Julio R. Banga

100 papers B 1Misc 3Journal 81Unranked 15
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Parameter Control Strategy for Parallel Island-Based Metaheuristics.
Expert Syst. J. Knowl. Eng.
Roberto Prado-Rodriguez, Patricia González, Julio R. Banga
2025 J jnl
Conformal prediction for uncertainty quantification in dynamic biological systems.
PLoS Comput. Biol.
Alberto Portela, Julio R. Banga, Marcos Matabuena
2025 J jnl
Generalized inverse optimal control and its application in biology.
Annu. Rev. Control.
Julio R. Banga, Sebastian Sager
2025 J jnl
Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.
PLoS Comput. Biol.
Ana Paredes-Vázquez, Eva Balsa-Canto, Julio R. Banga
2024 J jnl
Conformal Prediction in Dynamic Biological Systems.
CoRR
Alberto Portela, Julio R. Banga, Marcos Matabuena
2024 J jnl
Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications.
Expert Syst. J. Knowl. Eng.
Roberto Prado-Rodriguez, Patricia González, Julio R. Banga, Ramón Doallo
2024 J jnl
Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers.
PLoS Comput. Biol.
David R. Penas, Meysam Hashemi, Viktor K. Jirsa, Julio R. Banga
2024 J jnl
Population based metaheuristics in Spark: Towards a general framework using PSO as a case study.
Swarm Evol. Comput.
Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
2024 J jnl
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells.
PLoS Comput. Biol.
Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Béla Novák
2023 J jnl
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alejandro F. Villaverde, Elba Raimúndez-Álvarez, Jan Hasenauer, Julio R. Banga
2023 J jnl
Distilling identifiable and interpretable dynamic models from biological data.
PLoS Comput. Biol.
Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga
2023 J jnl
Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems.
IEEE ACM Trans. Comput. Biol. Bioinform.
Carlos Sequeiros, Irene Otero-Muras, Carlos Vázquez, Julio R. Banga
2023 J jnl
IDESS: a toolbox for identification and automated design of stochastic gene circuits.
Bioinform.
Carlos Sequeiros, Manuel Pájaro, Carlos Vázquez, Julio R. Banga, Irene Otero-Muras
2023 J jnl
Improving dynamic predictions with ensembles of observable models.
Bioinform.
Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga
2023 J jnl
Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants.
PLoS Comput. Biol.
Ahmed Taha, Mauricio Patón, David R. Penas, Julio R. Banga, Jorge Rodríguez
2022 J jnl
A protocol for dynamic model calibration.
Briefings Bioinform.
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga
2022 J jnl
An efficient ant colony optimization framework for HPC environments.
Appl. Soft Comput.
Patricia González, Roberto R. Osorio, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
2022 J jnl
Parallel ant colony optimization for the training of cell signaling networks.
Expert Syst. Appl.
Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
2021 J jnl
PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol.
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, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
2021 J jnl
Structural identifiability and observability of compartmental models of the COVID-19 pandemic.
Annu. Rev. Control.
Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde
2020 J jnl
Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights.
CoRR
Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde
2020 J jnl
Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment.
Swarm Evol. Comput.
Xoán C. Pardo, Pablo Argüeso-Alejandro, Patricia González, Julio R. Banga, Ramón Doallo
2020 J jnl
Using optimal control to understand complex metabolic pathways.
BMC Bioinform.
Nikolaos Tsiantis, Julio R. Banga
2019 J jnl
Benchmarking optimization methods for parameter estimation in large kinetic models.
Bioinform.
Alejandro Fernández Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R. Banga
2019 J jnl
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology.
J. Supercomput.
Patricia González, Pablo Argüeso-Alejandro, David R. Penas, Xoán C. Pardo, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
2019 J jnl
Input-Dependent Structural Identifiability of Nonlinear Systems.
IEEE Control. Syst. Lett.
Alejandro Fernández Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
2019 J jnl
Parameter estimation in models of biological oscillators: an automated regularised estimation approach.
BMC Bioinform.
Jake Alan Pitt, Julio R. Banga
2018 J jnl
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.
Bioinform.
Thomas S. Ligon, Fabian Fröhlich, Oana Chis, Julio R. Banga, Eva Balsa-Canto, Jan Hasenauer
2018 J jnl
Implementing cloud-based parallel metaheuristics: an overview.
J. Comput. Sci. Technol.
Patricia González, Xoán C. Pardo, Ramón Doallo, Julio R. Banga
2018 — conf
Multimethod Optimization for Reverse Engineering of Complex Biological Networks.
PBio@EuroMPI
Patricia González, David R. Penas, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
2018 J jnl
Multimethod optimization in the cloud: A case-study in systems biology modelling.
Concurr. Comput. Pract. Exp.
Patricia González, David R. Penas, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
2018 J jnl
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.
Bioinform.
Nikolaos Tsiantis, Eva Balsa-Canto, Julio R. Banga
2018 J jnl
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework.
Bioinform.
Nikolaos Tsiantis, Eva Balsa-Canto, Julio R. Banga
2018 J jnl
PREMER: A Tool to Infer Biological Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga
2018 J jnl
Towards cloud-based parallel metaheuristics.
Int. J. High Perform. Comput. Appl.
Diego Teijeiro, Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
2017 J jnl
A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology.
Clust. Comput.
Diego Teijeiro, Xoán C. Pardo, David R. Penas, Patricia González, Julio R. Banga, Ramón Doallo
2017 J jnl
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
PLoS Comput. Biol.
David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
2017 J jnl
Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.
PLoS Comput. Biol.
Alejandro Fernández Villaverde, Julio R. Banga
2017 J jnl
Dynamical compensation and structural identifiability: analysis, implications, and reconciliation.
CoRR
Alejandro Fernández Villaverde, Julio R. Banga
2017 J jnl
Dynamical compensation in biological systems as a particular case of structural non-identifiability.
CoRR
Alejandro Fernández Villaverde, Julio R. Banga
2017 J jnl
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.
BMC Bioinform.
David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga
2017 J jnl
Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems.
BMC Syst. Biol.
Attila Gábor, Alejandro Fernández Villaverde, Julio R. Banga
2017 B conf
Using the Cloud for parameter estimation problems: comparing Spark vs MPI with a case-study.
CCGrid
Patricia González, Xoán C. Pardo, David R. Penas, Diego Teijeiro, Julio R. Banga, Ramón Doallo
2016 J jnl
AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.
Bioinform.
Eva Balsa-Canto, David Henriques, Attila Gábor, Julio R. Banga
2016 — conf
Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark.
Euro-Par Workshops
Diego Teijeiro, Xoán C. Pardo, David R. Penas, Patricia González, Julio R. Banga, Ramón Doallo
2016 — conf
Implementing Parallel Differential Evolution on Spark.
EvoApplications (2)
Diego Teijeiro, Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
2016 — conf
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory.
CMSB
Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga
2016 J jnl
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits.
Bioinform.
Irene Otero-Muras, David Henriques, Julio R. Banga
2015 J jnl
A consensus approach for estimating the predictive accuracy of dynamic models in biology.
Comput. Methods Programs Biomed.
Alejandro Fernández Villaverde, Sophia Bongard, Klaus Mauch, Dirk Müller, Eva Balsa-Canto, Joachim Schmid, Julio R. Banga
2015 J jnl
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
BMC Syst. Biol.
Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga
2015 J jnl
Enabling network inference methods to handle missing data and outliers.
BMC Bioinform.
Abel Folch-Fortuny, Alejandro Fernández Villaverde, Alberto Ferrer, Julio R. Banga
2015 J jnl
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology.
Appl. Soft Comput.
David R. Penas, Julio R. Banga, Patricia González, Ramon Doallo
2015 J jnl
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.
BMC Bioinform.
Gundián M. de Hijas-Liste, Eva Balsa-Canto, Jan Ewald, Martin Bartl, Pu Li, Julio R. Banga, Christoph Kaleta
2015 Misc conf
Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method.
ICCS
David R. Penas, Patricia González, Jose A. Egea, Julio R. Banga, Ramon Doallo
2015 J jnl
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Bioinform.
David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
2015 J jnl
Robust and efficient parameter estimation in dynamic models of biological systems.
BMC Syst. Biol.
Attila Gábor, Julio R. Banga
2014 Misc conf
A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems.
PACBB
David R. Penas, Julio R. Banga, Patricia González, Ramon Doallo
2014 J jnl
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology.
CoRR
Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga
2014 J jnl
Global dynamic optimization approach to predict activation in metabolic pathways.
BMC Syst. Biol.
Gundián M. de Hijas-Liste, Edda Klipp, Eva Balsa-Canto, Julio R. Banga
2014 Misc conf
High-Confidence Predictions in Systems Biology Dynamic Models.
PACBB
Alejandro Fernández Villaverde, Sophia Bongard, Klaus Mauch, Dirk Müller, Eva Balsa-Canto, Joachim Schmid, Julio R. Banga
2014 — conf
Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods.
CMSB
Attila Gábor, Julio R. Banga
2014 J jnl
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC Bioinform.
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez
2014 J jnl
Multicriteria global optimization for biocircuit design.
BMC Syst. Biol.
Irene Otero-Muras, Julio R. Banga
2014 — conf
Optimization Based Design of Synthetic Oscillators from Standard Biological Parts.
CMSB
Irene Otero-Muras, Julio R. Banga
2013 J jnl
Computing All Sparse kinetic Structures for a Lorenz System using Optimization.
Int. J. Bifurc. Chaos
Zoltán András Tuza, Gábor Szederkényi, Katalin M. Hangos, Antonio A. Alonso, Julio R. Banga
2013 J jnl
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
CoRR
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez
2013 — conf
On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology.
CMSB
Attila Gábor, Katalin M. Hangos, Gábor Szederkényi, Julio R. Banga
2013 — conf
Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition.
MED
Gundián M. de Hijas-Liste, Eva Balsa-Canto, Julio R. Banga, Christoph Kaleta
2013 J jnl
Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in
PLoS Comput. Biol.
Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger
2013 J jnl
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems.
BMC Syst. Biol.
Maria Rodriguez-Fernandez, Markus Rehberg, Andreas Kremling, Julio R. Banga
2012 J jnl
A cooperative strategy for parameter estimation in large scale systems biology models.
BMC Syst. Biol.
Alejandro Fernández Villaverde, Jose A. Egea, Julio R. Banga
2012 J jnl
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.
Bioinform.
Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso
2012 J jnl
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.
BMC Syst. Biol.
Carlos Vilas, Eva Balsa-Canto, Maria-Sonia G. García, Julio R. Banga, Antonio A. Alonso
2011 J jnl
AMIGO, a toolbox for advanced model identification in systems biology using global optimization.
Bioinform.
Eva Balsa-Canto, Julio R. Banga
2011 J jnl
GenSSI: a software toolbox for structural identifiability analysis of biological models.
Bioinform.
Oana Chis, Julio R. Banga, Eva Balsa-Canto
2011 J jnl
Inference of complex biological networks: distinguishability issues and optimization-based solutions.
BMC Syst. Biol.
Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso
2010 J jnl
An evolutionary method for complex-process optimization.
Comput. Oper. Res.
Jose A. Egea, Rafael Martí, Julio R. Banga
2010 J jnl
An iterative identification procedure for dynamic modeling of biochemical networks.
BMC Syst. Biol.
Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga
2010 J jnl
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.
Bioinform.
Maria Rodriguez-Fernandez, Julio R. Banga
2009 J jnl
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinform.
Tomás Hirmajer, Eva Balsa-Canto, Julio R. Banga
2009 J jnl
Dynamic Optimization of Chemical and Bio-chemical Processes using an Efficient Global Optimization Metaheuristic.
Simul. Notes Eur.
Jose A. Egea, Eva Balsa-Canto, Julio R. Banga
2009 J jnl
Extended ant colony optimization for non-convex mixed integer nonlinear programming.
Comput. Oper. Res.
Martin Schlüter, Jose A. Egea, Julio R. Banga
2009 J jnl
Improved scatter search for the global optimization of computationally expensive dynamic models.
J. Glob. Optim.
Jose A. Egea, Emmanuel Vázquez, Julio R. Banga, Rafael Martí
2008 J jnl
A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design.
Comput. Chem. Eng.
Oliver Exler, Luis T. Antelo, Jose A. Egea, Antonio A. Alonso, Julio R. Banga
2008 — conf
Global Sensitivity Analysis of a Biochemical Pathway Model.
IWPACBB
Maria Rodriguez-Fernandez, Julio R. Banga
2008 J jnl
Hierarchical design of decentralized control structures for the Tennessee Eastman Process.
Comput. Chem. Eng.
Luis T. Antelo, Julio R. Banga, Antonio A. Alonso
2008 J jnl
Hybrid optimization method with general switching strategy for parameter estimation.
BMC Syst. Biol.
Eva Balsa-Canto, Martin Peifer, Julio R. Banga, Jens Timmer, Christian Fleck
2008 — conf
Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes.
IWPACBB
José-Oscar H. Sendín, Antonio A. Alonso, Julio R. Banga
2008 J jnl
Optimization in computational systems biology.
BMC Syst. Biol.
Julio R. Banga
2008 J jnl
The GLOBAL optimization method revisited.
Optim. Lett.
Tibor Csendes, László Pál, José-Oscar H. Sendín, Julio R. Banga
2007 J jnl
A systematic approach to plant-wide control based on thermodynamics.
Comput. Chem. Eng.
Luis T. Antelo, Irene Otero-Muras, Julio R. Banga, Antonio A. Alonso
2007 J jnl
Scatter search for chemical and bio-process optimization.
J. Glob. Optim.
Jose A. Egea, Maria Rodriguez-Fernandez, Julio R. Banga, Rafael Martí
2006 J jnl
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.
BMC Bioinform.
Maria Rodriguez-Fernandez, Jose A. Egea, Julio R. Banga
2006 — conf
Robust Parameter Estimation in a Model for Glucose Kinetics in Type 1 Diabetes Subjects.
EMBC
Cesar C. Palerm, Maria Rodriguez-Fernandez, Wendy C. Bevier, Howard C. Zisser, Julio R. Banga, Lois Jovanovic, Francis J. Doyle
2005 — conf
Global Optimization for Integrated Design and Control of Computationally Expensive Process Models.
CDC/ECC
Jose A. Egea, Dirk Vries, Antonio A. Alonso, Julio R. Banga
2005 — conf
State Reconstruction in Spatially Distributed BioProcess Systems using Reduced Order Models: Application to the Gluconic Acid Production.
CDC/ECC
Míriam R. García, Carlos Vilas, Julio R. Banga, Velislava N. Lyubenova, Maya N. Ignatova, Antonio A. Alonso
2004 J jnl
Optimal sensor location and reduced order observer design for distributed process systems.
Comput. Chem. Eng.
Antonio A. Alonso, Ioannis G. Kevrekidis, Julio R. Banga, Christos E. Frouzakis
2004 J jnl
Solving nonconvex climate control problems: pitfalls and algorithm performances.
Appl. Soft Comput.
Carmen G. Moles, Julio R. Banga, Klaus Keller
2001 — conf
Integrated process design and control via global optimization: A wastewater treatment plant case study.
ECC
Carmen G. Moles, G. Gutierrez, Antonio A. Alonso, Julio R. Banga
2001 — conf
Optimal control of distributed processes using reduced order models.
ECC
Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga