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Items: 1 to 50 of 65

1.

Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models.

Villaverde AF, Tsiantis N, Banga JR.

J R Soc Interface. 2019 Jul 26;16(156):20190043. doi: 10.1098/rsif.2019.0043. Epub 2019 Jul 3.

2.

Benchmarking optimization methods for parameter estimation in large kinetic models.

Villaverde AF, Fröhlich F, Weindl D, Hasenauer J, Banga JR.

Bioinformatics. 2019 Mar 1;35(5):830-838. doi: 10.1093/bioinformatics/bty736.

3.

Parameter estimation in models of biological oscillators: an automated regularised estimation approach.

Pitt JA, Banga JR.

BMC Bioinformatics. 2019 Feb 15;20(1):82. doi: 10.1186/s12859-019-2630-y.

4.

Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.

Tsiantis N, Balsa-Canto E, Banga JR.

Bioinformatics. 2018 Nov 1;34(21):3780. doi: 10.1093/bioinformatics/bty438. No abstract available.

PMID:
29917059
5.

Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.

Tsiantis N, Balsa-Canto E, Banga JR.

Bioinformatics. 2018 Jul 15;34(14):2433-2440. doi: 10.1093/bioinformatics/bty139. Erratum in: Bioinformatics. 2018 Nov 1;34(21):3780.

PMID:
29522196
6.

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.

Ligon TS, Fröhlich F, Chis OT, Banga JR, Balsa-Canto E, Hasenauer J.

Bioinformatics. 2018 Apr 15;34(8):1421-1423. doi: 10.1093/bioinformatics/btx735.

7.

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.

8.

PREMER: A Tool to Infer Biological Networks.

Villaverde AF, Becker K, Banga JR.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1193-1202. doi: 10.1109/TCBB.2017.2758786. Epub 2017 Oct 4.

PMID:
28981423
9.

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.

Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR.

PLoS One. 2017 Aug 15;12(8):e0182186. doi: 10.1371/journal.pone.0182186. eCollection 2017.

10.

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.

11.

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality.

Otero-Muras I, Banga JR.

ACS Synth Biol. 2017 Jul 21;6(7):1180-1193. doi: 10.1021/acssynbio.6b00306. Epub 2017 Apr 12.

PMID:
28350462
12.

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.

13.

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.

Penas DR, González P, Egea JA, Doallo R, Banga JR.

BMC Bioinformatics. 2017 Jan 21;18(1):52. doi: 10.1186/s12859-016-1452-4.

14.

Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis.

Otero-Muras I, Banga JR.

PLoS One. 2016 Dec 15;11(12):e0166867. doi: 10.1371/journal.pone.0166867. eCollection 2016.

15.

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
16.

SYNBADm: a tool for optimization-based automated design of synthetic gene circuits.

Otero-Muras I, Henriques D, Banga JR.

Bioinformatics. 2016 Nov 1;32(21):3360-3362. Epub 2016 Jul 8.

PMID:
27402908
17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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
39.

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
40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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
46.

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models.

Vera J, Rath O, Balsa-Canto E, Banga JR, Kolch W, Wolkenhauer O.

Mol Biosyst. 2010 Nov;6(11):2174-91. doi: 10.1039/c0mb00018c. Epub 2010 Aug 18.

PMID:
20717620
47.

A generalized Fisher equation and its utility in chemical kinetics.

Ross J, Fernández Villaverde A, Banga JR, Vázquez S, Morán F.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12777-81. doi: 10.1073/pnas.1008257107. Epub 2010 Jul 6.

48.

Multi-objective mixed integer strategy for the optimisation of biological networks.

Sendín JO, Exler O, Banga JR.

IET Syst Biol. 2010 May;4(3):236-48. doi: 10.1049/iet-syb.2009.0045.

PMID:
20500003
49.

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
50.

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.

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