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Results: 1 to 20 of 40

1.

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.

PMID:
24885957
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
24806471
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24586952
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
24393148
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
24307566
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
24204230
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23938131
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
24709703
[PubMed]
Free PMC Article
9.

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.

PMID:
22848435
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22802936
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22748139
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22727112
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
Free Article
14.

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
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
22132135
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
22034917
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21784792
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Use of a generalized fisher equation for global optimization in chemical kinetics.

Villaverde AF, Ross J, Morán F, Balsa-Canto E, Banga JR.

J Phys Chem A. 2011 Aug 4;115(30):8426-36. doi: 10.1021/jp203158r. Epub 2011 Jul 14.

PMID:
21711023
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
21685047
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Detailed kinetic model describing new oligosaccharides synthesis using different β-galactosidases.

Rodriguez-Fernandez M, Cardelle-Cobas A, Villamiel M, Banga JR.

J Biotechnol. 2011 May 20;153(3-4):116-24. doi: 10.1016/j.jbiotec.2011.03.012. Epub 2011 Mar 31.

PMID:
21440015
[PubMed - indexed for MEDLINE]

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