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Items: 19

1.

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

Villaverde AF, Banga JR.

PLoS Comput Biol. 2017 Nov 29;13(11):e1005878. doi: 10.1371/journal.pcbi.1005878. eCollection 2017 Nov.

2.

PREMER: a Tool to Infer Biological Networks.

Villaverde AF, Becker K, Banga JR.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Oct 4. doi: 10.1109/TCBB.2017.2758786. [Epub ahead of print]

PMID:
28981423
3.

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems.

Gábor A, Villaverde AF, Banga JR.

BMC Syst Biol. 2017 May 5;11(1):54. doi: 10.1186/s12918-017-0428-y.

4.

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.

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

PLoS Comput Biol. 2017 Feb 6;13(2):e1005379. doi: 10.1371/journal.pcbi.1005379. eCollection 2017 Feb.

5.

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.

6.

On the relationship between sloppiness and identifiability.

Chis OT, Villaverde AF, Banga JR, Balsa-Canto E.

Math Biosci. 2016 Dec;282:147-161. doi: 10.1016/j.mbs.2016.10.009. Epub 2016 Oct 24.

PMID:
27789352
7.

Metabolic engineering with multi-objective optimization of kinetic models.

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

J Biotechnol. 2016 Mar 20;222:1-8. doi: 10.1016/j.jbiotec.2016.01.005. Epub 2016 Jan 28.

PMID:
26826510
8.

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.

9.

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.

10.

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
11.

Acute lower gastrointestinal bleeding from a polyp.

Carrera VG, Villaverde AF, Campos AC, López SV.

Ann Gastroenterol. 2014;27(3):263. No abstract available.

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.

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.

14.

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.

15.

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.

16.

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.

17.

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.

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
19.

Acute hepatitis of cholestatic type possibly associated with the use of glucomannan (amorphophalus konjac).

Villaverde AF, Benlloch S, Berenguer M, Miguel Rayón J, Pina R, Berenguer J.

J Hepatol. 2004 Dec;41(6):1061-2. No abstract available.

PMID:
15582144

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