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Items: 1 to 20 of 139

1.

AMIGO, a toolbox for advanced model identification in systems biology using global optimization.

Balsa-Canto E, Banga JR.

Bioinformatics. 2011 Aug 15;27(16):2311-3. doi: 10.1093/bioinformatics/btr370. Epub 2011 Jun 17.

2.

GenSSI: a software toolbox for structural identifiability analysis of biological models.

Chiş O, Banga JR, Balsa-Canto E.

Bioinformatics. 2011 Sep 15;27(18):2610-1. doi: 10.1093/bioinformatics/btr431. Epub 2011 Jul 22.

3.

SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.

Rodriguez-Fernandez M, Banga JR.

Bioinformatics. 2010 Jul 1;26(13):1675-6. doi: 10.1093/bioinformatics/btq242. Epub 2010 May 5.

PMID:
20444837
4.

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.

Balsa-Canto E, Henriques D, Gábor A, Banga JR.

Bioinformatics. 2016 Nov 1;32(21):3357-3359. Epub 2016 Jul 4.

5.

CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.

Szederkényi G, Banga JR, Alonso AA.

Bioinformatics. 2012 Jun 1;28(11):1549-50. doi: 10.1093/bioinformatics/bts171. Epub 2012 Apr 6.

PMID:
22492646
6.

DOTcvpSB, a software toolbox for dynamic optimization in systems biology.

Hirmajer T, Balsa-Canto E, Banga JR.

BMC Bioinformatics. 2009 Jun 29;10:199. doi: 10.1186/1471-2105-10-199.

7.

Dynamical modeling and multi-experiment fitting with PottersWheel.

Maiwald T, Timmer J.

Bioinformatics. 2008 Sep 15;24(18):2037-43. doi: 10.1093/bioinformatics/btn350. Epub 2008 Jul 9.

8.

Computational procedures for optimal experimental design in biological systems.

Balsa-Canto E, Alonso AA, Banga JR.

IET Syst Biol. 2008 Jul;2(4):163-72. doi: 10.1049/iet-syb:20070069.

PMID:
18681746
9.

Identification of parameter correlations for parameter estimation in dynamic biological models.

Li P, Vu QD.

BMC Syst Biol. 2013 Sep 22;7:91. doi: 10.1186/1752-0509-7-91.

10.

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.

11.

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.

12.

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

Schmidt H, Jirstrand M.

Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.

PMID:
16317076
13.

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.

14.

Structural Identifiability of Dynamic Systems Biology Models.

Villaverde AF, Barreiro A, Papachristodoulou A.

PLoS Comput Biol. 2016 Oct 28;12(10):e1005153. doi: 10.1371/journal.pcbi.1005153. eCollection 2016 Oct.

15.

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
16.

Addressing parameter identifiability by model-based experimentation.

Raue A, Kreutz C, Maiwald T, Klingmuller U, Timmer J.

IET Syst Biol. 2011 Mar;5(2):120-30. doi: 10.1049/iet-syb.2010.0061.

PMID:
21405200
17.

An iterative identification procedure for dynamic modeling of biochemical networks.

Balsa-Canto E, Alonso AA, Banga JR.

BMC Syst Biol. 2010 Feb 17;4:11. doi: 10.1186/1752-0509-4-11.

18.

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.

19.

Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems.

Rodriguez-Fernandez M, Rehberg M, Kremling A, Banga JR.

BMC Syst Biol. 2013 Aug 12;7:76. doi: 10.1186/1752-0509-7-76.

20.

Experimental design for parameter estimation of gene regulatory networks.

Steiert B, Raue A, Timmer J, Kreutz C.

PLoS One. 2012;7(7):e40052. doi: 10.1371/journal.pone.0040052. Epub 2012 Jul 16.

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