Optimal control of distributed processes using reduced order models. - Eva Balsa-Canto; Antonio A. Alonso; Julio R. Banga (ECC, 2001)

Integrated process design and control via global optimization: A wastewater treatment plant case study. - Carmen G. Moles; G. Gutierrez; Antonio A. Alonso; Julio R. Banga (ECC, 2001)

Solving nonconvex climate control problems: pitfalls and algorithm performances. - Carmen G. Moles; Julio R. Banga; Klaus Keller (Appl. Soft Comput., 2004)

Optimal sensor location and reduced order observer design for distributed process systems. - Antonio A. Alonso; Ioannis G. Kevrekidis; Julio R. Banga; Christos E. Frouzakis (Comput. Chem. Eng., 2004)

Global Optimization for Integrated Design and Control of Computationally Expensive Process Models. - Jose A. Egea; Dirk Vries; Antonio A. Alonso; Julio R. Banga (CDC/ECC, 2005)

State Reconstruction in Spatially Distributed BioProcess Systems using Reduced Order Models: Application to the Gluconic Acid Production. - Míriam R. García; Carlos Vilas; Julio R. Banga; Velislava N. Lyubenova; Maya N. Ignatova; Antonio A. Alonso (CDC/ECC, 2005)

Robust Parameter Estimation in a Model for Glucose Kinetics in Type 1 Diabetes Subjects. - Cesar C. Palerm; Maria Rodriguez-Fernandez; Wendy C. Bevier; Howard C. Zisser; Julio R. Banga; Lois Jovanovic; Francis J. Doyle (EMBC, 2006)

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. - Maria Rodriguez-Fernandez; Jose A. Egea; Julio R. Banga (BMC Bioinform., 2006)

A systematic approach to plant-wide control based on thermodynamics. - Luis T. Antelo; Irene Otero-Muras; Julio R. Banga; Antonio A. Alonso (Comput. Chem. Eng., 2007)

Scatter search for chemical and bio-process optimization. - Jose A. Egea; Maria Rodriguez-Fernandez; Julio R. Banga; Rafael Martí (J. Glob. Optim., 2007)

Global Sensitivity Analysis of a Biochemical Pathway Model. - Maria Rodriguez-Fernandez; Julio R. Banga (IWPACBB, 2008)

Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes. - José-Oscar H. Sendín; Antonio A. Alonso; Julio R. Banga (IWPACBB, 2008)

Hybrid optimization method with general switching strategy for parameter estimation. - Eva Balsa-Canto; Martin Peifer; Julio R. Banga; Jens Timmer; Christian Fleck 001 (BMC Syst. Biol., 2008)

Optimization in computational systems biology. - Julio R. Banga (BMC Syst. Biol., 2008)

Hierarchical design of decentralized control structures for the Tennessee Eastman Process. - Luis T. Antelo; Julio R. Banga; Antonio A. Alonso (Comput. Chem. Eng., 2008)

A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design. - Oliver Exler; Luis T. Antelo; Jose A. Egea; Antonio A. Alonso; Julio R. Banga (Comput. Chem. Eng., 2008)

The GLOBAL optimization method revisited. - Tibor Csendes; László Pál; José-Oscar H. Sendín; Julio R. Banga (Optim. Lett., 2008)

DOTcvpSB, a software toolbox for dynamic optimization in systems biology. - Tomás Hirmajer; Eva Balsa-Canto; Julio R. Banga (BMC Bioinform., 2009)

Extended ant colony optimization for non-convex mixed integer nonlinear programming. - Martin Schlüter; Jose A. Egea; Julio R. Banga (Comput. Oper. Res., 2009)

Improved scatter search for the global optimization of computationally expensive dynamic models. - Jose A. Egea; Emmanuel Vázquez; Julio R. Banga; Rafael Martí (J. Glob. Optim., 2009)

Dynamic Optimization of Chemical and Bio-chemical Processes using an Efficient Global Optimization Metaheuristic. - Jose A. Egea; Eva Balsa-Canto; Julio R. Banga (Simul. Notes Eur., 2009)

SensSB: a software toolbox for the development and sensitivity analysis of systems biology models. - Maria Rodriguez-Fernandez; Julio R. Banga (Bioinform., 2010)

An iterative identification procedure for dynamic modeling of biochemical networks. - Eva Balsa-Canto; Antonio A. Alonso; Julio R. Banga (BMC Syst. Biol., 2010)

An evolutionary method for complex-process optimization. - Jose A. Egea; Rafael Martí; Julio R. Banga (Comput. Oper. Res., 2010)

AMIGO, a toolbox for advanced model identification in systems biology using global optimization. - Eva Balsa-Canto; Julio R. Banga (Bioinform., 2011)

GenSSI: a software toolbox for structural identifiability analysis of biological models. - Oana Chis; Julio R. Banga; Eva Balsa-Canto (Bioinform., 2011)

Inference of complex biological networks: distinguishability issues and optimization-based solutions. - Gábor Szederkényi; Julio R. Banga; Antonio A. Alonso (BMC Syst. Biol., 2011)

CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. - Gábor Szederkényi; Julio R. Banga; Antonio A. Alonso (Bioinform., 2012)

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. - Carlos Vilas; Eva Balsa-Canto; Maria-Sonia G. García; Julio R. Banga; Antonio A. Alonso (BMC Syst. Biol., 2012)

A cooperative strategy for parameter estimation in large scale systems biology models. - Alejandro Fernández Villaverde; Jose A. Egea; Julio R. Banga (BMC Syst. Biol., 2012)

On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology. - Attila Gábor; Katalin M. Hangos; Gábor Szederkényi; Julio R. Banga (CMSB, 2013)

Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition. - Gundián M. de Hijas-Liste; Eva Balsa-Canto; Julio R. Banga; Christoph Kaleta (MED, 2013)

Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. - Maria Rodriguez-Fernandez; Markus Rehberg; Andreas Kremling; Julio R. Banga (BMC Syst. Biol., 2013)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Julio R. Banga; Julio Saez-Rodriguez (CoRR, 2013)

Computing All Sparse kinetic Structures for a Lorenz System using Optimization. - Zoltán András Tuza; Gábor Szederkényi; Katalin M. Hangos; Antonio A. Alonso; Julio R. Banga (Int. J. Bifurc. Chaos, 2013)

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster. - Kolja Becker; Eva Balsa-Canto; Damjan Cicin-Sain; Astrid Hoermann; Hilde Janssens; Julio R. Banga; Johannes Jaeger (PLoS Comput. Biol., 2013)

Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. - Attila Gábor; Julio R. Banga (CMSB, 2014)

Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. - Irene Otero-Muras; Julio R. Banga (CMSB, 2014)

A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems. - David R. Penas; Julio R. Banga; Patricia González; Ramon Doallo (PACBB, 2014)

High-Confidence Predictions in Systems Biology Dynamic Models. - Alejandro Fernández Villaverde; Sophia Bongard; Klaus Mauch; Dirk Müller 004; Eva Balsa-Canto; Joachim Schmid 004; Julio R. Banga (PACBB, 2014)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Aidan MacNamara; Diana-Patricia Danciu; Julio R. Banga; Julio Saez-Rodriguez (BMC Bioinform., 2014)

Global dynamic optimization approach to predict activation in metabolic pathways. - Gundián M. de Hijas-Liste; Edda Klipp; Eva Balsa-Canto; Julio R. Banga (BMC Syst. Biol., 2014)

Multicriteria global optimization for biocircuit design. - Irene Otero-Muras; Julio R. Banga (BMC Syst. Biol., 2014)

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. - Alejandro Fernández Villaverde; David Henriques; Kieran Smallbone; Sophia Bongard; Joachim Schmid 004; Damjan Cicin-Sain; Anton Crombach; Julio Saez-Rodriguez; Klaus Mauch; Eva Balsa-Canto; Pedro Mendes 001; Johannes Jaeger; et al. (CoRR, 2014)

Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. - David R. Penas; Patricia González; Jose A. Egea; Julio R. Banga; Ramon Doallo (ICCS, 2015)

Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. - David R. Penas; Julio R. Banga; Patricia González; Ramon Doallo (Appl. Soft Comput., 2015)

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. - David Henriques; Miguel Rocha 001; Julio Saez-Rodriguez; Julio R. Banga (Bioinform., 2015)

Enabling network inference methods to handle missing data and outliers. - Abel Folch-Fortuny; Alejandro Fernández Villaverde; Alberto Ferrer 001; Julio R. Banga (BMC Bioinform., 2015)

Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. - Gundián M. de Hijas-Liste; Eva Balsa-Canto; Jan Ewald; Martin Bartl; Pu Li 001; Julio R. Banga; Christoph Kaleta (BMC Bioinform., 2015)

Robust and efficient parameter estimation in dynamic models of biological systems. - Attila Gábor; Julio R. Banga (BMC Syst. Biol., 2015)

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. - Alejandro Fernández Villaverde; David Henriques; Kieran Smallbone; Sophia Bongard; Joachim Schmid 004; Damjan Cicin-Sain; Anton Crombach; Julio Saez-Rodriguez; Klaus Mauch; Eva Balsa-Canto; Pedro Mendes 001; Johannes Jaeger; et al. (BMC Syst. Biol., 2015)

A consensus approach for estimating the predictive accuracy of dynamic models in biology. - Alejandro Fernández Villaverde; Sophia Bongard; Klaus Mauch; Dirk Müller 004; Eva Balsa-Canto; Joachim Schmid 004; Julio R. Banga (Comput. Methods Programs Biomed., 2015)

PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. - Alejandro Fernández Villaverde; Kolja Becker; Julio R. Banga (CMSB, 2016)

Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark. - Diego Teijeiro; Xoán C. Pardo; David R. Penas; Patricia González; Julio R. Banga; Ramón Doallo (Euro-Par Workshops, 2016)

Implementing Parallel Differential Evolution on Spark. - Diego Teijeiro; Xoán C. Pardo; Patricia González; Julio R. Banga; Ramón Doallo (EvoApplications (2), 2016)

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology. - Eva Balsa-Canto; David Henriques; Attila Gábor; Julio R. Banga (Bioinform., 2016)

SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. - Irene Otero-Muras; David Henriques; Julio R. Banga (Bioinform., 2016)

Using the Cloud for parameter estimation problems: comparing Spark vs MPI with a case-study. - Patricia González; Xoán C. Pardo; David R. Penas; Diego Teijeiro; Julio R. Banga; Ramón Doallo (CCGrid, 2017)

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. - David R. Penas; Patricia González; Jose A. Egea; Ramón Doallo; Julio R. Banga (BMC Bioinform., 2017)

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. - Attila Gábor; Alejandro Fernández Villaverde; Julio R. Banga (BMC Syst. Biol., 2017)

A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology. - Diego Teijeiro; Xoán C. Pardo; David R. Penas; Patricia González; Julio R. Banga; Ramón Doallo (Clust. Comput., 2017)

Dynamical compensation in biological systems as a particular case of structural non-identifiability. - Alejandro Fernández Villaverde; Julio R. Banga (CoRR, 2017)

Dynamical compensation and structural identifiability: analysis, implications, and reconciliation. - Alejandro Fernández Villaverde; Julio R. Banga (CoRR, 2017)

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. - David Henriques; Alejandro Fernández Villaverde; Miguel Rocha 001; Julio Saez-Rodriguez; Julio R. Banga (PLoS Comput. Biol., 2017)

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. - Alejandro Fernández Villaverde; Julio R. Banga (PLoS Comput. Biol., 2017)

Multimethod Optimization for Reverse Engineering of Complex Biological Networks. - Patricia González; David R. Penas; Xoán C. Pardo; Julio R. Banga; Ramón Doallo (PBio@EuroMPI, 2018)

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. - Thomas S. Ligon; Fabian Fröhlich; Oana Chis; Julio R. Banga; Eva Balsa-Canto; Jan Hasenauer (Bioinform., 2018)

Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. - Nikolaos Tsiantis; Eva Balsa-Canto; Julio R. Banga (Bioinform., 2018)

Multimethod optimization in the cloud: A case-study in systems biology modelling. - Patricia González; David R. Penas; Xoán C. Pardo; Julio R. Banga; Ramón Doallo (Concurr. Comput. Pract. Exp., 2018)

Towards cloud-based parallel metaheuristics. - Diego Teijeiro; Xoán C. Pardo; Patricia González; Julio R. Banga; Ramón Doallo (Int. J. High Perform. Comput. Appl., 2018)

Implementing cloud-based parallel metaheuristics: an overview. - Patricia González; Xoán C. Pardo; Ramón Doallo; Julio R. Banga (J. Comput. Sci. Technol., 2018)

PREMER: A Tool to Infer Biological Networks. - Alejandro Fernández Villaverde; Kolja Becker; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Benchmarking optimization methods for parameter estimation in large kinetic models. - Alejandro Fernández Villaverde; Fabian Fröhlich; Daniel Weindl; Jan Hasenauer; Julio R. Banga (Bioinform., 2019)

Parameter estimation in models of biological oscillators: an automated regularised estimation approach. - Jake Alan Pitt; Julio R. Banga (BMC Bioinform., 2019)

Input-Dependent Structural Identifiability of Nonlinear Systems. - Alejandro Fernández Villaverde; Neil D. Evans; Michael J. Chappell; Julio R. Banga (IEEE Control. Syst. Lett., 2019)

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. - Patricia González; Pablo Argüeso-Alejandro; David R. Penas; Xoán C. Pardo; Julio Saez-Rodriguez; Julio R. Banga; Ramón Doallo (J. Supercomput., 2019)

Using optimal control to understand complex metabolic pathways. - Nikolaos Tsiantis; Julio R. Banga (BMC Bioinform., 2020)

Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. - Gemma Massonis; Julio R. Banga; Alejandro Fernández Villaverde (CoRR, 2020)

Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment. - Xoán C. Pardo; Pablo Argüeso-Alejandro; Patricia González; Julio R. Banga; Ramón Doallo (Swarm Evol. Comput., 2020)

Structural identifiability and observability of compartmental models of the COVID-19 pandemic. - Gemma Massonis; Julio R. Banga; Alejandro Fernández Villaverde (Annu. Rev. Control., 2021)

PEtab - Interoperable specification of parameter estimation problems in systems biology. - Leonard Schmiester; Yannik Schälte; Frank T. Bergmann; Tacio Camba; Erika Dudkin; Janine Egert; Fabian Fröhlich; Lara Fuhrmann; Adrian L. Hauber; Svenja Kemmer; Polina A. Lakrisenko; Carolin Loos; et al. (PLoS Comput. Biol., 2021)

An efficient ant colony optimization framework for HPC environments. - Patricia González; Roberto R. Osorio; Xoán C. Pardo; Julio R. Banga; Ramón Doallo (Appl. Soft Comput., 2022)

A protocol for dynamic model calibration. - Alejandro F. Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R. Banga (Briefings Bioinform., 2022)

Parallel ant colony optimization for the training of cell signaling networks. - Patricia González; Roberto Prado-Rodriguez; Attila Gábor; Julio Saez-Rodriguez; Julio R. Banga; Ramón Doallo (Expert Syst. Appl., 2022)

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants. - Ahmed Taha; Mauricio Patón; David R. Penas; Julio R. Banga; Jorge Rodríguez (PLoS Comput. Biol., 2023)

Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems. - Carlos Sequeiros; Irene Otero-Muras; Carlos Vázquez 002; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. - Alejandro F. Villaverde; Elba Raimúndez-Álvarez; Jan Hasenauer; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Improving dynamic predictions with ensembles of observable models. - Gemma Massonis; Alejandro F. Villaverde; Julio R. Banga (Bioinform., 2023)

IDESS: a toolbox for identification and automated design of stochastic gene circuits. - Carlos Sequeiros; Manuel Pájaro; Carlos Vázquez 002; Julio R. Banga; Irene Otero-Muras (Bioinform., 2023)

Distilling identifiable and interpretable dynamic models from biological data. - Gemma Massonis; Alejandro F. Villaverde; Julio R. Banga (PLoS Comput. Biol., 2023)

Conformal Prediction in Dynamic Biological Systems. - Alberto Portela; Julio R. Banga; Marcos Matabuena (CoRR, 2024)

Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers. - David R. Penas; Meysam Hashemi; Viktor K. Jirsa; Julio R. Banga (PLoS Comput. Biol., 2024)

Population based metaheuristics in Spark: Towards a general framework using PSO as a case study. - Xoán C. Pardo; Patricia González; Julio R. Banga; Ramón Doallo (Swarm Evol. Comput., 2024)

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Paul F. Lang; David R. Penas; Julio R. Banga; Daniel Weindl; Béla Novák (PLoS Comput. Biol., 2024)

Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications. - Roberto Prado-Rodriguez; Patricia González; Julio R. Banga; Ramón Doallo (Expert Syst. J. Knowl. Eng., 2024)

A Parameter Control Strategy for Parallel Island-Based Metaheuristics. - Roberto Prado-Rodriguez; Patricia González; Julio R. Banga (Expert Syst. J. Knowl. Eng., 2025)