approximation is valid over limited times for any chemical system that is sufficiently large.

Wallace EW, Gillespie DT, Sanft KR, Petzold LR.

IET Syst Biol. 2012 Aug;6(4):102-15. doi: 10.1049/iet-syb.2011.0038.

PMID:
23039691
[PubMed - indexed for MEDLINE]
5.

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems.

Daigle BJ Jr, Roh MK, Petzold LR, Niemi J.

BMC Bioinformatics. 2012 May 1;13:68. doi: 10.1186/1471-2105-13-68.

PMID:
22548918
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems.

Harang R, Bonnet G, Petzold LR.

BMC Res Notes. 2012 Mar 26;5:163. doi: 10.1186/1756-0500-5-163.

PMID:
22448897
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Core module biomarker identification with network exploration for breast cancer metastasis.

Yang R, Daigle BJ Jr, Petzold LR, Doyle FJ 3rd.

BMC Bioinformatics. 2012 Jan 18;13:12. doi: 10.1186/1471-2105-13-12.

PMID:
22257533
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

Roh MK, Daigle BJ Jr, Gillespie DT, Petzold LR.

J Chem Phys. 2011 Dec 21;135(23):234108. doi: 10.1063/1.3668100.

PMID:
22191865
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Wavelet measurement suggests cause of period instability in mammalian circadian neurons.

Meeker K, Harang R, Webb AB, Welsh DK, Doyle FJ 3rd, Bonnet G, Herzog ED, Petzold LR.

J Biol Rhythms. 2011 Aug;26(4):353-62. doi: 10.1177/0748730411409863.

PMID:
21775294
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

StochKit2: software for discrete stochastic simulation of biochemical systems with events.

Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR.

Bioinformatics. 2011 Sep 1;27(17):2457-8. doi: 10.1093/bioinformatics/btr401. Epub 2011 Jul 4.

PMID:
21727139
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Automated estimation of rare event probabilities in biochemical systems.

Daigle BJ Jr, Roh MK, Gillespie DT, Petzold LR.

J Chem Phys. 2011 Jan 28;134(4):044110. doi: 10.1063/1.3522769.

PMID:
21280690
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Legitimacy of the stochastic Michaelis-Menten approximation.

Sanft KR, Gillespie DT, Petzold LR.

IET Syst Biol. 2011 Jan;5(1):58. doi: 10.1049/iet-syb.2009.0057.

PMID:
21261403
[PubMed - in process]
13.

Confidence from uncertainty--a multi-target drug screening method from robust control theory.

Luni C, Shoemaker JE, Sanft KR, Petzold LR, Doyle FJ 3rd.

BMC Syst Biol. 2010 Nov 24;4:161. doi: 10.1186/1752-0509-4-161.

PMID:
21106087
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

Roh MK, Gillespie DT, Petzold LR.

J Chem Phys. 2010 Nov 7;133(17):174106. doi: 10.1063/1.3493460.

PMID:
21054005
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Velocity response curves support the role of continuous entrainment in circadian clocks.

Taylor SR, Webb AB, Smith KS, Petzold LR, Doyle FJ 3rd.

J Biol Rhythms. 2010 Apr;25(2):138-49. doi: 10.1177/0748730409360949.

PMID:
20348465
[PubMed - indexed for MEDLINE]
16.

Refining the weighted stochastic simulation algorithm.

Gillespie DT, Roh M, Petzold LR.

J Chem Phys. 2009 May 7;130(17):174103. doi: 10.1063/1.3116791.

PMID:
19425765
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Effect of excluded volume on 2D discrete stochastic chemical kinetics.

Lampoudi S, Gillespie DT, Petzold LR.

J Comput Phys. 2009;228(10):3656-3668.

PMID:
19360139
[PubMed]
Free PMC Article
18.

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.

Lampoudi S, Gillespie DT, Petzold LR.

J Chem Phys. 2009 Mar 7;130(9):094104. doi: 10.1063/1.3074302.

PMID:
19275393
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The subtle business of model reduction for stochastic chemical kinetics.

Gillespie DT, Cao Y, Sanft KR, Petzold LR.

J Chem Phys. 2009 Feb 14;130(6):064103. doi: 10.1063/1.3072704.

PMID:
19222263
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Oscillator model reduction preserving the phase response: application to the circadian clock.

Taylor SR, Doyle FJ 3rd, Petzold LR.

Biophys J. 2008 Aug;95(4):1658-73. doi: 10.1529/biophysj.107.128678. Epub 2008 May 16.

PMID:
18487303
[PubMed - indexed for MEDLINE]
Free PMC Article

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