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Results: 1 to 20 of 311

1.

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

Thomas P, Matuschek H, Grima R.

PLoS One. 2012;7(6):e38518. doi: 10.1371/journal.pone.0038518. Epub 2012 Jun 12.

PMID:
22723865
[PubMed - indexed for MEDLINE]
Free PMC Article
2.
3.

How reliable is the linear noise approximation of gene regulatory networks?

Thomas P, Matuschek H, Grima R.

BMC Genomics. 2013;14 Suppl 4:S5. doi: 10.1186/1471-2164-14-S4-S5. Epub 2013 Oct 1.

PMID:
24266939
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Salis H, Sotiropoulos V, Kaznessis YN.

BMC Bioinformatics. 2006 Feb 24;7:93.

PMID:
16504125
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions.

Thomas P, Straube AV, Grima R.

BMC Syst Biol. 2012 May 14;6:39. doi: 10.1186/1752-0509-6-39.

PMID:
22583770
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations.

Gómez-Uribe CA, Verghese GC.

J Chem Phys. 2007 Jan 14;126(2):024109.

PMID:
17228945
[PubMed - indexed for MEDLINE]
7.

A study of the accuracy of moment-closure approximations for stochastic chemical kinetics.

Grima R.

J Chem Phys. 2012 Apr 21;136(15):154105. doi: 10.1063/1.3702848.

PMID:
22519313
[PubMed - indexed for MEDLINE]
8.

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

Adalsteinsson D, McMillen D, Elston TC.

BMC Bioinformatics. 2004 Mar 8;5:24.

PMID:
15113411
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

COPASI--a COmplex PAthway SImulator.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U.

Bioinformatics. 2006 Dec 15;22(24):3067-74. Epub 2006 Oct 10.

PMID:
17032683
[PubMed - indexed for MEDLINE]
Free Article
10.

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.

Mendes P.

Comput Appl Biosci. 1993 Oct;9(5):563-71.

PMID:
8293329
[PubMed - indexed for MEDLINE]
11.

StochSens--Matlab package for sensitivity analysis of stochastic chemical systems.

Komorowski M, Zurauskiene J, Stumpf MP.

Bioinformatics. 2012 Mar 1;28(5):731-3. doi: 10.1093/bioinformatics/btr714.

PMID:
22378710
[PubMed - indexed for MEDLINE]
Free Article
12.

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

Eccher C, Priami C.

Bioinformatics. 2006 Dec 15;22(24):3075-81. Epub 2006 Oct 17.

PMID:
17046974
[PubMed - indexed for MEDLINE]
Free Article
13.

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.

PMID:
17586553
[PubMed - indexed for MEDLINE]
Free Article
14.

Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

Klim S, Mortensen SB, Kristensen NR, Overgaard RV, Madsen H.

Comput Methods Programs Biomed. 2009 Jun;94(3):279-89. doi: 10.1016/j.cmpb.2009.02.001. Epub 2009 Mar 5.

PMID:
19268387
[PubMed - indexed for MEDLINE]
15.

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

Komorowski M, Costa MJ, Rand DA, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8645-50. doi: 10.1073/pnas.1015814108. Epub 2011 May 6.

PMID:
21551095
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

Erhard F, Friedel CC, Zimmer R.

BMC Bioinformatics. 2008 Aug 29;9:356. doi: 10.1186/1471-2105-9-356.

PMID:
18755046
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Stochastic reduction method for biological chemical kinetics using time-scale separation.

Pahlajani CD, Atzberger PJ, Khammash M.

J Theor Biol. 2011 Mar 7;272(1):96-112. doi: 10.1016/j.jtbi.2010.11.023. Epub 2010 Nov 30.

PMID:
21126524
[PubMed - indexed for MEDLINE]
18.

GraphCrunch: a tool for large network analyses.

Milenković T, Lai J, Przulj N.

BMC Bioinformatics. 2008 Jan 30;9:70. doi: 10.1186/1471-2105-9-70.

PMID:
18230190
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

Sekiguchi T, Okamoto M.

J Bioinform Comput Biol. 2006 Jun;4(3):621-38.

PMID:
16960966
[PubMed - indexed for MEDLINE]
20.

Solving the chemical master equation using sliding windows.

Wolf V, Goel R, Mateescu M, Henzinger TA.

BMC Syst Biol. 2010 Apr 8;4:42. doi: 10.1186/1752-0509-4-42.

PMID:
20377904
[PubMed - indexed for MEDLINE]
Free PMC Article

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