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Results: 1 to 20 of 33

1.

Systems biology approach to understanding post-traumatic stress disorder.

Thakur GS, Daigle BJ Jr, Dean KR, Zhang Y, Rodriguez-Fernandez M, Hammamieh R, Yang R, Jett M, Palma J, Petzold LR, Doyle Iii FJ.

Mol Biosyst. 2015 Mar 17;11(4):980-93. doi: 10.1039/c4mb00404c.

PMID:
25627823
2.

Inferring single-cell gene expression mechanisms using stochastic simulation.

Daigle BJ Jr, Soltani M, Petzold LR, Singh A.

Bioinformatics. 2015 May 1;31(9):1428-35. doi: 10.1093/bioinformatics/btv007. Epub 2015 Jan 7.

PMID:
25573914
3.

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.

4.

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.

5.

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.

6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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
15.

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.

16.

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.

17.

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
18.

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.

19.

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

Lampoudi S, Gillespie DT, Petzold LR.

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

20.

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.

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