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1.

Lessons learned from quantitative dynamical modeling in systems biology.

Raue A, Schilling M, Bachmann J, Matteson A, Schelker M, Kaschek D, Hug S, Kreutz C, Harms BD, Theis FJ, Klingmüller U, Timmer J.

PLoS One. 2013 Sep 30;8(9):e74335. doi: 10.1371/journal.pone.0074335. eCollection 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/ea0193d8-1f7f-492a-b0b7-d877629fdcee. Schelke, Max [corrected to Schelker, Max].

2.

An improved swarm optimization for parameter estimation and biological model selection.

Abdullah A, Deris S, Mohamad MS, Anwar S.

PLoS One. 2013 Apr 11;8(4):e61258. doi: 10.1371/journal.pone.0061258. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/0e890aa4-232d-4fd3-bb82-675dd9fc33ff.

3.

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling.

Streif S, Savchenko A, Rumschinski P, Borchers S, Findeisen R.

Bioinformatics. 2012 May 1;28(9):1290-1. doi: 10.1093/bioinformatics/bts137. Epub 2012 Mar 25.

4.

Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis.

Tashkova K, Korošec P, Silc J, Todorovski L, Džeroski S.

BMC Syst Biol. 2011 Oct 11;5:159. doi: 10.1186/1752-0509-5-159.

5.

Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Chou IC, Voit EO.

Math Biosci. 2009 Jun;219(2):57-83. doi: 10.1016/j.mbs.2009.03.002. Epub 2009 Mar 25. Review.

6.

Robust optimal design of experiments for model discrimination using an interactive software tool.

Stegmaier J, Skanda D, Lebiedz D.

PLoS One. 2013;8(2):e55723. doi: 10.1371/journal.pone.0055723. Epub 2013 Feb 4.

7.

Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

Zhang Q, Bhattacharya S, Andersen ME, Conolly RB.

J Toxicol Environ Health B Crit Rev. 2010 Feb;13(2-4):253-76. doi: 10.1080/10937404.2010.483943.

PMID:
20574901
8.

Global optimization in systems biology: stochastic methods and their applications.

Balsa-Canto E, Banga JR, Egea JA, Fernandez-Villaverde A, de Hijas-Liste GM.

Adv Exp Med Biol. 2012;736:409-24. doi: 10.1007/978-1-4419-7210-1_24.

PMID:
22161343
9.

Differential simulated annealing: a robust and efficient global optimization algorithm for parameter estimation of biological networks.

Dai Z, Lai L.

Mol Biosyst. 2014 Jun;10(6):1385-92. doi: 10.1039/c4mb00100a. Epub 2014 Apr 9.

PMID:
24714701
10.

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models.

Erguler K, Stumpf MP.

Mol Biosyst. 2011 May;7(5):1593-602. doi: 10.1039/c0mb00107d. Epub 2011 Mar 4.

PMID:
21380410
11.

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41. doi: 10.1186/1752-0509-2-41.

12.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.

BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136.

13.

A continuous optimization approach for inferring parameters in mathematical models of regulatory networks.

Deng Z, Tian T.

BMC Bioinformatics. 2014 Jul 29;15:256. doi: 10.1186/1471-2105-15-256.

14.

ODEion--a software module for structural identification of ordinary differential equations.

Gennemark P, Wedelin D.

J Bioinform Comput Biol. 2014 Feb;12(1):1350015. doi: 10.1142/S0219720013500157. Epub 2013 Nov 12.

PMID:
24467754
15.

A cooperative strategy for parameter estimation in large scale systems biology models.

Villaverde AF, Egea JA, Banga JR.

BMC Syst Biol. 2012 Jun 22;6:75. doi: 10.1186/1752-0509-6-75.

16.

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

Vilas C, Balsa-Canto E, García MS, Banga JR, Alonso AA.

BMC Syst Biol. 2012 Jul 2;6:79. doi: 10.1186/1752-0509-6-79.

17.

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model.

Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, Tyson JJ.

BMC Syst Biol. 2013 Jun 28;7:53. doi: 10.1186/1752-0509-7-53.

18.

System estimation from metabolic time-series data.

Goel G, Chou IC, Voit EO.

Bioinformatics. 2008 Nov 1;24(21):2505-11. doi: 10.1093/bioinformatics/btn470. Epub 2008 Sep 4.

19.

Computational modeling of biochemical networks using COPASI.

Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U.

Methods Mol Biol. 2009;500:17-59. doi: 10.1007/978-1-59745-525-1_2.

PMID:
19399433
20.

BioBayes: a software package for Bayesian inference in systems biology.

Vyshemirsky V, Girolami M.

Bioinformatics. 2008 Sep 1;24(17):1933-4. doi: 10.1093/bioinformatics/btn338. Epub 2008 Jul 16.

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