Publications

• González-Rodríguez B., J. Ossorio-Castillo, J. González-Díaz, A.M. González-Rueda, D.R. Penas, and D. Rodríguez-Martínez (2022) Computational advances in polynomial optimization: RAPOSa, a freely available global solver. Journal of Global Optimization, accepted, in press. (article)

• Otero-Muras, I., R. Perez-Carrasco, J. R. Banga, C. P. Barnes (2022) Automated design of gene circuits with optimal mushroom-bifurcation behaviour. bioRxiv 2022.05.09.490426. (article)

• Gonzalez, P., Prado-Rodriguez, R., Gabor, A., Saez-Rodriguez, J., Banga, J. R., & Doallo, R. (2022). Parallel ant colony optimization for the training of cell signaling networks. Expert Systems with Applications, 208, 118199. (article)

• Sequeiros, C., Vázquez, C., Banga, J. R., & Otero-Muras, I. (2022). Automated design of synthetic biocircuits in the stochastic regime. IFAC-PapersOnLine, 55(20), 630-634. (article)

• Jiang, S., I. Otero-Muras, J. R. Banga, Y. Wang, M. Kaiser, N. Krasnogor (2022) OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production. ACS Synthetic Biology 11 (4), 1531-1541. (article)

• Villaverde, A.F., D. Pathirana, F. Frohlich, J. Hasenauer, J. R. Banga (2022) A protocol for dynamic model calibration. Briefings in Bioinformatics, 23(1), bbab387. (article)

• Hasenauer, J., & Banga, J. R. (2022) Editorial overview: Mathematical modelling of high-throughput and high-content data. Current Opinion in Systems Biology, 29, 100405. (article)  

• Gonzalez, P., Osorio, R. R., Pardo, X. C., Banga, J. R., & Doallo, R. (2022) An efficient ACO framework for high performance computing environments. Applied Soft Computing, 114, 108058. (article) 

• Schmiester L, Schaelte Y, Bergmann FT, Camba T, Dudkin E, Egert J, F. Froehlich, L. Fuhrmann, A.L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos, S. Merkt, W. Mueller, D. Pathirana, E. Raimundez, L. Refisch, M. Rosenblatt, P.L. Stapor, P. Staedter, D. Wang, F.-G. Wieland, J.R. Banga, J. Timmer, A.F. Villaverde, S. Sahle, C. Kreutz, J. Hasenauer, D. Weindl (2021) PEtab - interoperable specification of parameter estimation problems in systems biology. PLoS Computational Biology 17(1): e1008646. (article) (software) 

• Massonis, G., Banga, J.R., Villaverde, A.F. (2021) Structural Identifiability and Observability of Compartmental Models of the COVID-19 Pandemic. Annual Reviews in Control, 51:441-459. (article) 

• Otero-Muras I., Banga J.R. (2021) Automated Biocircuit Design with SYNBADm. In: Menolascina F. (eds) Synthetic Gene Circuits. Methods in Molecular Biology, vol 2229. Humana, New York, NY. (article) 

• Otero-Muras I., Banga J.R. (2021) Synthetic Gene Circuit Analysis and Optimization. In: Marchisio M.A. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 2189. Humana, New York, NY.. (article) 

• Massonis, G., Banga, J.R., Villaverde, A.F. (2020) Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. arXiv preprint arXiv:2012.09826. (article) 

• Tsiantis, N., J.R. Banga (2020) Using optimal control to understand complex metabolic pathways. BMC Bioinformatics, 21:472. (article)

• Pardo, X. C., P. Argueso-Alejandro, P. Gonzalez, J. R. Banga, R. Doallo (2020) Spark implementation of the enhanced scatter search metaheuristic: methodology and assessment. Swarm and Evolutionary Computation, 59:100748. (article) 

• Tsipa, A., J.A. Pitt, J.R. Banga, A. Mantalaris (2020) A dual-parameter identification approach for data-based predictive modeling of hybrid gene regulatory network-growth kinetics in Pseudomonas putida mt-2. Bioprocess and Biosystems Engineering, 43:1671-1688. (article) 

• Villaverde, A.F., N. Tsiantis, J.R. Banga (2019) Full observability and estimation of unknown inputs, states, and parameters of nonlinear biological models. Journal of the Royal Society Interface, 16:20190043. (article) (software) 

• Villaverde, A.F., F. Froehlich, D. Weindl, J. Hasenauer, J.R. Banga (2019) Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinformatics, 35(5):830-838. (article) (software) 

• Pitt, J.A., Banga, J.R. (2019) Parameter estimation in models of biological oscillators: an automated regularised estimation approach. BMC Bioinformatics, 20:82. (article)

• Villaverde, A.F., N.D. Evans, M. Chappell, J.R. Banga (2019) Input-Dependent Structural Identifiability of Nonlinear Systems. IEEE Control Systems Letters, 3(2):272-277. (article) 

• Gonzalez P., P. Argueso-Alejandro, D.R. Penas, X.C. Pardo, J. Saez-Rodriguez, J.R. Banga, R. Doallo (2019) Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. The Journal of Supercomputing, 35(5):830-838. (article) 

• Otero-Muras, I., Banga, J.R. (2019) Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization. Processes, 7(2):92. (article) 

• Otero-Muras, I., Mannan, A.A., Banga, J.R., Oyarzún, D.A. (2019) Multiobjective optimization of gene circuits for metabolic engineering

(2019) IFAC-PapersOnLine, 52 (26), pp. 13-16. (article)

• Villaverde, A.F., Raimúndez, E., Hasenauer, J., Banga, J.R. (2019) A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology. IFAC-PapersOnLine, 52 (26), pp. 45-51. (article)

• Banga, J.R. , F. Menolascina (2019) (2019) Editorial - Computational Methods Enabling Next-Generation Bioprocesses. Processes, 7(4):214. (article) 

• Tsiantis, N., E. Balsa-Canto and J. R. Banga (2018) Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinformatics, 34(14):2433-2440. (article) (software) (erratum)

• Ligon, T.S., F. Frohlich, O.T. Chis, J.R. Banga, E. Balsa-Canto, J. Hasenauer (2018) GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. Bioinformatics, 34(8):1421-1423. (article) (software) 

• Villaverde A.F., K. Becker, J.R. Banga (2018) PREMER: a Tool to Infer Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4):1193-1202. (article) (software) 

•  Teijeiro, D., Pardo, X.C., Gonzalez, P., Banga, J.R., Doallo, R. (2018) Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark. International Journal of High Performance Computing Applications, 32(5):693-705. (article)

• Gonzalez, P., Martinez, X. C. P., Doallo, R., & Banga, J.R. (2018) Implementing cloud-based parallel metaheuristics: an overview. Journal of Computer Science and Technology., 18(03):e26-e26. (article) 

• Gonzalez, P., D.R. Penas, X.C. Pardo, J.R. Banga, R. Doallo (2018) Multimethod optimization in the cloud: A case-study in systems biology modelling. Concurrency Computat. Pract. Exper., 2018;e4488. (article) (software) 

• Villaverde, A.F., Evans, N.D., Chappell, M.J., Banga, J.R. (2018) Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models. IFAC-PapersOnLine 51 (19), pp. 16-19. https://doi.org/10.1016/j.ifacol.2018.09.015

• Pitt, J.A., Gomoescu, L., Pantelides, C.C., Chachuat, B., Banga, J.R. (2018) Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators. IFAC-PapersOnLine 51 (19), pp. 72-75. https://doi.org/10.1016/j.ifacol.2018.09.040

• Otero-Muras, I., Banga, J.R. (2018) Optimization-based prediction of fold bifurcations in nonlinear ODE models. IFAC-PapersOnLine 51 (15), pp. 485-490. https://doi.org/10.1016/j.ifacol.2018.09.192

• Otero-Muras, I., Banga, J.R. (2018) Mixed Integer Multiobjective Optimization Approaches for Systems and Synthetic Biology. IFAC-PapersOnLine 51 (19), pp. 58-61. https://doi.org/10.1016/j.ifacol.2018.09.042

• Villaverde A.F., J.R. Banga (2017) Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. PLoS Computational Biology, 13(11): e1005878. (article) 

• Penas DR, Henriques D, Gonzalez P, Doallo R, Saez-Rodriguez J, Banga JR (2017) A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology. PLoS ONE, 12(8):e0182186. (article) 

• Villaverde, A.F. and J.R. Banga (2017) Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions. Processes, 5(2):29. (article) 

• Gabor, A., A.F. Villaverde and J.R. Banga (2017) Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. BMC Systems Biology, 11:54. (article) (software) 

• Otero-Muras, I. and J.R. Banga (2017) Automated Design Framework for Synthetic Biology exploiting Pareto Optimality. ACS Synthetic Biology, 6(7):1180-1193. (article) 

• Henriques, D., A.F. Villaverde, M. Rocha, J. Saez-Rodriguez , J.R. Banga (2017) Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Computational Biology, 13(2):e1005379. (article)

• Teijeiro, D., X.C. Pardo, D.R. Penas, P. González, J.R. Banga, R. Doallo (2017) A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology. Cluster Computing, 20(3):1937-1950. (article) 

•  Penas, D.R., P. Gonzalez, J.A. Egea, R. Doallo and J. R. Banga (2017) Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. BMC Bioinformatics, 18:52. (article) 

•  Teijeiro, D., Pardo, X.C., Penas, D.R., González, P., Banga, J.R., Doallo, R. (2017) Evaluation of parallel differential evolution implementations on MapReduce and Spark. Lecture Notes in Computer Science, 10104 LNCS, pp. 397-408. https://doi.org/10.1007/978-3-319-58943-5_32

• Otero-Muras, I. and J.R. Banga (2016) Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis. PLoS ONE, 11(12):e0166867. (article) 

• Teijeiro, D., X.C. Pardo, P. Gonzalez, J.R. Banga and R. Doallo (2016) Towards cloud-based parallel metaheuristics: a case study in computational biology with Differential Evolution and Spark. Int. J. of High Performance Computing Applications, 1094342016679011. (article) 

• Chis, O.T., A.F. Villaverde, J.R. Banga, E. Balsa-Canto (2016) On the relationship between sloppiness and identifiability. Mathematical Biosciences, 282:147-161. (article)

• Villaverde, A.F., K. Becker, J.R. Banga (2016) PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. Computational Methods in Systems Biology, Lecture Notes in Computer Science 9859:323-329 . (article) (software) 

• Otero-Muras, I., D. Henriques and J. R. Banga (2016) SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinformatics, 32(21):3360-3362 . (article) (software)

• Balsa-Canto, E., D. Henriques, A. Gabor, J.R. Banga (2016) AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology. Bioinformatics, 32(21):3357-3359. (article) (software)

• Teijeiro, D., X.C. Pardo, P. Gonzalez, J.R. Banga, R. Doallo (2016) Implementing parallel differential evolution on Spark. Lecture Notes in Computer Science, 9598:75-90. (article) 

• Villaverde, A.F., S. Bongard, K. Mauch, E. Balsa-Canto, J.R. Banga (2016) Metabolic engineering with multi-objective optimization of kinetic models. Journal of biotechnology, 222:1-8. (article) 

• Gabor, A. and J. R. Banga (2015) Robust and efficient parameter estimation in dynamic models of biological systems. BMC Systems Biology, 9:74. (article)

• Folch-Fortuny A, AF Villaverde, A Ferrer, JR Banga (2015) Enabling network inference methods to handle missing data and outliers. BMC Bioinformatics, 16(1):283. (article)

• Henriques, D., M. Rocha, J. Saez-Rodriguez and J.R. Banga (2015) Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimisation approach. Bioinformatics, 31(18):2999-3007. (article)

• Penas DR, P Gonzalez, JA Egea, JR Banga, R Doallo (2015) Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. Procedia Computer Science, 51:630-639. (article)

• Gabor, A., K.M. Hangos, J.R. Banga, Gabor Szederkenyi (2015) Reaction Network Realizations of Rational Biochemical Systems and Their Structural Properties. Journal of Mathematical Chemistry, 53:1657-1686. (article)

• de Hijas Liste, G.M., E. Balsa-Canto, J. Ewald, M. Bartl, P. Li, J.R. Banga and C. Kaleta (2015) Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. BMC Bioinformatics 16:163. (article)

• Penas, D.R., J.R. Banga, P. González, R. Doallo (2015) Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. Applied Soft Computing 33:86-99. (article)

• Villaverde AF, D Henriques, K Smallbone, S Bongard, J Schmid, D Cicin-Sain, A Crombach, J Saez-Rodriguez, K Mauch, E Balsa-Canto, P Mendes, J Jaeger and JR Banga (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology 9:8. (article) (software)

• Villaverde AF, S Bongard, K Mauch, D Muller, E Balsa-Canto, J Schmid, JR Banga (2015) A consensus approach for estimating the predictive accuracy of dynamic models in biology. Computer Methods and Programs in Biomedicine 8:113. (article)

• Otero-Muras, I. and J. R. Banga (2014) Multicriteria global optimization for biocircuit design. BMC Systems Biology 8:113. (article)

•  Otero-Muras, I. and J. R. Banga (2014) Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. In "Computational Methods in Systems Biology", (Editors: Pedro Mendes, Joseph O. Dada, Kieran Smallbone), Lecture Notes in Computer Science, Volume 8859, pp. 225-238. (article)

•  Gabor, A. and J. R. Banga (2014) Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. In "Computational Methods in Systems Biology", (Editors: Pedro Mendes, Joseph O. Dada, Kieran Smallbone), Lecture Notes in Computer Science, Volume 8859, pp. 45-60. (article)

•  Villaverde, A., Ross, J., Moran, F., and Banga, J.R. (2014) MIDER: network inference with mutual information distance and entropy reduction. PLOS ONE 9(5):e96732. (article)

•  Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR and Saez-Rodriguez J (2014) MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics 15:136. (article)

•  de Hijas-Liste, G.M., E. Klipp, E. Balsa-Canto, J.R. Banga (2014) Global dynamic optimization approach to predict activation in metabolic pathways. BMC Systems Biology 8:1. (article)

•  Villaverde, A.F. and J.R. Banga (2014) Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J. Royal Soc. Interface 11(91):20130505. (article)

•  Heermann, R., K. Zigann, S., M. Rodriguez-Fernandez, J.R. Banga, A. Kremling, K. Jung (2014) Dynamics of an Interactive Network Composed of a Bacterial Two-Component System, a Transporter and K+ as Mediator. PLoS ONE 9(2):e89671. (article)

• Becker, K., E. Balsa-Canto, D. Cicin-Sain, A. Hoermann, H. Janssens, J.R. Banga, J. Jaeger (2013) Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster. PLoS Computational Biology 9(10): e1003281. (article)

• Egea, J.A., D. Henriques, T. Cokelaer, A.F. Villaverde, J.R. Banga, J. Saez-Rodriguez (2013) MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. arXiv:1311.5735 . (article)

• Gabor, A., K.M. Hangos, G. Szederkenyi, J.R. Banga (2013) On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology. Computational Methods in Systems Biology. Lecture Notes in Computer Science 8130:206-219. (article)

• Balsa-Canto, E. and J.R. Banga (2013) Optimal Dynamic Experiments. In "Encyclopedia of Systems Biology", W. Dubitzky, O. Wolkenhauer, K.-H. Cho, H. Yokota (Eds.) pp. 1569-1572. (article)

• Tuza, Z.A., G. Szederkenyi, K.M. Hangos, A.A. Alonso, J.R. Banga (2013) Computing all Sparse Kinetic Structures for a Lorenz System Using Optimization. Int. Journal of Bifurcation and Chaos 23(8):1350141. (article)

• Rodriguez-Fernandez, M., M. Rehberg, A. Kremling, J.R. Banga (2013) Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Systems Biology 7:76. (article)

• Villaverde, A.F., J. Ross and J. R. Banga (2013) Reverse Engineering Cellular Networks with Information Theoretic Methods. Cells 2(2):306-329.  (article)

• Higuera, C., A.F. Villaverde, J.R. Banga, J. Ross, and F. Morán (2012) Multi-Criteria Optimization of Regulation in Metabolic Networks. PLoS ONE 7(7): e41122.  (article)

• Villaverde, A.F., J.A. Egea and J.R. Banga (2012) A cooperative strategy for parameter estimation in large scale systems biology models. BMC Systems Biology 6:75.  (article)

• Vilas, C., E. Balsa-Canto, M. S. G. Garcia, J. R. Banga and A. A. Alonso (2012) Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. BMC Systems Biology 6:79.  (article)

• Otero-Muras, I., Julio R. Banga and Antonio A. Alonso (2012) Characterizing Multistationarity Regimes in Biochemical Reaction Networks. PLoS ONE 7(7):e39194.  (article)

• Szederkenyi G., Banga J.R., Alonso A.A. (2012) CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. Bioinformatics 28(11):1549-1550.  (article) (software)

• Rodriguez-Fernandez, M., Banga, J. R., and Doyle, F. J. (2012) Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: application to systems biology models. Int. J. of Robust and Nonlinear Control 22(10):1082-1102.  (article)

• Balsa-Canto, E., J.R. Banga, J.A. Egea, A. Fernandez-Villaverde and G.M. de Hijas-Liste (2012) Global optimization in systems biology: stochastic methods and their applications. Advances in Experimental Medicine and Biology 736:409-424.  (article)

• Szederkenyi G., Banga J.R., Alonso A.A. (2011) Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Systems Biology 5:177.  (article)

• Kothare, M.V. and Banga, J.R. (2011) Editorial - DYCOPS and CAB Special Issue. Journal of Process Control 21(10):1359-1360.  (article)

• Chis, Oana, Julio R. Banga, and Eva Balsa-Canto (2011) Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PLoS ONE 27(18):2610-2611.  (article)

• Chis, Oana, Julio R. Banga, and Eva Balsa-Canto (2011) GenSSI: a software toolbox for structural identifiability analysis of biological models. Bioinformatics 27(18):2610-2611.  (article) (*software*)

• Villaverde, A., J. Ross, F. Morán, E. Balsa-Canto, J.R. Banga (2011) Use of a Generalized Fisher Equation for Global Optimization in Chemical Kinetics. Journal of Physical Chemistry A115(30):8426-8436.  (article)

• Balsa-Canto, E. and Julio R. Banga (2011) AMIGO, a toolbox for Advanced Model Identification in systems biology using Global Optimization. Bioinformatics 27(16):2311-2313.  (article) (*software*)

• De Hijas-Liste, G. M., Balsa-Canto, E., & Banga, J. R. (2011) Prediction of activation of metabolic pathways via dynamic optimization. Computer Aided Chemical Engineering 29:1386-1390.  (article)

• Rodriguez-Fernandez, M., Cardelle-Cobas, A., Villamiel, M., & Banga, J. R. (2011) Detailed kinetic model describing new oligosaccharides synthesis using different ß-galactosidases. Journal of Biotechnology 153(3-4):116-124.  (article)

• Nicolai, B. M., Egea, J. A., Scheerlinck, N., Banga, J. R., & Datta, A. K. (2011) Fuzzy finite element analysis of heat conduction problems with uncertain parameters. Journal of Food Engineering 103(1):38-46. 

• Ross, J., A.F. Villaverde, J.R. Banga, S. Vazquez, F. Moran (2010) A generalized Fisher equation and its utility in chemical kinetics. Proc. Natl. Acad. Sci. USA 107(29):12777-12781.  (article)

• Georgiadis, Michael C., Julio R. Banga and Efstratios N. Pistikopoulos (Eds) (2010) DYNAMIC PROCESS MODELLING. Wiley-VCH, Weinheim, ISBN-10: 3-527-31684-1.  (BOOK site)

• Vera, J., O. Rath, E. Balsa-Canto, J. R. Banga, W. Kolch and Olaf Wolkenhauer (2010) Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models. Molecular BioSystems 6:2174–2191.  (article)

• Rodriguez-Fernandez, M. and J.R. Banga (2010). SensSB: A software toolbox for the development and sensitivity analysis of systems biology models. Bioinformatics 26(13):1675-1676. (article) (software)

• Sendin, J.O.H., O. Exler & J.R. Banga (2010). Multi-objective mixed integer strategy for the optimisation of biological networks. IET Systems Biology 4(3):236-248. (article)

• Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2010). An iterative identification procedure for dynamic modeling of biochemical networks. BMC Systems Biology 4:11. (article)

• Egea, J.A., Martí, R., & Banga, J.R. (2010). An evolutionary method for complex-process optimization. Computers and Operations Research 37(2):315-324. (article)

• Balsa-Canto E., J.R. Banga and M.R. García (2010). Dynamic Model Building Using Optimal Identification Strategies, with Applications in Bioprocess Engineering. In "Dynamic Process Modelling", Banga J.R., Georgiadis M., Pistikopoulos E. (eds.), Wiley-VCH, Weinheim.. 

• Balsa-Canto, E., Banga, J.R. (2010). Computational Procedures for Model Identification. In "Systems Biology for Signaling Networks", Sangdun Choi (Ed.), (pp: 111-138), Springer. ISBN: 978-1-4419-5796-2. 

• Sendin, J. O. H., Alonso, A. A., & Banga, J. R. (2010). Efficient and robust multi-objective optimization of food processing: A novel approach with application to thermal sterilization. Journal of Food Engineering 98(3):317-324. 

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