DYNAMO-bio: research outputs

Journal papers

19. R Prado-Rodriguez, P Gonzalez, XC Pardo, JR Banga (2026) Efficient cooperative strategies for parallel metaheuristics using MPI-3 features. Int. J. of High Performance Computing Applications, in press, online first doi:10.1177/10943420261431588
18. J Pico, A Arboleda-Garcıa, DR Penas, JR, Banga, A Vignoni, Y Boada, P de Valencia (2026). Host-aware Identification of Intrinsic Gene Expression Biopart Parameters from Combinatorial Libraries. Nature Communications, 17 (1), 9656 doi:10.1038/s41467-026-76332-7
17. A Polo-Rodríguez, DR Penas, JR Banga (2026). An adaptive multi-strategy metaheuristic for robust model calibration in large-scale systems biology. Swarm and Evolutionary Computation, under review, bioRxiv preprint: doi:10.64898/2026.01.27.701977
16. A Paredes-Vázquez, E Balsa-Canto, JR Banga (2026) Robust Calibration of Generalised Lotka-Volterra Models. NPJ Systems Biology and Applications, doi:10.1038/s41540-026-00816-x
15. JR Banga, F Pena-Brage, JM Rodríguez-Reinoso (2026) Bayesian optimization for parameter estimation in the Brusselator model using finite element simulations. Journal of Computational Physics, under review
14. R Prado-Rodriguez, P Gonzalez, JR Banga, R Doallo (2026) Parallel ACO-VNS for the solution of binary combinatorial optimization problems in computational systems biology. Applied Soft Computing, under review
13. XR Barreiro, J Faro, AF Villaverde (2026). Leveraging mathematical models to predict and control T-cell activation. PLOS Computational Biology, 22(4):e1013769, doi:10.1371/journal.pcbi.1013769
12. XR Barreiro, J Faro, AF Villaverde (2026). Response metrics of T-cell activation models. Royal Society Open Science, 13:250910, doi:10.1098/rsos.250910
11. M Shams Falavarjani, A González Vázquez, AF Villaverde (2025). Assessment of computational tools for analysing the observability and accessibility of nonlinear systems. Computation, 13(12), 281 doi:10.3390/computation13120281
10. S Díaz-Seoane, A Barreiro, AF Villaverde, M Chatzis (2025). On the relation between the accessibility and input observability tests in ODE systems. Systems Science & Control Engineering, 13(1):2579995 doi:10.1080/21642583.2025.2579995
9. H Faquir, Ma Pájaro, I Otero-Muras (2025). A computational framework for Optimal and Model Predictive Control of stochastic gene regulatory networks. IEEE-ACM Transactions on Computational Biology & Bioinformatics, 22(6):2630-2641 doi:10.1109/TCBBIO.2025.3598449
8. A González Vázquez, AF Villaverde (2025). Analysing the Structural Identifiability and Observability of Mechanistic Models of Tumour Growth. Bioengineering, 12(10), 1048 doi:10.3390/bioengineering12101048
7. JR Banga, AF Villaverde (2025). Mechanistic dynamic modelling of biological systems: the road ahead. Current Opinion in Systems Biology, doi:10.1016/j.coisb.2025.100553
6. AF Villaverde (2025). Employing Observability Rank Conditions for Taking into Account Experimental Information a priori. Bulletin of Mathematical Biology, 87, 39: doi:10.1007/s11538-025-01415-3
5. Prado-Rodriguez, R., Gonzalez, P., Banga, J. R. (2025) A Parameter Control Strategy for Parallel Island‐Based Metaheuristics. Expert Systems 42:e70061 https://doi.org/10.1111/exsy.70061
4. Fernández de Dios, M., A. M. González-Rueda, J. R. Banga, J. González-Díaz, D. R. Penas (2025) Parameter estimation in ODEs: assessing the potential of local and global solvers. Optimization and Engineering 26, 2663–2701 https://doi.org/10.1007/s11081-025-09978-9
3. Portela, A., J.R. Banga, M. Matabuena (2025) Conformal Prediction for Uncertainty Quantification in Dynamic Biological Systems. PLOS Computational Biology 21(5): e1013098. https://doi.org/10.1371/journal.pcbi.1013098
2. Banga, J. R. and S. Sager (2025) Generalized Inverse Optimal Control and its Application in Biology. Annual Reviews in Control 60:101029 https://doi.org/10.1016/j.arcontrol.2025.101029
1. Paredes-Vázquez, A., E. Balsa-Canto, J. R. Banga (2025) Identification of dynamic models of microbial communities: a workflow addressing identifiability and modeling pitfalls. PLOS Computational Biology 21(12): e1013204 https://doi.org/10.1371/journal.pcbi.1013204

Conference papers

5. M Shams Falavarjani, P Sánchez Calvo, AF Villaverde (2026). Symmetry-Based Structural Identifiability and Observability Analysis of PDE and ODE Models in STRIKE-GOLDD. XLVII Jornadas de Automática (JA’26), Córdoba, Spain, September 2–4, 2026. doi:10.17979/ja-cea.2026.47.13688.
4. Rey Barreiro, N Baberuxki, M Abebaw Mebratie, AF Villaverde, W Seiler (2026). Structural identifiability and discrete symmetries. European Control Conference (ECC 2026), Reykjavík, Iceland, July 7-10, 2026, pp. 2226-2232. ISBN:978-3-907144-13-8
3. A González Vázquez, AF Villaverde (2025). Structural identifiability and observability of tumour growth models with and without chemotherapy. XLVI Jornadas de Automática (JA’25), Cartagena, Spain, September 3–5, 2025.
2. DA Ionescu Leoca, M Shams Falavarjani, AF Villaverde (2025). Comparativa de metodologías de análisis de identificabilidad estructural y observabilidad para modelos no lineales. XLVI Jornadas de Automática (JA’25), Cartagena, Spain, September 3–5, 2025.
1. A Pardo, S Díaz-Seoane, DA Ionescu, A Papachristodoulou, AF Villaverde (2025). Analysing control-theoretic properties of nonlinear synthetic biology circuits. 14th IFAC Symposium on Dynamics and Control of Process Systems, including Biosystems (DYCOPS 2025), Bratislava, Slovakia, June 16-19, 2025.

Doctoral dissertations (completed)

3. Sandra Díaz Seoane, "Computational methods for the study of observability and controllability of biological systems" Supervised by AF Villaverde. Universidade de Vigo. Thesis completed, viva expected for December 2026.
2. Xabier Rey Barreiro, "Computational modelling of the dynamics of immune reactions: methodologies for identifiability and robustness analysis" Supervised by AF Villaverde and J Faro Rivas. Universidade de Vigo, September 2026. Grade: cum laude with international distinction.
1. Roberto Prado Rodríguez, "Exploiting HPC capabilities for combinatorial optimization in computational systems biology" Supervised by Patricia González (UDC) and Julio R. Banga (MBG-CSIC). Universidade da Coruña, September 2025. Grade: cum laude.