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2020 – today
- 2024
[j70]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)- [j69]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) - [j68]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: 101483 (2024) - [i6]Alberto Portela, Julio R. Banga, Marcos Matabuena:
Conformal Prediction in Dynamic Biological Systems. CoRR abs/2409.02644 (2024) - 2023
- [j67]Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga:
Improving dynamic predictions with ensembles of observable models. Bioinform. 39(1) (2023) - [j66]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) - [j65]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) - [j64]Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga:
Distilling identifiable and interpretable dynamic models from biological data. PLoS Comput. Biol. 19(10) (2023) - [j63]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): 1725-1736 (2023) - [j62]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): 1971-1982 (2023) - 2022
- [j61]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: 108058 (2022) - [j60]Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga:
A protocol for dynamic model calibration. Briefings Bioinform. 23(1) (2022) - [j59]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: 118199 (2022) - 2021
- [j58]Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde:
Structural identifiability and observability of compartmental models of the COVID-19 pandemic. Annu. Rev. Control. 51: 441-459 (2021) - [j57]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:
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j56]Nikolaos Tsiantis, Julio R. Banga:
Using optimal control to understand complex metabolic pathways. BMC Bioinform. 21(1): 472 (2020) - [j55]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: 100748 (2020) - [i5]Gemma Massonis, Julio R. Banga, Alejandro Fernández Villaverde:
Repairing dynamic models: a method to obtain identifiable and observable reparameterizations with mechanistic insights. CoRR abs/2012.09826 (2020)
2010 – 2019
- 2019
- [j54]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): 830-838 (2019) - [j53]Jake Alan Pitt, Julio R. Banga:
Parameter estimation in models of biological oscillators: an automated regularised estimation approach. BMC Bioinform. 20(1): 82:1-82:17 (2019) - [j52]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): 272-277 (2019) - [j51]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): 3471-3498 (2019) - 2018
- [j50]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): 1421-1423 (2018) - [j49]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): 2433-2440 (2018) - [j48]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): 3780 (2018) - [j47]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) - [j46]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): 693-705 (2018) - [j45]Patricia González, Xoán C. Pardo, Ramón Doallo, Julio R. Banga:
Implementing cloud-based parallel metaheuristics: an overview. J. Comput. Sci. Technol. 18(03): 26 (2018) - [j44]Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga:
PREMER: A Tool to Infer Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1193-1202 (2018) - [c19]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: 11-18 - 2017
- [j43]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): 52:1-52:24 (2017) - [j42]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): 54:1-54:16 (2017) - [j41]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): 1937-1950 (2017) - [j40]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) - [j39]Alejandro Fernández Villaverde, Julio R. Banga:
Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation. PLoS Comput. Biol. 13(11) (2017) - [c18]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: 797-806 - [i4]Alejandro Fernández Villaverde, Julio R. Banga:
Dynamical compensation in biological systems as a particular case of structural non-identifiability. CoRR abs/1701.02562 (2017) - [i3]Alejandro Fernández Villaverde, Julio R. Banga:
Dynamical compensation and structural identifiability: analysis, implications, and reconciliation. CoRR abs/1703.08415 (2017) - 2016
- [j38]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): 3357-3359 (2016) - [j37]Irene Otero-Muras, David Henriques, Julio R. Banga:
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinform. 32(21): 3360-3362 (2016) - [c17]Alejandro Fernández Villaverde, Kolja Becker, Julio R. Banga:
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. CMSB 2016: 323-329 - [c16]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: 397-408 - [c15]Diego Teijeiro, Xoán C. Pardo, Patricia González, Julio R. Banga, Ramón Doallo:
Implementing Parallel Differential Evolution on Spark. EvoApplications (2) 2016: 75-90 - 2015
- [j36]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: 86-99 (2015) - [j35]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): 2999-3007 (2015) - [j34]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: 163:1-163:13 (2015) - [j33]Abel Folch-Fortuny, Alejandro Fernández Villaverde, Alberto Ferrer, Julio R. Banga:
Enabling network inference methods to handle missing data and outliers. BMC Bioinform. 16: 283:1-283:12 (2015) - [j32]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: 8 (2015) - [j31]Attila Gábor, Julio R. Banga:
Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst. Biol. 9: 74 (2015) - [j30]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): 17-28 (2015) - [c14]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: 630-639 - 2014
- [j29]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: 136 (2014) - [j28]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: 1 (2014) - [j27]Irene Otero-Muras, Julio R. Banga:
Multicriteria global optimization for biocircuit design. BMC Syst. Biol. 8: 113 (2014) - [c13]Attila Gábor, Julio R. Banga:
Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. CMSB 2014: 45-60 - [c12]Irene Otero-Muras, Julio R. Banga:
Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. CMSB 2014: 225-238 - [c11]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: 161-171 - [c10]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: 173-181 - [i2]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 abs/1407.5856 (2014) - 2013
- [j26]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: 76 (2013) - [j25]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) - [j24]Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger:
Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster. PLoS Comput. Biol. 9(10) (2013) - [c9]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: 206-219 - [c8]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: 237-242 - [i1]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 abs/1311.5735 (2013) - 2012
- [j23]Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso:
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. Bioinform. 28(11): 1549-1550 (2012) - [j22]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: 75 (2012) - [j21]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: 79 (2012) - 2011
- [j20]Eva Balsa-Canto, Julio R. Banga:
AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinform. 27(16): 2311-2313 (2011) - [j19]Oana Chis, Julio R. Banga, Eva Balsa-Canto:
GenSSI: a software toolbox for structural identifiability analysis of biological models. Bioinform. 27(18): 2610-2611 (2011) - [j18]Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso:
Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Syst. Biol. 5: 177 (2011) - 2010
- [j17]Maria Rodriguez-Fernandez, Julio R. Banga:
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models. Bioinform. 26(13): 1675-1676 (2010) - [j16]Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga:
An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst. Biol. 4: 11 (2010) - [j15]Jose A. Egea, Rafael Martí, Julio R. Banga:
An evolutionary method for complex-process optimization. Comput. Oper. Res. 37(2): 315-324 (2010)
2000 – 2009
- 2009
- [j14]Tomás Hirmajer, Eva Balsa-Canto, Julio R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology. BMC Bioinform. 10 (2009) - [j13]Martin Schlüter, Jose A. Egea, Julio R. Banga:
Extended ant colony optimization for non-convex mixed integer nonlinear programming. Comput. Oper. Res. 36(7): 2217-2229 (2009) - [j12]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): 175-190 (2009) - [j11]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): 41-46 (2009) - 2008
- [j10]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: 26 (2008) - [j9]Julio R. Banga:
Optimization in computational systems biology. BMC Syst. Biol. 2: 47 (2008) - [j8]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): 1877-1891 (2008) - [j7]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): 1995-2015 (2008) - [j6]Tibor Csendes, László Pál, José-Oscar H. Sendín, Julio R. Banga:
The GLOBAL optimization method revisited. Optim. Lett. 2(4): 445-454 (2008) - [c7]José-Oscar H. Sendín, Antonio A. Alonso, Julio R. Banga:
Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes. IWPACBB 2008: 197-205 - [c6]Maria Rodriguez-Fernandez, Julio R. Banga:
Global Sensitivity Analysis of a Biochemical Pathway Model. IWPACBB 2008: 233-242 - 2007
- [j5]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): 677-691 (2007) - [j4]Jose A. Egea, Maria Rodriguez-Fernandez, Julio R. Banga, Rafael Martí:
Scatter search for chemical and bio-process optimization. J. Glob. Optim. 37(3): 481-503 (2007) - 2006
- [j3]Maria Rodriguez-Fernandez, Jose A. Egea, Julio R. Banga:
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinform. 7: 483 (2006) - [c5]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: 319-322 - 2005
- [c4]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: 6256-6261 - [c3]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: 6899-6904 - 2004
- [j2]Carmen G. Moles, Julio R. Banga, Klaus Keller:
Solving nonconvex climate control problems: pitfalls and algorithm performances. Appl. Soft Comput. 5(1): 35-44 (2004) - [j1]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): 27-35 (2004) - 2001
- [c2]Eva Balsa-Canto, Antonio A. Alonso, Julio R. Banga:
Optimal control of distributed processes using reduced order models. ECC 2001: 2511-2516 - [c1]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: 2994-2999
Coauthor Index
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