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Items: 1 to 20 of 40


Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification.

Doostparast Torshizi A, Petzold LR.

J Am Med Inform Assoc. 2017 May 13. doi: 10.1093/jamia/ocx032. [Epub ahead of print]


Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.

Drawert B, Hellander A, Bales B, Banerjee D, Bellesia G, Daigle BJ Jr, Douglas G, Gu M, Gupta A, Hellander S, Horuk C, Nath D, Takkar A, Wu S, Lötstedt P, Krintz C, Petzold LR.

PLoS Comput Biol. 2016 Dec 8;12(12):e1005220. doi: 10.1371/journal.pcbi.1005220. eCollection 2016 Dec.


Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion.

Golkaram M, Hellander S, Drawert B, Petzold LR.

PLoS Comput Biol. 2016 Nov 28;12(11):e1005122. doi: 10.1371/journal.pcbi.1005122. eCollection 2016 Nov.


Functional network inference of the suprachiasmatic nucleus.

Abel JH, Meeker K, Granados-Fuentes D, St John PC, Wang TJ, Bales BB, Doyle FJ 3rd, Herzog ED, Petzold LR.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4512-7. doi: 10.1073/pnas.1521178113. Epub 2016 Apr 4.


On the Inference of Functional Circadian Networks Using Granger Causality.

Pourzanjani A, Herzog ED, Petzold LR.

PLoS One. 2015 Sep 28;10(9):e0137540. doi: 10.1371/journal.pone.0137540. eCollection 2015.


Adaptive deployment of model reductions for tau-leaping simulation.

Wu S, Fu J, Petzold LR.

J Chem Phys. 2015 May 28;142(20):204108. doi: 10.1063/1.4921638.


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 FJ 3rd.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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