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Items: 1 to 20 of 48

1.

Metabolic engineering with multi-objective optimization of kinetic models.

Villaverde AF, Bongard S, Mauch K, Balsa-Canto E, Banga JR.

J Biotechnol. 2016 Jan 28;222:1-8. doi: 10.1016/j.jbiotec.2016.01.005. [Epub ahead of print]

PMID:
26826510
2.

Robust and efficient parameter estimation in dynamic models of biological systems.

Gábor A, Banga JR.

BMC Syst Biol. 2015 Oct 29;9:74. doi: 10.1186/s12918-015-0219-2.

3.

Enabling network inference methods to handle missing data and outliers.

Folch-Fortuny A, Villaverde AF, Ferrer A, Banga JR.

BMC Bioinformatics. 2015 Sep 3;16:283. doi: 10.1186/s12859-015-0717-7.

4.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

Henriques D, Rocha M, Saez-Rodriguez J, Banga JR.

Bioinformatics. 2015 Sep 15;31(18):2999-3007. doi: 10.1093/bioinformatics/btv314. Epub 2015 May 21.

5.

Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.

de Hijas-Liste GM, Balsa-Canto E, Ewald J, Bartl M, Li P, Banga JR, Kaleta C.

BMC Bioinformatics. 2015 May 16;16:163. doi: 10.1186/s12859-015-0587-z.

6.

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 Feb 20;9:8. doi: 10.1186/s12918-015-0144-4.

7.

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
8.

Multicriteria global optimization for biocircuit design.

Otero-Muras I, Banga JR.

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

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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