Julio R. Banga

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 50

Top Topics

Parameter Estimation

Reverse Engineer

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

Publications

Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
Population based metaheuristics in Spark: Towards a general framework using PSO as a case study. Swarm Evol. Comput. 85 (2024)
Roberto Prado-Rodriguez, Patricia González, Julio R. Banga, Ramón Doallo
Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications. Expert Syst. J. Knowl. Eng. 41 (8) (2024)
Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Béla Novák
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLoS Comput. Biol. 20 (1) (2024)
Carlos Sequeiros, Irene Otero-Muras, Carlos Vázquez, Julio R. Banga
Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga
Distilling identifiable and interpretable dynamic models from biological data. PLoS Comput. Biol. 19 (10) (2023)
Carlos Sequeiros, Manuel Pájaro, Carlos Vázquez, Julio R. Banga, Irene Otero-Muras
IDESS: a toolbox for identification and automated design of stochastic gene circuits. Bioinform. 39 (10) (2023)
Ahmed Taha, Mauricio Patón, David R. Penas, Julio R. Banga, Jorge Rodríguez
Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants. PLoS Comput. Biol. 19 (7) (2023)
Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga
Improving dynamic predictions with ensembles of observable models. Bioinform. 39 (1) (2023)
Alejandro F. Villaverde, Elba Raimúndez-Álvarez, Jan Hasenauer, Julio R. Banga
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
Parallel ant colony optimization for the training of cell signaling networks. Expert Syst. Appl. 208 (2022)
Patricia González, Roberto R. Osorio, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
An efficient ant colony optimization framework for HPC environments. Appl. Soft Comput. 114 (2022)
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga
A protocol for dynamic model calibration. Briefings Bioinform. 23 (1) (2022)
Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde
Structural identifiability and observability of compartmental models of the COVID-19 pandemic. Annu. Rev. Control. 51 (2021)
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 L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17 (1) (2021)
Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde
Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. CoRR (2020)
Xoán C. Pardo, Pablo Argüeso-Alejandro, Patricia González, Julio R. Banga, Ramón Doallo
Spark implementation of the enhanced Scatter Search metaheuristic: Methodology and assessment. Swarm Evol. Comput. 59 (2020)
Nikolaos Tsiantis, Julio R. Banga
Using optimal control to understand complex metabolic pathways. BMC Bioinform. 21 (1) (2020)
Alejandro Fernández Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R. Banga
Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinform. 35 (5) (2019)
Jake Alan Pitt, Julio R. Banga
Parameter estimation in models of biological oscillators: an automated regularised estimation approach. BMC Bioinform. 20 (1) (2019)
Alejandro Fernández Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Input-Dependent Structural Identifiability of Nonlinear Systems. IEEE Control. Syst. Lett. 3 (2) (2019)
Patricia González, Pablo Argüeso-Alejandro, David R. Penas, Xoán C. Pardo, Julio Saez-Rodriguez, Julio R. Banga, Ramón Doallo
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. J. Supercomput. 75 (7) (2019)
Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga
PREMER: A Tool to Infer Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Patricia González, David R. Penas, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
Multimethod Optimization for Reverse Engineering of Complex Biological Networks. PBio@EuroMPI (2018)
Thomas S. Ligon, Fabian Fröhlich, Oana Chis, Julio R. Banga, Eva Balsa-Canto, Jan Hasenauer
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. Bioinform. 34 (8) (2018)
Nikolaos Tsiantis, Eva Balsa-Canto, Julio R. Banga
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinform. 34 (14) (2018)
Diego Teijeiro, Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
Towards cloud-based parallel metaheuristics. Int. J. High Perform. Comput. Appl. 32 (5) (2018)
Patricia González, Xoán Carlos Pardo Martínez, Ramón Doallo, Julio R. Banga
Implementing cloud-based parallel metaheuristics: an overview. J. Comput. Sci. Technol. 18 (03) (2018)
Nikolaos Tsiantis, Eva Balsa-Canto, Julio R. Banga
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinform. 34 (21) (2018)
Patricia González, David R. Penas, Xoán C. Pardo, Julio R. Banga, Ramón Doallo
Multimethod optimization in the cloud: A case-study in systems biology modelling. Concurr. Comput. Pract. Exp. 30 (12) (2018)
David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. BMC Bioinform. 18 (1) (2017)
Alejandro Fernández Villaverde, Julio R. Banga
Dynamical compensation and structural identifiability: analysis, implications, and reconciliation. CoRR (2017)
David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Comput. Biol. 13 (2) (2017)
Diego Teijeiro, Xoán C. Pardo, David R. Penas, Patricia González, Julio R. Banga, Ramón Doallo
A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology. Clust. Comput. 20 (3) (2017)
Patricia González, Xoán C. Pardo, David R. Penas, Diego Teijeiro, Julio R. Banga, Ramón Doallo
Using the Cloud for parameter estimation problems: comparing Spark vs MPI with a case-study. CCGrid (2017)
Alejandro Fernández Villaverde, Julio R. Banga
Dynamical compensation in biological systems as a particular case of structural non-identifiability. CoRR (2017)
Alejandro Fernández Villaverde, Julio R. Banga
Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. PLoS Comput. Biol. 13 (11) (2017)
Attila Gábor, Alejandro Fernández Villaverde, Julio R. Banga
Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. BMC Syst. Biol. 11 (1) (2017)
Eva Balsa-Canto, David Henriques, Attila Gábor, Julio R. Banga
AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology. Bioinform. 32 (21) (2016)
Diego Teijeiro, Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo
Implementing Parallel Differential Evolution on Spark. EvoApplications (2) (2016)
Diego Teijeiro, Xoán C. Pardo, David R. Penas, Patricia González, Julio R. Banga, Ramón Doallo
Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark. Euro-Par Workshops (2016)
Irene Otero-Muras, David Henriques, Julio R. Banga
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinform. 32 (21) (2016)
Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. CMSB (2016)
Gundián M. de Hijas-Liste, Eva Balsa-Canto, Jan Ewald, Martin Bartl, Pu Li, Julio R. Banga, Christoph Kaleta
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. BMC Bioinform. 16 (2015)
Abel Folch-Fortuny, Alejandro Fernández Villaverde, Alberto Ferrer, Julio R. Banga
Enabling network inference methods to handle missing data and outliers. BMC Bioinform. 16 (2015)
David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinform. 31 (18) (2015)
Alejandro Fernández Villaverde, Sophia Bongard, Klaus Mauch, Dirk Müller, Eva Balsa-Canto, Joachim Schmid, Julio R. Banga
A consensus approach for estimating the predictive accuracy of dynamic models in biology. Comput. Methods Programs Biomed. 119 (1) (2015)
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
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst. Biol. 9 (2015)
David R. Penas, Patricia González, Jose A. Egea, Julio R. Banga, Ramon Doallo
Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. ICCS (2015)
Attila Gábor, Julio R. Banga
Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst. Biol. 9 (2015)
David R. Penas, Julio R. Banga, Patricia González, Ramon Doallo
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. Appl. Soft Comput. 33 (2015)
Gundián M. de Hijas-Liste, Edda Klipp, Eva Balsa-Canto, Julio R. Banga
Global dynamic optimization approach to predict activation in metabolic pathways. BMC Syst. Biol. 8 (2014)
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
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. CoRR (2014)
Attila Gábor, Julio R. Banga
Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. CMSB (2014)
David R. Penas, Julio R. Banga, Patricia González, Ramon Doallo
A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems. PACBB (2014)
Irene Otero-Muras, Julio R. Banga
Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. CMSB (2014)
Alejandro Fernández Villaverde, Sophia Bongard, Klaus Mauch, Dirk Müller, Eva Balsa-Canto, Joachim Schmid, Julio R. Banga
High-Confidence Predictions in Systems Biology Dynamic Models. PACBB (2014)
Irene Otero-Muras, Julio R. Banga
Multicriteria global optimization for biocircuit design. BMC Syst. Biol. 8 (2014)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinform. 15 (2014)
Maria Rodriguez-Fernandez, Markus Rehberg, Andreas Kremling, Julio R. Banga
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Syst. Biol. 7 (2013)
Zoltán András Tuza, Gábor Szederkényi, Katalin M. Hangos, Antonio A. Alonso, Julio R. Banga
Computing All Sparse kinetic Structures for a Lorenz System using Optimization. Int. J. Bifurc. Chaos 23 (8) (2013)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. CoRR (2013)
Gundián M. de Hijas-Liste, Eva Balsa-Canto, Julio R. Banga, Christoph Kaleta
Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition. MED (2013)
Attila Gábor, Katalin M. Hangos, Gábor Szederkényi, Julio R. Banga
On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology. CMSB (2013)
Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger
. PLoS Comput. Biol. 9 (10) (2013)
Alejandro Fernández Villaverde, Jose A. Egea, Julio R. Banga
A cooperative strategy for parameter estimation in large scale systems biology models. BMC Syst. Biol. 6 (2012)
Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. Bioinform. 28 (11) (2012)
Carlos Vilas, Eva Balsa-Canto, Maria-Sonia G. García, Julio R. Banga, Antonio A. Alonso
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. BMC Syst. Biol. 6 (2012)
Eva Balsa-Canto, Julio R. Banga
AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinform. 27 (16) (2011)
Oana Chis, Julio R. Banga, Eva Balsa-Canto
GenSSI: a software toolbox for structural identifiability analysis of biological models. Bioinform. 27 (18) (2011)
Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso
Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Syst. Biol. 5 (2011)
Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga
An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst. Biol. 4 (2010)
Jose A. Egea, Rafael Martí, Julio R. Banga
An evolutionary method for complex-process optimization. Comput. Oper. Res. 37 (2) (2010)
Maria Rodriguez-Fernandez, Julio R. Banga
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models. Bioinform. 26 (13) (2010)
Jose A. Egea, Eva Balsa-Canto, Julio R. Banga
Dynamic Optimization of Chemical and Bio-chemical Processes using an Efficient Global Optimization Metaheuristic. Simul. Notes Eur. 19 (3-4) (2009)
Martin Schlüter, Jose A. Egea, Julio R. Banga
Extended ant colony optimization for non-convex mixed integer nonlinear programming. Comput. Oper. Res. 36 (7) (2009)
Jose A. Egea, Emmanuel Vázquez, Julio R. Banga, Rafael Martí
Improved scatter search for the global optimization of computationally expensive dynamic models. J. Glob. Optim. 43 (2-3) (2009)
Tomás Hirmajer, Eva Balsa-Canto, Julio R. Banga
DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinform. 10 (2009)
Maria Rodriguez-Fernandez, Julio R. Banga
Global Sensitivity Analysis of a Biochemical Pathway Model. IWPACBB (2008)
Oliver Exler, Luis T. Antelo, Jose A. Egea, Antonio A. Alonso, Julio R. Banga
A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design. Comput. Chem. Eng. 32 (8) (2008)
José-Oscar H. Sendín, Antonio A. Alonso, Julio R. Banga
Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes. IWPACBB (2008)
Tibor Csendes, László Pál, José-Oscar H. Sendín, Julio R. Banga
The GLOBAL optimization method revisited. Optim. Lett. 2 (4) (2008)
Luis T. Antelo, Julio R. Banga, Antonio A. Alonso
Hierarchical design of decentralized control structures for the Tennessee Eastman Process. Comput. Chem. Eng. 32 (9) (2008)
Eva Balsa-Canto, Martin Peifer, Julio R. Banga, Jens Timmer, Christian Fleck
Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst. Biol. 2 (2008)
Julio R. Banga
Optimization in computational systems biology. BMC Syst. Biol. 2 (2008)
Jose A. Egea, Maria Rodriguez-Fernandez, Julio R. Banga, Rafael Martí
Scatter search for chemical and bio-process optimization. J. Glob. Optim. 37 (3) (2007)
Luis T. Antelo, Irene Otero-Muras, Julio R. Banga, Antonio A. Alonso
A systematic approach to plant-wide control based on thermodynamics. Comput. Chem. Eng. 31 (5-6) (2007)
Cesar C. Palerm, Maria Rodriguez-Fernandez, Wendy C. Bevier, Howard C. Zisser, Julio R. Banga, Lois Jovanovic, Francis J. Doyle
Robust Parameter Estimation in a Model for Glucose Kinetics in Type 1 Diabetes Subjects. EMBC (2006)
Maria Rodriguez-Fernandez, Jose A. Egea, Julio R. Banga
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinform. 7 (2006)
Míriam R. García, Carlos Vilas, Julio R. Banga, Velislava N. Lyubenova, Maya N. Ignatova, Antonio A. Alonso
State Reconstruction in Spatially Distributed BioProcess Systems using Reduced Order Models: Application to the Gluconic Acid Production. CDC/ECC (2005)
Jose A. Egea, Dirk Vries, Antonio A. Alonso, Julio R. Banga
Global Optimization for Integrated Design and Control of Computationally Expensive Process Models. CDC/ECC (2005)
Antonio A. Alonso, Ioannis G. Kevrekidis, Julio R. Banga, Christos E. Frouzakis
Optimal sensor location and reduced order observer design for distributed process systems. Comput. Chem. Eng. 28 (1-2) (2004)
Carmen G. Moles, Julio R. Banga, Klaus Keller
Solving nonconvex climate control problems: pitfalls and algorithm performances. Appl. Soft Comput. 5 (1) (2004)
Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga
Optimal control of distributed processes using reduced order models. ECC (2001)
Carmen G. Moles, G. Gutierrez, Antonio A. Alonso, Julio R. Banga
Integrated process design and control via global optimization: A wastewater treatment plant case study. ECC (2001)