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Results: 1 to 20 of 43

1.

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.

BMC Syst Biol. 2015 Dec;9(1):144. doi: 10.1186/s12918-015-0144-4. Epub 2015 Feb 20.

2.

A consensus approach for estimating the predictive accuracy of dynamic models in biology.

Villaverde AF, Bongard S, Mauch K, Müller D, Balsa-Canto E, Schmid J, Banga JR.

Comput Methods Programs Biomed. 2015 Apr;119(1):17-28. doi: 10.1016/j.cmpb.2015.02.001. Epub 2015 Feb 11.

PMID:
25716416
3.

Multicriteria global optimization for biocircuit design.

Otero-Muras I, Banga JR.

BMC Syst Biol. 2014 Sep 24;8(1):113. doi: 10.1186/s12918-014-0113-3.

4.

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.

5.

MIDER: network inference with mutual information distance and entropy reduction.

Villaverde AF, Ross J, Morán F, Banga JR.

PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

6.

Dynamics of an interactive network composed of a bacterial two-component system, a transporter and K+ as mediator.

Heermann R, Zigann K, Gayer S, Rodriguez-Fernandez M, Banga JR, Kremling A, Jung K.

PLoS One. 2014 Feb 28;9(2):e89671. doi: 10.1371/journal.pone.0089671. eCollection 2014.

7.

Global dynamic optimization approach to predict activation in metabolic pathways.

de Hijas-Liste GM, Klipp E, Balsa-Canto E, Banga JR.

BMC Syst Biol. 2014 Jan 6;8:1. doi: 10.1186/1752-0509-8-1.

8.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

Villaverde AF, Banga JR.

J R Soc Interface. 2013 Dec 4;11(91):20130505. doi: 10.1098/rsif.2013.0505. Print 2014 Feb 6. Review.

9.

Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster.

Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J.

PLoS Comput Biol. 2013 Oct;9(10):e1003281. doi: 10.1371/journal.pcbi.1003281. Epub 2013 Oct 31.

10.

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.

11.

Reverse engineering cellular networks with information theoretic methods.

Villaverde AF, Ross J, Banga JR.

Cells. 2013 May 10;2(2):306-29. doi: 10.3390/cells2020306.

12.

Multi-criteria optimization of regulation in metabolic networks.

Higuera C, Villaverde AF, Banga JR, Ross J, Morán F.

PLoS One. 2012;7(7):e41122. doi: 10.1371/journal.pone.0041122. Epub 2012 Jul 26. Erratum in: PLoS One. 2012;7(11). doi:10.1371/annotation/ab5c1e64-2c46-421e-a1f7-e79cc415534d.

13.

Characterizing multistationarity regimes in biochemical reaction networks.

Otero-Muras I, Banga JR, Alonso AA.

PLoS One. 2012;7(7):e39194. doi: 10.1371/journal.pone.0039194. Epub 2012 Jul 3. Erratum in: PLoS One. 2013;8(1). doi:10.1371/annotation/b5283cc5-5a93-4c96-abc4-c5112266fabe.

14.

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.

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.

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.

17.

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
18.

Structural identifiability of systems biology models: a critical comparison of methods.

Chis OT, Banga JR, Balsa-Canto E.

PLoS One. 2011;6(11):e27755. doi: 10.1371/journal.pone.0027755. Epub 2011 Nov 22.

19.

Inference of complex biological networks: distinguishability issues and optimization-based solutions.

Szederkényi G, Banga JR, Alonso AA.

BMC Syst Biol. 2011 Oct 28;5:177. doi: 10.1186/1752-0509-5-177.

20.

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.

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