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Results: 1 to 20 of 284

1.

Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise.

Leier A, Marquez-Lago TT, Burrage K.

J Chem Phys. 2008 May 28;128(20):205107. doi: 10.1063/1.2919124.

PMID:
18513050
[PubMed - indexed for MEDLINE]
2.

Efficient binomial leap method for simulating chemical kinetics.

Peng X, Zhou W, Wang Y.

J Chem Phys. 2007 Jun 14;126(22):224109.

PMID:
17581046
[PubMed - indexed for MEDLINE]
3.

Unbiased tau-leap methods for stochastic simulation of chemically reacting systems.

Xu Z, Cai X.

J Chem Phys. 2008 Apr 21;128(15):154112. doi: 10.1063/1.2894479.

PMID:
18433195
[PubMed - indexed for MEDLINE]
4.

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

Marquez-Lago TT, Burrage K.

J Chem Phys. 2007 Sep 14;127(10):104101.

PMID:
17867731
[PubMed]
5.

Exact stochastic simulation of coupled chemical reactions with delays.

Cai X.

J Chem Phys. 2007 Mar 28;126(12):124108.

PMID:
17411109
[PubMed]
6.

Binomial leap methods for simulating stochastic chemical kinetics.

Tian T, Burrage K.

J Chem Phys. 2004 Dec 1;121(21):10356-64.

PMID:
15549913
[PubMed]
7.

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior.

McCollum JM, Peterson GD, Cox CD, Simpson ML, Samatova NF.

Comput Biol Chem. 2006 Feb;30(1):39-49.

PMID:
16321569
[PubMed - indexed for MEDLINE]
8.

Simulation methods with extended stability for stiff biochemical Kinetics.

Rué P, Villà-Freixa J, Burrage K.

BMC Syst Biol. 2010 Aug 11;4:110. doi: 10.1186/1752-0509-4-110.

PMID:
20701766
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A rigorous framework for multiscale simulation of stochastic cellular networks.

Chevalier MW, El-Samad H.

J Chem Phys. 2009 Aug 7;131(5):054102. doi: 10.1063/1.3190327.

PMID:
19673546
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Multinomial tau-leaping method for stochastic kinetic simulations.

Pettigrew MF, Resat H.

J Chem Phys. 2007 Feb 28;126(8):084101.

PMID:
17343434
[PubMed - indexed for MEDLINE]
11.

Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression.

Roussel MR, Zhu R.

Phys Biol. 2006 Dec 8;3(4):274-84.

PMID:
17200603
[PubMed - indexed for MEDLINE]
12.

A multi-scaled approach for simulating chemical reaction systems.

Burrage K, Tian T, Burrage P.

Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):217-34.

PMID:
15142745
[PubMed - indexed for MEDLINE]
13.

K-leap method for accelerating stochastic simulation of coupled chemical reactions.

Cai X, Xu Z.

J Chem Phys. 2007 Feb 21;126(7):074102.

PMID:
17328588
[PubMed]
14.

A markov model based analysis of stochastic biochemical systems.

Ghosh P, Ghosh S, Basu K, Das SK.

Comput Syst Bioinformatics Conf. 2007;6:121-32.

PMID:
17951818
[PubMed - indexed for MEDLINE]
Free Article
15.

Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

Zhu R, Ribeiro AS, Salahub D, Kauffman SA.

J Theor Biol. 2007 Jun 21;246(4):725-45. Epub 2007 Feb 6.

PMID:
17350653
[PubMed - indexed for MEDLINE]
16.

Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.

Chatterjee A, Mayawala K, Edwards JS, Vlachos DG.

Bioinformatics. 2005 May 1;21(9):2136-7. Epub 2005 Feb 4.

PMID:
15699024
[PubMed - indexed for MEDLINE]
Free Article
17.

Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways.

Chiam KH, Tan CM, Bhargava V, Rajagopal G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Nov;74(5 Pt 1):051910. Epub 2006 Nov 14.

PMID:
17279942
[PubMed - indexed for MEDLINE]
18.

In silico simulation of biological network dynamics.

Salwinski L, Eisenberg D.

Nat Biotechnol. 2004 Aug;22(8):1017-9. Epub 2004 Jul 4.

PMID:
15235611
[PubMed - indexed for MEDLINE]
19.

Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm.

Sehl M, Alekseyenko AV, Lange KL.

J Comput Biol. 2009 Sep;16(9):1195-208. doi: 10.1089/cmb.2008.0249.

PMID:
19772431
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks.

Slepoy A, Thompson AP, Plimpton SJ.

J Chem Phys. 2008 May 28;128(20):205101. doi: 10.1063/1.2919546.

PMID:
18513044
[PubMed - indexed for MEDLINE]
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