Publications

2025

• Parameter estimation in ODEs: assessing the potential of local and global solvers. M. Fernández de Dios, A. M. González-Rueda, J. R. Banga, J. González-Díaz, D. R. Penas. Optimization and engineering, 2025.  [article] 

• Testing for genetic interactions in complex disease with distance correlation. F. Castro-Prado, J. Costas, D. Edelmann, W. González-Manteiga, and D. R. Penas.  Biometrical Journal, 2025. (Accepted, in press).  [preprint]

2024

• Parameter estimation in a whole-brain network model of epilepsy: comparison of parallel global optimization solvers. D. R. Penas, M. Hashemi, V. K. Jirsa, and J. R. Banga. PLOS Computational Biology, 20(7):e1011642, 2024. [article] [software]

• Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. P.F. Lang, D.R. Penas, J.R. Banga, D. Weindl,  and B. Novak. PLOS Computational Biology, 20(1): e1011151, 2024. [article] [software]

2023

• Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants.  A. Taha, M. Patón, D.R. Penas,  J.R. Banga, J. Rodríguez. PLOS Computational Biology, 19(7): e1011264, 2023. [article] 

• Application of decomposition techniques in a wildfire suppression optimization model. J. Rodríguez-Veiga, D. R. Penas, A. M. González-Rueda, and M.  Ginzo-Villamayor. Optimization and engineering, 2023. [article] [software]

• A new two-phase heuristic for a problem of food distribution with compartmentalized trucks and trailers. L. Davila-Pena, D. R. Penas and B. Casas-Méndez. International Transactions in Operational Research, 30: 1031-1064, 2023.   [article] [software]
  
  

2022

• Computational advances in polynomial optimization: RAPOSa, a freely available global solver. B.  González-Rodríguez, J. Ossorio-Castillo, J. González-Díaz, A. M. González-Rueda, D R. Penas, and D. Rodríguez-Martínez. Journal of Global Optimization, 85, 541–568 ,2022. [article] [software]
  
  

2020

• A metaheuristic penalty approach for the starting point in nonlinear programming. D.R. Penas and M. Raydan. RAIRO Operations Research, 54 (2) 451-469, 2020. [article]
  
  

2019

• Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology. P. González, P. Argüeso-Alejandro, D.R. Penas, X.C. Pardo, J. Saez-Rodriguez, J.R. Banga, and R. Doallo. The Journal of Supercomputing, 75(7), pp 3471-3498, 2019. [article] 

• Enhanced global optimization methods applied to complex fisheries stock assessment models. D.R. Penas, A. Gómez, B.B. Fraguela, M.J. Martín, and S. Cerviño. Applied Soft Computing, 77, pp 50-66, 2019. [article] [software]

2018

• Multimethod optimization in the cloud: A case-study in systems biology modelling. P. González, D.R. Penas, X.C. Pardo, J.R. Banga, and R. Doallo. Concurrency and Computation: Practice and Experience. 30(12): e4488, 2018. [article] [software]

• Multimethod Optimization for Reverse Engineering of Complex Biological Networks. P. González, D.R. Penas, X. Pardo, J.R. Banga and R. Doallo. Proceedings of the 6th International Workshop on Parallelism in Bioinformatics. pp. 11 - 18. ACM Digital Library, 2018. [article]

2017

• A parallel metaheuristic for large mixed-integer nonlinear dynamic optimization problems, with applications in computational biology. D.R. Penas, D. Henriques, P. González, R. Doallo, J. Saez-Rodriguez, and J.R. Banga. PLOS ONE, 12(8): e0182186, 2017. [article] [software]

• A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology. D. Teijeiro, X. Pardo, D.R. Penas, P. González, J.R. Banga and R. Doallo. Cluster Computing, 20(3), pp 1937-1950, 2017. [article][software]

• Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. D.R. Penas, P. González, J.A. Egea, R. Doallo and J.R. Banga. BMC bioinformatics. 18:52, 2017. [article] [software]

• Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study. P. González, X. Pardo, D.R. Penas, D. Teijeiro, J.R. Banga and R. Doallo. Proceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. pp. 797 - 806. ACM Digital Library, 2017. [article]

2016

• Evaluation of parallel Differential Evolution implementation on MapReduce and Spark. D. Teijeiro, X. C. Pardo, D.R. Penas, P. González, J.R. Banga and R. Doallo. Euro-Par 2016: Parallel Processing Workshops. Lecture Notes in Computer science. 10104, pp. 397 - 408. Springer, 2016. [article]

2015

• Enhanced parallel Differential Evolution algorithm for problems in computational systems biology. D.R. Penas, J.R. Banga, P. González, and R. Doallo. Applied Soft Computing. 33-0, pp. 86 - 99, 2015. [article] [software]

• Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method. D.R. Penas, P. González, J.A. Egea, J.R. Banga, and R. Doallo. Procedia Computer Science. 51, pp. 630 - 639. Elsevier, 2015. [article]

2014

• A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems. D.R. Penas, J.R. Banga, P. González, and R. Doallo. Advances in Intelligent Systems and Computing. 294, pp. 173 - 181. Springer, 2014. [article]

2013

• A Study of Semantic Proximity between Archetype Terms Based on SNOMED CT Relationships. J.L. Allones, D.R. Penas, M. Taboada, D. Martínez, and S. Tellado. Lecture Notes in Computer Science, 7738, pp. 98 - 112. Springer Berlin Heidelberg, 2013. [article]

• Deployment of HPC services in multipurpose cloud environments. David R. Penas and Natalia Costas Lago. CESGA technical report / Master’s Thesis, 2012. [article]

• Networking virtualization technologies analysis and their application to NREN networks. David R. Penas and Natalia Costas Lago. CESGA technical report, 2011. [article] 

• Greedy Differential Evolution for the multiple allocation p-hub median problem. D. R. Penas, and S. García. (preparing).