Portela, A., Banga, J. R., & Matabuena, M. (2025). Conformal prediction for uncertainty quantification in dynamic biological systems. PLOS Computational Biology, 21(5), e1013098. https://doi.org/10.1371/journal.pcbi.1013098

Banga, J. R., & Villaverde, A. F. (2025). Mechanistic dynamic modelling of biological systems: The road ahead. Current Opinion in Systems Biology, 42, 100553. https://doi.org/10.1016/j.coisb.2025.100553

Lang, P. F., Penas, D. R., Banga, J. R., Weindl, D., & Novak, B. (2024). Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLOS Computational Biology, 20(1), e1011151. https://doi.org/10.1371/journal.pcbi.1011151

Prado‐Rodríguez, R., González, P., Banga, J. R., & Doallo, R. (2024). Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications. Expert Systems, 41(8). Portico. https://doi.org/10.1111/exsy.13554

Pardo, X. C., González, P., Banga, J. R., & Doallo, R. (2024). Population based metaheuristics in Spark: Towards a general framework using PSO as a case study. Swarm and Evolutionary Computation, 85, 101483. https://doi.org/10.1016/j.swevo.2024.101483

Penas, D. R., Hashemi, M., Jirsa, V. K., & Banga, J. R. (2024). Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers. PLOS Computational Biology, 20(7), e1011642. https://doi.org/10.1371/journal.pcbi.1011642

Sequeiros, C., Otero-Muras, I., Vázquez, C., & Banga, J. R. (2023). Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(3), 1971–1982. https://doi.org/10.1109/tcbb.2022.3225675

Villaverde, A. F., Raimúndez, E., Hasenauer, J., & Banga, J. R. (2023). Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(3), 1725–1736. https://doi.org/10.1109/tcbb.2022.3213914

Taha, A., Patón, M., Penas, D. R., Banga, J. R., & Rodríguez, J. (2023). Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants. PLOS Computational Biology, 19(7), e1011264. https://doi.org/10.1371/journal.pcbi.1011264

Massonis, G., Villaverde, A. F., & Banga, J. R. (2023). Distilling identifiable and interpretable dynamic models from biological data. PLOS Computational Biology, 19(10), e1011014. https://doi.org/10.1371/journal.pcbi.1011014

Sequeiros, C., Vázquez, C., Banga, J. R., & Otero-Muras, I. (2023). Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise. ACS Synthetic Biology, 12(10), 2865–2876. https://doi.org/10.1021/acssynbio.3c00033

Sequeiros, C., Pájaro, M., Vázquez, C., Banga, J. R., & Otero-Muras, I. (2023). IDESS: a toolbox for identification and automated design of stochastic gene circuits. Bioinformatics, 39(11). https://doi.org/10.1093/bioinformatics/btad682

Hasenauer, J., & Banga, J. R. (2022). Editorial overview: ‘Mathematical modelling of high-throughput and high-content data.’ Current Opinion in Systems Biology, 29, 100405. https://doi.org/10.1016/j.coisb.2021.100405

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. https://doi.org/10.1016/j.ifacol.2022.09.166

González, P., Osorio, R. R., Pardo, X. C., Banga, J. R., & Doallo, R. (2022). An efficient ant colony optimization framework for HPC environments. Applied Soft Computing, 114, 108058. https://doi.org/10.1016/j.asoc.2021.108058

Jiang, S., Otero-Muras, I., Banga, J. R., Wang, Y., Kaiser, M., & Krasnogor, N. (2022). OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production. ACS Synthetic Biology, 11(4), 1531–1541. https://doi.org/10.1021/acssynbio.1c00610

González, P., Prado-Rodriguez, R., Gábor, 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. https://doi.org/10.1016/j.eswa.2022.118199

Massonis, G., Villaverde, A. F., & Banga, J. R. (2022). Improving dynamic predictions with ensembles of observable models. Bioinformatics, 39(1). https://doi.org/10.1093/bioinformatics/btac755

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. https://doi.org/10.1016/j.arcontrol.2020.12.001

Schmiester, L., Schälte, Y., Bergmann, F. T., Camba, T., Dudkin, E., Egert, J., Fröhlich, F., Fuhrmann, L., Hauber, A. L., Kemmer, S., Lakrisenko, P., Loos, C., Merkt, S., Müller, W., Pathirana, D., Raimúndez, E., Refisch, L., Rosenblatt, M., Stapor, P. L., … Weindl, D. (2021). PEtab—Interoperable specification of parameter estimation problems in systems biology. PLOS Computational Biology, 17(1), e1008646. https://doi.org/10.1371/journal.pcbi.1008646

Ogunnaike, B., Banga, J. R., Bogle, D., & Parker, R. (2021). Editorial: Biological Control Systems and Disease Modeling. Frontiers in Bioengineering and Biotechnology, 9. https://doi.org/10.3389/fbioe.2021.677976

Otero-Muras, I., & Banga, J. R. (2021). Automated Biocircuit Design with SYNBADm. Synthetic Gene Circuits, 119–136. https://doi.org/10.1007/978-1-0716-1032-9_4

Massonis, G., Banga, J. R., & Villaverde, A. F. (2021). AutoRepar: A method to obtain identifiable and observable reparameterizations of dynamic models with mechanistic insights. International Journal of Robust and Nonlinear Control, 33(9), 5039–5057. Portico. https://doi.org/10.1002/rnc.5887

Villaverde, A. F., Pathirana, D., Fröhlich, F., Hasenauer, J., & Banga, J. R. (2021). A protocol for dynamic model calibration. Briefings in Bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab387

Pardo, X. C., Argüeso-Alejandro, P., González, P., Banga, J. R., & Doallo, R. (2020). Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment. Swarm and Evolutionary Computation, 59, 100748. https://doi.org/10.1016/j.swevo.2020.100748

Tsipa, A., Pitt, J. A., Banga, J. R., & Mantalaris, A. (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(9), 1671–1688. https://doi.org/10.1007/s00449-020-02360-2

Tsiantis, N., & Banga, J. R. (2020). Using optimal control to understand complex metabolic pathways. https://doi.org/10.1101/2020.05.07.082198

Otero-Muras, I., & Banga, J. R. (2020). Synthetic Gene Circuit Analysis and Optimization. Computational Methods in Synthetic Biology, 89–103. https://doi.org/10.1007/978-1-0716-0822-7_8

Pitt, J. A., & Banga, J. R. (2019). Parameter estimation in models of biological oscillators: an automated regularised estimation approach. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-2630-y

Otero-Muras, I., Mannan, A. A., Banga, J. R., & Oyarzún, D. A. (2019). Multiobjective optimization of gene circuits for metabolic engineering. IFAC-PapersOnLine, 52(26), 13–16. https://doi.org/10.1016/j.ifacol.2019.12.229

González, P., Argüeso-Alejandro, P., Penas, D. R., Pardo, X. C., Saez-Rodriguez, J., Banga, J. R., & Doallo, R. (2019). Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. The Journal of Supercomputing, 75(7), 3471–3498. https://doi.org/10.1007/s11227-019-02871-0

Villaverde, A. F., Tsiantis, N., & Banga, J. R. (2019). Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models. Journal of The Royal Society Interface, 16(156), 20190043. https://doi.org/10.1098/rsif.2019.0043

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), 45–51. https://doi.org/10.1016/j.ifacol.2019.12.234

Otero-Muras, I., & Banga, J. R. (2019). Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization. Processes, 7(2), 92. https://doi.org/10.3390/pr7020092

Villaverde, A. F., Evans, N. D., Chappell, M. J., & Banga, J. R. (2019). Input-Dependent Structural Identifiability of Nonlinear Systems. IEEE Control Systems Letters, 3(2), 272–277. https://doi.org/10.1109/lcsys.2018.2868608

Banga, J. R., & Menolascina, F. (2019). Computational Methods Enabling Next-Generation Bioprocesses. Processes, 7(4), 214. https://doi.org/10.3390/pr7040214

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), 16–19. https://doi.org/10.1016/j.ifacol.2018.09.015

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

González, P., Penas, D. R., Pardo, X. C., Banga, J. R., & Doallo, R. (2018). Multimethod optimization in the cloud: A case‐study in systems biology modelling. Concurrency and Computation: Practice and Experience, 30(12). Portico. https://doi.org/10.1002/cpe.4488

González, P., Penas, D. R., Pardo, X. C., Banga, J. R., & Doallo, R. (2018). Multimethod Optimization for Reverse Engineering of Complex Biological Networks. Proceedings of the 6th International Workshop on Parallelism in Bioinformatics, 11–18. https://doi.org/10.1145/3235830.3235832

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

Tsiantis, N., Balsa-Canto, E., & Banga, J. R. (2018). Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinformatics, 34(21), 3780–3780. https://doi.org/10.1093/bioinformatics/bty438

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), 72–75. https://doi.org/10.1016/j.ifacol.2018.09.040

Wierling, C., Herault, Y., Jonkers, J., Ploubidou, A., Frappart, L., Hasenauer, J., Banga, J., Rinner, O., Naumova, V., Koubi, D., & Lange, B. (2018). Abstract 1296: CanPathPro—development of a platform for predictive pathway modelling using genetically engineered mouse models. Cancer Research, 78(13_Supplement), 1296–1296. https://doi.org/10.1158/1538-7445.am2018-1296

Villaverde, A. F., Fröhlich, F., Weindl, D., Hasenauer, J., & Banga, J. R. (2018). Benchmarking optimization methods for parameter estimation in large kinetic models. https://doi.org/10.1101/295006

Villaverde, A. F., Becker, K., & Banga, J. R. (2018). PREMER: A Tool to Infer Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4), 1193–1202. https://doi.org/10.1109/tcbb.2017.2758786

Tsiantis, N., Balsa-Canto, E., & Banga, J. R. (2018). Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinformatics, 34(14), 2433–2440. https://doi.org/10.1093/bioinformatics/bty139

Gonzalez, P., Pardo, X. C., Penas, D. R., Teijeiro, D., Banga, J. R., & Doallo, R. (2017). Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study. 2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), 797–806. https://doi.org/10.1109/ccgrid.2017.58

Gábor, A., Villaverde, A. F., & Banga, J. R. (2017). Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. BMC Systems Biology, 11(1). https://doi.org/10.1186/s12918-017-0428-y

Penas, D. R., González, P., Egea, J. A., Doallo, R., & Banga, J. R. (2017). Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. BMC Bioinformatics, 18(1). https://doi.org/10.1186/s12859-016-1452-4

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. Euro-Par 2016: Parallel Processing Workshops, 397–408. https://doi.org/10.1007/978-3-319-58943-5_32

Henriques, D., Villaverde, A. F., Rocha, M., Saez-Rodriguez, J., & Banga, J. R. (2017). Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLOS Computational Biology, 13(2), e1005379. https://doi.org/10.1371/journal.pcbi.1005379

Penas, D. R., Henriques, D., González, P., Doallo, R., Saez-Rodriguez, J., & Banga, J. R. (2017). A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology. PLOS ONE, 12(8), e0182186. https://doi.org/10.1371/journal.pone.0182186

Teijeiro, D., Pardo, X. C., Penas, D. R., González, P., Banga, J. R., & Doallo, R. (2017). A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology. Cluster Computing, 20(3), 1937–1950. https://doi.org/10.1007/s10586-017-0860-1

Villaverde, A. F., & Banga, J. R. (2017). Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions. Processes, 5(2), 29. https://doi.org/10.3390/pr5020029

Otero-Muras, I., & Banga, J. R. (2017). Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality. ACS Synthetic Biology, 6(7), 1180–1193. https://doi.org/10.1021/acssynbio.6b00306

Villaverde, A. F., & Banga, J. R. (2017). Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. PLOS Computational Biology, 13(11), e1005878. https://doi.org/10.1371/journal.pcbi.1005878

Ligon, T. S., Fröhlich, F., Chiş, O. T., Banga, J. R., Balsa-Canto, E., & Hasenauer, J. (2017). GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. Bioinformatics, 34(8), 1421–1423. https://doi.org/10.1093/bioinformatics/btx735

Otero-Muras, I., Henriques, D., & Banga, J. R. (2016). SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinformatics, 32(21), 3360–3362. https://doi.org/10.1093/bioinformatics/btw415

Villaverde, A. F., Becker, K., & Banga, J. R. (2016). PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. Computational Methods in Systems Biology, 323–329. https://doi.org/10.1007/978-3-319-45177-0_21

Teijeiro, D., Pardo, X. C., González, P., Banga, J. R., & Doallo, R. (2016). Implementing Parallel Differential Evolution on Spark. Applications of Evolutionary Computation, 75–90. https://doi.org/10.1007/978-3-319-31153-1_6

Otero-Muras, I., & Banga, J. R. (2016). Exploring Design Principles of Gene Regulatory Networks via Pareto Optimality**We acknowledge funding from the Spanish MINECO (and the European Regional Development Fund) project SYNBIOFACTORY (grant number DPI2014-55276-C5-2-R). IFAC-PapersOnLine, 49(7), 809–814. https://doi.org/10.1016/j.ifacol.2016.07.289

Otero-Muras, I., & Banga, J. R. (2016). Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis. PLOS ONE, 11(12), e0166867. https://doi.org/10.1371/journal.pone.0166867

Balsa-Canto, E., Henriques, D., Gábor, A., & Banga, J. R. (2016). AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology. Bioinformatics, 32(21), 3357–3359. https://doi.org/10.1093/bioinformatics/btw411

Villaverde, A. F., Bongard, S., Mauch, K., Balsa-Canto, E., & Banga, J. R. (2016). Metabolic engineering with multi-objective optimization of kinetic models. Journal of Biotechnology, 222, 1–8. https://doi.org/10.1016/j.jbiotec.2016.01.005

Chis, O.-T., Villaverde, A. F., Banga, J. R., & Balsa-Canto, E. (2016). On the relationship between sloppiness and identifiability. Mathematical Biosciences, 282, 147–161. https://doi.org/10.1016/j.mbs.2016.10.009

Teijeiro, D., Pardo, X. C., González, P., Banga, J. R., & Doallo, R. (2016). Towards cloud-based parallel metaheuristics. The International Journal of High Performance Computing Applications, 32(5), 693–705. https://doi.org/10.1177/1094342016679011

Gábor, A., & Banga, J. R. (2015). Robust and efficient parameter estimation in dynamic models of biological systems. BMC Systems Biology, 9(1). https://doi.org/10.1186/s12918-015-0219-2

Gábor, A., Hangos, K. M., Banga, J. R., & Szederkényi, G. (2015). Reaction network realizations of rational biochemical systems and their structural properties. Journal of Mathematical Chemistry, 53(8), 1657–1686. https://doi.org/10.1007/s10910-015-0511-9

Penas, D. R., González, P., Egea, J. A., Banga, J. R., & Doallo, R. (2015). Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. Procedia Computer Science, 51, 630–639. https://doi.org/10.1016/j.procs.2015.05.331

de Hijas-Liste, G. M., Balsa-Canto, E., Ewald, J., Bartl, M., Li, P., Banga, J. R., & Kaleta, C. (2015). Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. BMC Bioinformatics, 16(1). https://doi.org/10.1186/s12859-015-0587-z

Penas, D. R., Banga, J. R., González, P., & Doallo, R. (2015). Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. Applied Soft Computing, 33, 86–99. https://doi.org/10.1016/j.asoc.2015.04.025

Folch-Fortuny, A., Villaverde, A. F., Ferrer, A., & Banga, J. R. (2015). Enabling network inference methods to handle missing data and outliers. BMC Bioinformatics, 16(1). https://doi.org/10.1186/s12859-015-0717-7

Villaverde, A. F., 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, J. R. (2015). BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology, 9(1). https://doi.org/10.1186/s12918-015-0144-4

Villaverde, A. F., Bongard, S., Mauch, K., Müller, D., Balsa-Canto, E., Schmid, J., & Banga, J. R. (2015). A consensus approach for estimating the predictive accuracy of dynamic models in biology. Computer Methods and Programs in Biomedicine, 119(1), 17–28. https://doi.org/10.1016/j.cmpb.2015.02.001

Henriques, D., Rocha, M., Saez-Rodriguez, J., & Banga, J. R. (2015). Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinformatics, 31(18), 2999–3007. https://doi.org/10.1093/bioinformatics/btv314

Villaverde, A. F., & Banga, J. R. (2014). Reverse engineering and identification in systems biology: strategies, perspectives and challenges. Journal of The Royal Society Interface, 11(91), 20130505. https://doi.org/10.1098/rsif.2013.0505

Otero-Muras, I., & Banga, J. R. (2014). Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. Computational Methods in Systems Biology, 225–238. https://doi.org/10.1007/978-3-319-12982-2_16

Otero-Muras, I., & Banga, J. R. (2014). Multicriteria global optimization for biocircuit design. BMC Systems Biology, 8(1). https://doi.org/10.1186/s12918-014-0113-3

Villaverde, A. F., Ross, J., Morán, F., & Banga, J. R. (2014). MIDER: Network Inference with Mutual Information Distance and Entropy Reduction. PLoS ONE, 9(5), e96732. https://doi.org/10.1371/journal.pone.0096732

Egea, J. A., Henriques, D., Cokelaer, T., Villaverde, A. F., MacNamara, A., Danciu, D.-P., Banga, J. R., & Saez-Rodriguez, J. (2014). MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics, 15(1). https://doi.org/10.1186/1471-2105-15-136

Gábor, A., & Banga, J. R. (2014). Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. Computational Methods in Systems Biology, 45–60. https://doi.org/10.1007/978-3-319-12982-2_4

Villaverde, A. F., Bongard, S., Mauch, K., Müller, D., Balsa-Canto, E., Schmid, J., & Banga, J. R. (2014). High-Confidence Predictions in Systems Biology Dynamic Models. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), 161–171. https://doi.org/10.1007/978-3-319-07581-5_20

de Hijas-Liste, G. M., Klipp, E., Balsa-Canto, E., & Banga, J. R. (2014). Global dynamic optimization approach to predict activation in metabolic pathways. BMC Systems Biology, 8(1). https://doi.org/10.1186/1752-0509-8-1

Heermann, R., Zigann, K., Gayer, S., Rodriguez-Fernandez, M., Banga, J. R., Kremling, A., & Jung, K. (2014). Dynamics of an Interactive Network Composed of a Bacterial Two-Component System, a Transporter and K+ as Mediator. PLoS ONE, 9(2), e89671. https://doi.org/10.1371/journal.pone.0089671

Penas, D. R., Banga, J. R., González, P., & Doallo, R. (2014). A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), 173–181. https://doi.org/10.1007/978-3-319-07581-5_21

Rodriguez-Fernandez, M., Rehberg, M., Kremling, A., & Banga, J. R. (2013). Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Systems Biology, 7(1). https://doi.org/10.1186/1752-0509-7-76

Rodríez‐Fernáez, M., Alonso, A. A., & Banga, J. R. (2013). Robust Identification in Nonlinear Dynamic Process Models. Taming Heterogeneity and Complexity of Embedded Control, 635–644. Portico. https://doi.org/10.1002/9780470612217.ch35

Becker, K., Balsa-Canto, E., Cicin-Sain, D., Hoermann, A., Janssens, H., Banga, J. R., & Jaeger, J. (2013). Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster. PLoS Computational Biology, 9(10), e1003281. https://doi.org/10.1371/journal.pcbi.1003281

Villaverde, A., Ross, J., & Banga, J. (2013). Reverse Engineering Cellular Networks with Information Theoretic Methods. Cells, 2(2), 306–329. https://doi.org/10.3390/cells2020306

de Hijas-Liste, G. M., Balsa-Canto, E., Banga, J. R., & Kaleta, C. (2013). Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition. 21st Mediterranean Conference on Control and Automation, 237–242. https://doi.org/10.1109/med.2013.6608728

Gábor, A., Hangos, K. M., Szederkényi, G., & Banga, J. R. (2013). On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology. Computational Methods in Systems Biology, 206–219. https://doi.org/10.1007/978-3-642-40708-6_16

Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2013). Correction: Characterizing Multistationarity Regimes in Biochemical Reaction Networks. PLoS ONE, 8(1). https://doi.org/10.1371/annotation/b5283cc5-5a93-4c96-abc4-c5112266fabe

García, M. G., Balsa‐Canto, E., Alonso, A. A., & Banga, J. R. (2013). Dynamic Optimization of Nonlinear Bioreactors. Taming Heterogeneity and Complexity of Embedded Control, 307–327. Portico. https://doi.org/10.1002/9780470612217.ch18

TUZA, Z. A., SZEDERKÉNYI, G., HANGOS, K. M., ALONSO, A. A., & BANGA, J. R. (2013). COMPUTING ALL SPARSE KINETIC STRUCTURES FOR A LORENZ SYSTEM USING OPTIMIZATION. International Journal of Bifurcation and Chaos, 23(08), 1350141. https://doi.org/10.1142/s0218127413501411

Vilas, C., Balsa-Canto, E., Banga, J. R., & Alonso, A. A. (2012). Robust and efficient numerical methods for the optimal control of spatially distributed biological systems. 2012 20th Mediterranean Conference on Control & Automation (MED), 163–168. https://doi.org/10.1109/med.2012.6265632

Rodriguez‐Fernandez, M., Banga, J. R., & 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. International Journal of Robust and Nonlinear Control, 22(10), 1082–1102. Portico. https://doi.org/10.1002/rnc.2797

Higuera, C., Villaverde, A. F., Banga, J. R., Ross, J., & Morán, F. (2012). Multi-Criteria Optimization of Regulation in Metabolic Networks. PLoS ONE, 7(7), e41122. https://doi.org/10.1371/journal.pone.0041122

Vilas, C., Balsa-Canto, E., García, M.-S. G., Banga, J. R., & Alonso, A. A. (2012). Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. BMC Systems Biology, 6(1). https://doi.org/10.1186/1752-0509-6-79

Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2012). Characterizing Multistationarity Regimes in Biochemical Reaction Networks. PLoS ONE, 7(7), e39194. https://doi.org/10.1371/journal.pone.0039194

Szederkényi, 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. https://doi.org/10.1093/bioinformatics/bts171

Villaverde, A. F., Egea, J. A., & Banga, J. R. (2012). A cooperative strategy for parameter estimation in large scale systems biology models. BMC Systems Biology, 6(1). https://doi.org/10.1186/1752-0509-6-75

Villaverde, A. F., Ross, J., Morán, F., Balsa-Canto, E., & Banga, J. R. (2011). Use of a Generalized Fisher Equation for Global Optimization in Chemical Kinetics. The Journal of Physical Chemistry A, 115(30), 8426–8436. https://doi.org/10.1021/jp203158r

Chis, O.-T., Banga, J. R., & Balsa-Canto, E. (2011). Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PLoS ONE, 6(11), e27755. https://doi.org/10.1371/journal.pone.0027755

De Hijas-Liste, G. M., Balsa-Canto, E., & Banga, J. R. (2011). Prediction of activation of metabolic pathways via dynamic optimization. 21st European Symposium on Computer Aided Process Engineering, 1386–1390. https://doi.org/10.1016/b978-0-444-54298-4.50056-8

Chis, O., Banga, J. R., & Balsa-Canto, E. (2011). Methods for checking structural identifiability of nonlinear biosystems: A critical comparison. IFAC Proceedings Volumes, 44(1), 10585–10590. https://doi.org/10.3182/20110828-6-it-1002.00800

Uhr, M., Villaverde, A. F., Egea, J. A., Banga, J. R., & Stelling, J. (2011). Inference of Transcriptional Control Design of Metabolic Networks. IFAC Proceedings Volumes, 44(1), 10448–10453. https://doi.org/10.3182/20110828-6-it-1002.01588

Szederkényi, G., Banga, J. R., & Alonso, A. A. (2011). Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Systems Biology, 5(1), 177. https://doi.org/10.1186/1752-0509-5-177

Chiş, O., Banga, J. R., & Balsa-Canto, E. (2011). GenSSI: a software toolbox for structural identifiability analysis of biological models. Bioinformatics, 27(18), 2610–2611. https://doi.org/10.1093/bioinformatics/btr431

Nicolaï, 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. https://doi.org/10.1016/j.jfoodeng.2010.09.017

Rodriguez-Fernandez, M., Cardelle-Cobas, A., Villamiel, M., & Banga, J. R. (2011). Detailed kinetic model describing new oligosaccharides synthesis using different β-galactosidases. Journal of Biotechnology, 153(3–4), 116–124. https://doi.org/10.1016/j.jbiotec.2011.03.012

Balsa-Canto, E., & Banga, J. R. (2011). AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinformatics, 27(16), 2311–2313. https://doi.org/10.1093/bioinformatics/btr370

Kothare, M. V., & Banga, J. R. (2011). 9th IFAC International Symposium on Dynamics and Control of Process Systems (DYCOPS) & 11th IFAC International Symposium on Computer Applications in Biotechnology (CAB). Journal of Process Control, 21(10), 1359–1360. https://doi.org/10.1016/j.jprocont.2011.10.009

Balsa-Canto, E., Banga, J. R., Egea, J. A., Fernandez-Villaverde, A., & de Hijas-Liste, G. M. (2011). Global Optimization in Systems Biology: Stochastic Methods and Their Applications. Advances in Systems Biology, 409–424. https://doi.org/10.1007/978-1-4419-7210-1_24

Rodriguez-Fernandez, M., & Banga, J. R. (2010). SensSB: a software toolbox for the development and sensitivity analysis of systems biology models. Bioinformatics, 26(13), 1675–1676. https://doi.org/10.1093/bioinformatics/btq242

Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2010). Parametric Condition for Multistationarity in Biochemical Reaction Networks*. IFAC Proceedings Volumes, 43(6), 30–35. https://doi.org/10.3182/20100707-3-be-2012.0008

Sendín, J. O. H., Exler, O., & Banga, J. R. (2010). Multi-objective mixed integer strategy for the optimisation of biological networks. IET Systems Biology, 4(3), 236–248. https://doi.org/10.1049/iet-syb.2009.0045

Vera, J., Rath, O., Balsa-Canto, E., Banga, J. R., Kolch, W., & Wolkenhauer, O. (2010). Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models. Molecular BioSystems, 6(11), 2174. https://doi.org/10.1039/c0mb00018c

Sendín, 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. https://doi.org/10.1016/j.jfoodeng.2010.01.007

Balsa-Canto, E., & Banga, J. R. (2010). Computational Procedures for Model Identification. Systems Biology for Signaling Networks, 111–137. https://doi.org/10.1007/978-1-4419-5797-9_5

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2010). An iterative identification procedure for dynamic modeling of biochemical networks. BMC Systems Biology, 4(1). https://doi.org/10.1186/1752-0509-4-11

Egea, J. A., Martí, R., & Banga, J. R. (2010). An evolutionary method for complex-process optimization. Computers & Operations Research, 37(2), 315–324. https://doi.org/10.1016/j.cor.2009.05.003

Balsa-Canto, E., & Banga, J. R. (2010). AMIGO: A model identification toolbox based on global optimization and its applications in biosystems. IFAC Proceedings Volumes, 43(6), 132–137. https://doi.org/10.3182/20100707-3-be-2012.0053

Ross, J., Villaverde, A. F., Banga, J. R., Vázquez, S., & Morán, F. (2010). A generalized Fisher equation and its utility in chemical kinetics. Proceedings of the National Academy of Sciences, 107(29), 12777–12781. https://doi.org/10.1073/pnas.1008257107

Georgiadis, M. C., Banga, J. R., & Pistikopoulos, E. N. (Eds.). (2010). Process Systems Engineering. https://doi.org/10.1002/9783527631339

Front Matter: Volume 7: Dynamic Process Modeling. (2010). Process Systems Engineering. Portico. https://doi.org/10.1002/9783527631209.fmatter7

Sendín, J.-O. H., Banga, J. R., & Csendes, T. (2009). Extensions of a Multistart Clustering Algorithm for Constrained Global Optimization Problems. Industrial & Engineering Chemistry Research, 48(6), 3014–3023. https://doi.org/10.1021/ie800319m

Schlüter, M., Egea, J. A., & Banga, J. R. (2009). Extended ant colony optimization for non-convex mixed integer nonlinear programming. Computers & Operations Research, 36(7), 2217–2229. https://doi.org/10.1016/j.cor.2008.08.015

Otero‐Muras, I., Banga, J. R., & Alonso, A. A. (2009). Exploring multiplicity conditions in enzymatic reaction networks. Biotechnology Progress, 25(3), 619–631. Portico. https://doi.org/10.1002/btpr.112

Egea, J. A., Balsa-Canto, E., García, M.-S. G., & Banga, J. R. (2009). Dynamic Optimization of Nonlinear Processes with an Enhanced Scatter Search Method. Industrial & Engineering Chemistry Research, 48(9), 4388–4401. https://doi.org/10.1021/ie801717t

Hirmajer, T., Balsa-Canto, E., & Banga, J. R. (2009). DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinformatics, 10(1). https://doi.org/10.1186/1471-2105-10-199

Schlüter, M., Egea, J. A., Antelo, L. T., Alonso, A. A., & Banga, J. R. (2009). An Extended Ant Colony Optimization Algorithm for Integrated Process and Control System Design. Industrial & Engineering Chemistry Research, 48(14), 6723–6738. https://doi.org/10.1021/ie8016785

Vilas, C., García, M. R., Banga, J. R., & Alonso, A. A. (2008). Robust feed-back control of travelling waves in a class of reaction–diffusion distributed biological systems. Physica D: Nonlinear Phenomena, 237(18), 2353–2364. https://doi.org/10.1016/j.physd.2008.02.019

Banga, J. R., Balsa‐Canto, E., & Alonso, A. A. (2008). Quality and Safety Models and Optimization as Part of Computer‐Integrated Manufacturing. Comprehensive Reviews in Food Science and Food Safety, 7(1), 168–174. Portico. https://doi.org/10.1111/j.1541-4337.2007.00023.x

Banga, J. R., & Balsa-Canto, E. (2008). Parameter estimation and optimal experimental design. Essays in Biochemistry, 45, 195–210. https://doi.org/10.1042/bse0450195

Banga, J. R. (2008). Optimization in computational systems biology. BMC Systems Biology, 2(1). https://doi.org/10.1186/1752-0509-2-47

Scheerlinck, N., Berhane, N. H., Moles, C. G., Banga, J. R., & Nicolaï, B. M. (2008). Optimal dynamic heat generation profiles for simultaneous estimation of thermal food properties using a hotwire probe: Computation, implementation and validation. Journal of Food Engineering, 84(2), 297–306. https://doi.org/10.1016/j.jfoodeng.2007.05.019

Antelo, L. T., Exler, O., Banga, J. R., & Alonso, A. A. (2008). Optimal tuning of thermodynamic‐based decentralized PI control loops: Application to the Tennessee Eastman Process. AIChE Journal, 54(11), 2904–2924. Portico. https://doi.org/10.1002/aic.11588

Balsa-Canto, E., Peifer, M., Banga, J. R., Timmer, J., & Fleck, C. (2008). Hybrid optimization method with general switching strategy for parameter estimation. BMC Systems Biology, 2(1). https://doi.org/10.1186/1752-0509-2-26

Antelo, L. T., Banga, J. R., & Alonso, A. A. (2008). Hierarchical design of decentralized control structures for the Tennessee Eastman Process. Computers & Chemical Engineering, 32(9), 1995–2015. https://doi.org/10.1016/j.compchemeng.2007.10.021

García, M. R., Vilas, C., Banga, J. R., & Alonso, A. A. (2008). Exponential observers for distributed tubular (bio)reactors. AIChE Journal, 54(11), 2943–2956. Portico. https://doi.org/10.1002/aic.11571

Vilas, C., García, M. R., Banga, J. R., & Alonso, A. A. (2008). Desarrollo De Una Librería De Componentes En Ecosimpro Para La Operación De Plantas De Procesamiento Térmico De Alimentos. Revista Iberoamericana de Automática e Informática Industrial RIAI, 5(1), 51–65. https://doi.org/10.1016/s1697-7912(08)70123-7

BALSA‐CANTO, E., ALONSO, A. A., & BANGA, J. R. (2008). COMPUTING OPTIMAL DYNAMIC EXPERIMENTS FOR MODEL CALIBRATION IN PREDICTIVE MICROBIOLOGY. Journal of Food Process Engineering, 31(2), 186–206. Portico. https://doi.org/10.1111/j.1745-4530.2007.00147.x

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2008). Computational procedures for optimal experimental design in biological systems. IET Systems Biology, 2(4), 163–172. https://doi.org/10.1049/iet-syb:20070069

Exler, O., Antelo, L. T., Egea, J. A., Alonso, A. A., & Banga, J. R. (2008). A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design. Computers & Chemical Engineering, 32(8), 1877–1891. https://doi.org/10.1016/j.compchemeng.2007.10.008

Vilas, C., García, M. R., Banga, J. R., & Alonso, A. A. (2008). A LIBRARY OF SOFTWARE COMPONENTS FOR THE OPERATION OF THERMAL FOOD PROCESSING PLANTS. Acta Horticulturae, 802, 141–146. https://doi.org/10.17660/actahortic.2008.802.16

Cortie, M. B. (2007). Welcome and introduction. Materials Science and Engineering: B, 140(3), 137. https://doi.org/10.1016/j.mseb.2007.03.012

Vilas, C., García, M. R., Banga, J. R., & Alonso, A. A. (2007). Robust feed-back control of distributed chemical reaction systems. Chemical Engineering Science, 62(11), 2941–2957. https://doi.org/10.1016/j.ces.2007.02.042

Vera, J., Balsa-Canto, E., Wellstead, P., Banga, J. R., & Wolkenhauer, O. (2007). Power-law models of signal transduction pathways. Cellular Signalling, 19(7), 1531–1541. https://doi.org/10.1016/j.cellsig.2007.01.029

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2007). OPTIMAL DYNAMIC EXPERIMENTAL DESIGN IN SYSTEMS BIOLOGY: APPLICATIONS IN CELL SIGNALING. IFAC Proceedings Volumes, 40(4), 73–78. https://doi.org/10.3182/20070604-3-mx-2914.00081

Balsa-Canto, E., Rodriguez-Fernandez, M., & Banga, J. R. (2007). Optimal design of dynamic experiments for improved estimation of kinetic parameters of thermal degradation. Journal of Food Engineering, 82(2), 178–188. https://doi.org/10.1016/j.jfoodeng.2007.02.006

García, M.-S. G., Balsa-Canto, E., Wouwer, A. V., & Banga, J. R. (2007). OPTIMAL CONTROL of the SIMULATED MOVING BED (SMB) CHROMATOGRAPHIC SEPARATION PROCESS. IFAC Proceedings Volumes, 40(5), 183–188. https://doi.org/10.3182/20070606-3-mx-2915.00029

Antelo, L. T., Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2007). La teoría de redes en ingeniería de control: aplicación al análisis dinámico y al control de procesos. Revista Iberoamericana de Automática e Informática Industrial RIAI, 4(1), 24–34. https://doi.org/10.1016/s1697-7912(07)70189-9

Ellaia, R., El Mouatasim, A., Banga, J. R., & Sendin, O. H. (2007). NBI-RPRGM for Multi-objective Optimization Design of Bio-Processes. ESAIM: Proceedings, 20, 118–128. https://doi.org/10.1051/proc:072011

Rodríguez-Fernández, M., Balsa-Canto, E., Egea, J. A., & Banga, J. R. (2007). Identifiability and robust parameter estimation in food process modeling: Application to a drying model. Journal of Food Engineering, 83(3), 374–383. https://doi.org/10.1016/j.jfoodeng.2007.03.023

Csendes, T., Pál, L., Sendín, J. O. H., & Banga, J. R. (2007). The GLOBAL optimization method revisited. Optimization Letters, 2(4), 445–454. https://doi.org/10.1007/s11590-007-0072-3

Egea, J. A., Vazquez, E., Banga, J. R., & Martí, R. (2007). Improved scatter search for the global optimization of computationally expensive dynamic models. Journal of Global Optimization, 43(2–3), 175–190. https://doi.org/10.1007/s10898-007-9172-y

Rodriguez-Fernandez, M., Mendes, P., & Banga, J. R. (2006). A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems, 83(2–3), 248–265. https://doi.org/10.1016/j.biosystems.2005.06.016

Vilas, C., García, M. R., Banga, J. R., & Alonso, A. A. (2006). Stabilization of inhomogeneous patterns in a diffusion–reaction system under structural and parametric uncertainties. Journal of Theoretical Biology, 241(2), 295–306. https://doi.org/10.1016/j.jtbi.2005.11.030

Palerm, C. C., Rodriguez-Fernandez, M., Bevier, W. C., Zisser, H., Banga, J. R., Jovanovic, L., & Doyle, F. J. (2006). Robust Parameter Estimation in a Model for Glucose Kinetics in Type 1 Diabetes Subjects. 2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 319–322. https://doi.org/10.1109/iembs.2006.260045

Rodriguez-Fernandez, M., Egea, J. A., & Banga, J. R. (2006). Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-483

Sendín, O. H., Vera, J., Torres, N. V., & Banga, J. R. (2006). Model based optimization of biochemical systems using multiple objectives: a comparison of several solution strategies. Mathematical and Computer Modelling of Dynamical Systems, 12(5), 469–487. https://doi.org/10.1080/13873950600723442

Sendín, J.-O. H., Otero-Muras, I., Alonso, A. A., & Banga, J. R. (2006). Improved Optimization Methods for the Multiobjective Design of Bioprocesses. Industrial & Engineering Chemistry Research, 45(25), 8594–8603. https://doi.org/10.1021/ie0605433

García, M.-S. G., Balsa-Canto, E., Banga, J. R., & Vande Wouwer, A. (2006). Dynamic Optimization of a Simulated Moving Bed (SMB) Chromatographic Separation Process. Industrial & Engineering Chemistry Research, 45(26), 9033–9041. https://doi.org/10.1021/ie060576i

García, M.-S. G., Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2006). Computing optimal operating policies for the food industry. Journal of Food Engineering, 74(1), 13–23. https://doi.org/10.1016/j.jfoodeng.2005.02.011

Antelo, L. T., Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2006). A thermodynamic based plant-wide control design procedure of the tennessee eastman process. 16th European Symposium on Computer Aided Process Engineering and 9th International Symposium on Process Systems Engineering, 1413–1418. https://doi.org/10.1016/s1570-7946(06)80245-2

Egea, J. A., Rodríguez-Fernández, M., Banga, J. R., & Martí, R. (2006). Scatter search for chemical and bio-process optimization. Journal of Global Optimization, 37(3), 481–503. https://doi.org/10.1007/s10898-006-9075-3

García, M. R., Vilas, C., Banga, J. R., & Alonso, A. A. (2006). Optimal Field Reconstruction of Distributed Process Systems from Partial Measurements. Industrial & Engineering Chemistry Research, 46(2), 530–539. https://doi.org/10.1021/ie0604167

Rodríguez-Fernández, M., Alonso, A. A., & Banga, J. R. (2005). Robust parameter estimation in nonlinear dynamic process models. European Symposium on Computer-Aided Process Engineering-15, 38th European Symposium of the Working Party on Computer Aided Process Engineering, 37–42. https://doi.org/10.1016/s1570-7946(05)80128-2

Balsa-Canto, E., Vassiliadis, V. S., & Banga, J. R. (2005). Dynamic Optimization of Single- and Multi-Stage Systems Using a Hybrid Stochastic−Deterministic Method. Industrial & Engineering Chemistry Research, 44(5), 1514–1523. https://doi.org/10.1021/ie0493659

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2005). Dynamic Optimization of Complex Distributed Process Systems. Chemical Engineering Research and Design, 83(6), 724–729. https://doi.org/10.1205/cherd.04378

Banga, J. R., Balsa-Canto, E., Moles, C. G., & Alonso, A. A. (2005). Dynamic optimization of bioprocesses: Efficient and robust numerical strategies. Journal of Biotechnology, 117(4), 407–419. https://doi.org/10.1016/j.jbiotec.2005.02.013

García, M. R., Balsa-Canto, E., Vilas, C., Banga, J. R., & Alonso, A. A. (2005). An efficient real-time dynamic optimization architecture for the control of non-isothermal tubular reactors. European Symposium on Computer-Aided Process Engineering-15, 38th European Symposium of the Working Party on Computer Aided Process Engineering, 1333–1338. https://doi.org/10.1016/s1570-7946(05)80064-1

Antelo, L. T., Otero-Muras, I., Banga, J. R., & Alonso, A. A. (2005). A systematic approach to plant-wide control based on thermodynamics. European Symposium on Computer-Aided Process Engineering-15, 38th European Symposium of the Working Party on Computer Aided Process Engineering, 1105–1110. https://doi.org/10.1016/s1570-7946(05)80026-4

García, M.-S. G., Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2005). A software toolbox for the dynamic optimization of nonlinear processes. European Symposium on Computer-Aided Process Engineering-15, 38th European Symposium of the Working Party on Computer Aided Process Engineering, 121–126. https://doi.org/10.1016/s1570-7946(05)80142-7

Banga, J. R., Moles, C. G., & Alonso, A. A. (2004). Global Optimization of Bioprocesses using Stochastic and Hybrid Methods. Frontiers in Global Optimization, 45–70. https://doi.org/10.1007/978-1-4613-0251-3_3

Moles, C. G., Banga, J. R., & Keller, K. (2004). Solving nonconvex climate control problems: pitfalls and algorithm performances. Applied Soft Computing, 5(1), 35–44. https://doi.org/10.1016/j.asoc.2004.03.011

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2004). Reduced-Order Models for Nonlinear Distributed Process Systems and Their Application in Dynamic Optimization. Industrial & Engineering Chemistry Research, 43(13), 3353–3363. https://doi.org/10.1021/ie049946y

Vilas, C., García, M. R., Fernández, M. R., Balsa-Canto, E., Banga, J. R., & Alonso, A. A. (2004). On systematic model reduction techniques for dynamic optimization and robust control of distributed process systems. European Symposium on Computer-Aided Process Engineering-14, 37th European Symposium of the Working Party on Computer-Aided Process Engineering, 841–846. https://doi.org/10.1016/s1570-7946(04)80206-2

Sendín, O. H., Otero, I., Alonso, A. A., & Banga, J. R. (2004). Multi-objective optimization for the design of bio-processes. European Symposium on Computer-Aided Process Engineering-14, 37th European Symposium of the Working Party on Computer-Aided Process Engineering, 283–288. https://doi.org/10.1016/s1570-7946(04)80113-5

Balsa-Canto, E., Banga, J. R., Alonso, A. A., & Vassiliadis, V. S. (2004). Dynamic Optimization of Distributed Parameter Systems Using Second-Order Directional Derivatives. Industrial & Engineering Chemistry Research, 43(21), 6756–6765. https://doi.org/10.1021/ie0497590

Sendin, O. H., Moles, C. G., Alonso, A. A., & Banga, J. R. (2004). Multi-objective integrated design and control using stochastic global optimization methods. The Integration of Process Design and Control, 555–581. https://doi.org/10.1016/s1570-7946(04)80074-9

Scheerlinck, N., Marquenie, D., Jancsók, P. T., Verboven, P., Moles, C. G., Banga, J. R., & Nicolaı̈, B. M. (2004). A model-based approach to develop periodic thermal treatments for surface decontamination of strawberries. Postharvest Biology and Technology, 34(1), 39–52. https://doi.org/10.1016/j.postharvbio.2004.04.004

Moles, C. G., Mendes, P., & Banga, J. R. (2003). Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods. Genome Research, 13(11), 2467–2474. https://doi.org/10.1101/gr.1262503

Vera, J., Torres, N. V., Moles, C. G., & Banga, J. (2003). Integrated nonlinear optimization of bioprocesses via linear programming. AIChE Journal, 49(12), 3173–3187. Portico. https://doi.org/10.1002/aic.690491217

Banga, J. R., Balsa-Canto, E., Moles, C. G., & Alonso, A. A. (2003). Improving food processing using modern optimization methods. Trends in Food Science & Technology, 14(4), 131–144. https://doi.org/10.1016/s0924-2244(03)00048-7

Moles, C. G., Lieber, A. S., Banga, J. R., & Keller, K. (2003). Global optimization of climate control problems using evolutionary and stochastic algorithms. Advances in Soft Computing, 331–342. https://doi.org/10.1007/978-1-4471-3744-3_32

Zorrilla, S. E., Banga, J. R., & Singh, R. P. (2003). Dynamic optimization of double-sided cooking of meat patties. Journal of Food Engineering, 58(2), 173–182. https://doi.org/10.1016/s0260-8774(02)00342-4

A. Alonso, A., V. Fernandez, C., & R. Banga, J. (2003). Dissipative systems: from physics to robust nonlinear control. International Journal of Robust and Nonlinear Control, 14(2), 157–179. Portico. https://doi.org/10.1002/rnc.868

Alonso, A. A., Kevrekidis, I., Balsa-Canto, E., & Banga, J. R. (2002). ROBUST NONLINEAR CONTROL DESIGN OF DISTRIBUTED PROCESS SYSTEMS WITH INPUT CONSTRAINTS. IFAC Proceedings Volumes, 35(1), 477–482. https://doi.org/10.3182/20020721-6-es-1901.00648

Balsa Canto, E., Banga, J. R., Alonso, A. A., & Vassiliadis, V. S. (2002). Restricted second order information for the solution of optimal control problems using control vector parameterization. Journal of Process Control, 12(2), 243–255. https://doi.org/10.1016/s0959-1524(01)00008-7

Alonso, A. A., Kevrekidis, I., Banga, J. R., & Frouzakis, C. (2002). Optimal Sensor Location and Reduced Order Observer Design for Distributed Process Systems. European Symposium on Computer Aided Process Engineering-12, 35th European Symposium of the Working Party on Computer Aided Process Engineering, 415–420. https://doi.org/10.1016/s1570-7946(02)80097-9

Alonso, A. A., Ydstie, B. E., & Banga, J. R. (2002). From irreversible thermodynamics to a robust control theory for distributed process systems. Journal of Process Control, 12(4), 507–517. https://doi.org/10.1016/s0959-1524(01)00017-8

Banga, J. R., Versyck, K. J., & Van Impe, J. F. (2002). Computation of Optimal Identification Experiments for Nonlinear Dynamic Process Models:  a Stochastic Global Optimization Approach. Industrial & Engineering Chemistry Research, 41(10), 2425–2430. https://doi.org/10.1021/ie010183d

Wäppling-Raaholt, B., ScheerHawk, N., Galt, S., Banga, J. R., Alonso, A., Balsa-Canto, E., Van Impe, J., Ohlsson, T., & Nicolaï, B. M. (2002). A Combined Electromagnetic and Heat Transfer Model for Heating of Foods in Microwave Combination Ovens. Journal of Microwave Power and Electromagnetic Energy, 37(2), 97–111. https://doi.org/10.1080/08327823.2002.11688473

Balsa-Canto, E., Alonso, A. A., & Banga, J. R. (2001). Optimal control of distributed processes using reduced order models. 2001 European Control Conference (ECC), 2511–2516. https://doi.org/10.23919/ecc.2001.7076305

Banga, J. R., Pan, Z., & Singh, R. P. (2001). On the Optimal Control of Contact-Cooking Processes. Food and Bioproducts Processing, 79(3), 145–151. https://doi.org/10.1205/096030801750425235

Moles, C. G., Gutierrez, G., Alonso, A. A., & Banga, J. R. (2001). Integrated process design and control via global optimization: A wastewater treatment plant case study. 2001 European Control Conference (ECC), 2994–2999. https://doi.org/10.23919/ecc.2001.7076389

Sanchez, I., Banga, J. R., & Alonso, A. A. (2000). Temperature control in microwave combination ovens. Journal of Food Engineering, 46(1), 21–29. https://doi.org/10.1016/s0260-8774(00)00065-0

Alonso, A. A., Banga, J. R., & Sanchez, I. (2000). Passive control design for distributed process systems: Theory and applications. AIChE Journal, 46(8), 1593–1606. Portico. https://doi.org/10.1002/aic.690460811

Barton, P. I., Banga, J. R., & Galán, S. (2000). Optimization of hybrid discrete/continuous dynamic systems. Computers & Chemical Engineering, 24(9–10), 2171–2182. https://doi.org/10.1016/s0098-1354(00)00586-x

Banga, J. R., Versyck, K. J., & Van Impe, J. F. (2000). Numerical strategies for optimal experimental design for parameter identification of non-linear dynamic (Bio-)chemical processes. European Symposium on Computer Aided Process Engineering-10, 37–42. https://doi.org/10.1016/s1570-7946(00)80008-5

Balsa-Canto, E., Banga, J. R., Alonso, A. A., & Vassiliadis, V. S. (2000). Efficient Optimal Control of Bioprocesses Using Second-Order Information. Industrial & Engineering Chemistry Research, 39(11), 4287–4295. https://doi.org/10.1021/ie990658p

Vassiliadis, V. S., Canto, E. B., & Banga, J. R. (1999). Second-order sensitivities of general dynamic systems with application to optimal control problems. Chemical Engineering Science, 54(17), 3851–3860. https://doi.org/10.1016/s0009-2509(98)00432-1

Banga, J. R., Irizarry-Rivera, R., & Seider, W. D. (1998). Stochastic optimization for optimal and model-predictive control. Computers & Chemical Engineering, 22(4–5), 603–612. https://doi.org/10.1016/s0098-1354(97)00226-3

Banga, J. R., & Carrasco, E. F. (1998). Rebuttal to the Comments of Rein Luus on “Dynamic Optimization of Batch Reactors Using Adaptive Stochastic Algorithms.” Industrial & Engineering Chemistry Research, 37(1), 306–307. https://doi.org/10.1021/ie970822d

Alonso, A. A., Banga, J. R., & Perez-Martin, R. (1998). Modeling and adaptive control for batch sterilization. Computers & Chemical Engineering, 22(3), 445–458. https://doi.org/10.1016/s0098-1354(97)00250-0

Alonso, A. A., & Banga, J. R. (1998). Design of a Class of Stabilizing Nonlinear State Feedback Controllers with Bounded Inputs. Industrial & Engineering Chemistry Research, 37(1), 131–144. https://doi.org/10.1021/ie9605591

Carrasco, E. F. (1998). A hybrid method for the optimal control of chemical processes. UKACC International Conference on Control (CONTROL ’98), 1998, 925–930. https://doi.org/10.1049/cp:19980352

Carrasco, E. F., & Banga, J. R. (1997). Dynamic Optimization of Batch Reactors Using Adaptive Stochastic Algorithms. Industrial & Engineering Chemistry Research, 36(11), 5047–5047. https://doi.org/10.1021/ie970827a

Alonso, A. A., Banga, J. R., & Perez-Martin, R. (1997). A complete dynamic model for the thermal processing of bioproducts in batch units and its application to controller design. Chemical Engineering Science, 52(8), 1307–1322. https://doi.org/10.1016/s0009-2509(96)00484-8

Banga, J. R., & Seider, W. D. (1996). Global Optimization of Chemical Processes using Stochastic Algorithms. State of the Art in Global Optimization, 563–583. https://doi.org/10.1007/978-1-4613-3437-8_33

Torres, J. A., Bouzas, J., Kirby, C., Almonacid Merino, S. F., Kantt, C. A., Simpson, R., & Banga, J. R. (1995). Time-Temperature Effects on Microbial, Chemical and Sensory Changes During Cooling and Aging of Cheddar Cheese. Chemistry of Structure-Function Relationships in Cheese, 123–159. https://doi.org/10.1007/978-1-4615-1913-3_9

Banga, J. R., Alonso, A. A., Pérez-Martín, R. I., & Paul Singh, R. (1994). Optimal control of heat and mass transfer in food and bioproducts processing. Computers & Chemical Engineering, 18, S699–S705. https://doi.org/10.1016/0098-1354(94)80114-2

Banga, J. R., & Paul Singh, R. (1994). Optimization of air drying of foods. Journal of Food Engineering, 23(2), 189–211. https://doi.org/10.1016/0260-8774(94)90086-8

Banga, J. R., Pérez-Martín, R. I., & Singh, R. P. (1994). ICRS/DS: A Computer Package for the Optimization of Batch Processes and its Applications in Food Processing. Developments in Food Engineering, 730–732. https://doi.org/10.1007/978-1-4615-2674-2_237

Alonso, A. A., Banga, J. R., & Perez-Martin, R. I. (1994). Different Strategies for Controlling Pressure during the Cooling Stage in Batch Retorts. Developments in Food Engineering, 724–726. https://doi.org/10.1007/978-1-4615-2674-2_235

Banga, J. R., Alonso, A. A., Gallardo, J. M., & Perez-Martín, R. I. (1994). Computer Aided Design and Optimization of Sterilization of Canned Tuna. Developments in Food Engineering, 721–723. https://doi.org/10.1007/978-1-4615-2674-2_234

Banga, J. R., Alonso, A. A., Gallardo, J. M., & Perez-Martin, R. I. (1993). Mathematical modelling and simulation of the thermal processing of anisotropic and non-homogeneous conduction-heated canned foods: Application to canned tuna. Journal of Food Engineering, 18(4), 369–387. https://doi.org/10.1016/0260-8774(93)90053-m

Banga, J. R., Alonso, A. A., Gallardo, J. M., & P�rez-Mart�n, R. I. (1993). Kinetics of thermal degradation of thiamine and surface colour in canned tuna. Zeitschrift F�r Lebensmittel-Untersuchung Und -Forschung, 197(2), 127–131. https://doi.org/10.1007/bf01260307

BANGA, J. R., ALONSO, A. A., GALLARDO, J. M., & PEREZ‐MARTIN, R. I. (1992). Degradation Kinetics of Protein Digestibility and Available Lysine During Thermal Processing of Tuna. Journal of Food Science, 57(4), 913–915. Portico. https://doi.org/10.1111/j.1365-2621.1992.tb14321.x

Perez-Mart�n, R. I., Gallardo, J. M., Banga, J. R., & Casares, J. (1989). Determination of thermal conductivity, specific heat and thermal diffusivity of albacore (Thunnus alalunga). Zeitschrift F�r Lebensmittel-Untersuchung Und -Forschung, 189(6), 525–529. https://doi.org/10.1007/bf01274270

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Garcia, M. R., Vilas, C., Banga, J. R., Lyubenova, V. N., Ignatova, M. N., & Alonso, A. A. (n.d.). State Reconstruction in Spatially Distributed BioProcess Systems using Reduced Order Models: Application to the Gluconic Acid Production. Proceedings of the 44th IEEE Conference on Decision and Control, 6256–6261. https://doi.org/10.1109/cdc.2005.1583164

Egea, J. A., Vries, D., Alonso, A. A., & Banga, J. R. (n.d.). Global Optimization for Integrated Design and Control of Computationally Expensive Process Models. Proceedings of the 44th IEEE Conference on Decision and Control, 6899–6904. https://doi.org/10.1109/cdc.2005.1583272

Technology and society. (n.d.). Energy, Society and Environment, 3. https://doi.org/10.4324/9780203183168_chapter_1

Sendín, J.-O. H., Alonso, A. A., & Banga, J. R. (n.d.). Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), 197–205. https://doi.org/10.1007/978-3-540-85861-4_24

Rodriguez-Fernandez, M., & Banga, J. R. (n.d.). Global Sensitivity Analysis of a Biochemical Pathway Model. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), 233–242. https://doi.org/10.1007/978-3-540-85861-4_28