Working Papers
- Ripples in water: epidemiological forecasting with wastewater signals and hybrid neural-compartmental networks.
- Integrating genome-scale metabolic models into multi-scale simulations.
- Extreme-scale calibration of Epidemic Simulations.
- A Methodological Framework to Guide Air Pollution Exposure Assessment Integrating Population Mobility.
Publications
Systems Biology and Cancer Modeling
- Hayoun-Mya, O., Montagud, A., Valencia, A., & Ponce-de-León, M. (2026). Experimentally calibrated multiscale model predicts schedule dependent drug combination effects. NPJ Systems Biology and Applications. [DOI]
- Benedicto, X., Flobak, Å., Ponce-de-León, M.✉︎, & Valencia, A. (2025). Constraint based modeling of drug induced metabolic changes in a cancer cell line. NPJ Systems Biology and Applications. [DOI]
- Niarakis, A., et al. (2024). Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology. [DOI]
- Ponce-de-León, M., Montagud, A., Noël, V., Meert, A., Pradas, G., Barillot, E., Calzone, L., & Valencia, A. (2023). PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. NPJ Systems Biology and Applications. [DOI]
- Ponce-de-León, M.✉︎, Montagud, A., Akasiadis, C., Schreiber, J., Ntiniakou, T., & Valencia, A. (2022). Optimizing dosage-specific treatments in a multi-scale model of a tumor growth. Frontiers in Molecular Biosciences. [DOI]
- Montagud, A., Ponce-de-León, M., & Valencia, A. (2021). Systems Biology at the giga-scale: large multi-scale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology. [DOI]
- Ponce-de-León, M., Apaolaza, I., Valencia, A., & Planes, F. J. (2020). On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinformatics. [DOI]
- Ponce-de-León, M.✉︎, et al. (2017). Determinism and contingency shape metabolic complementation in an endosymbiotic consortium. Frontiers in Microbiology. [DOI]
- Mori, M., Ponce-de-León, M., Peretó, J., & Montero, F. (2016). Metabolic complementation in bacterial communities: necessary conditions and optimality. Frontiers in Microbiology. [DOI]
- Calle-Espinosa, J., Ponce-de-León, M., et al. (2016). Nature lessons: The whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics. Journal of Theoretical Biology. [DOI]
- Ponce-de-León, M., Calle-Espinosa, J., Peretó, J., & Montero, F. (2015). Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PLOS ONE. [DOI]
- Ponce-de-León, M.✉︎, Montero, F., & Peretó, J. (2013). Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. BMC Systems Biology, 7(1), 114. [DOI]
- Ponce-de-León, M., Cancela, H., & Acerenza, L. (2008). A strategy to calculate the patterns of nutrient consumption by microorganisms applying a two-level optimisation principle to reconstructed metabolic networks. Journal of Biological Physics. [DOI]
Epidemiology, Mobility and Urban Health
- Ponce-de-León, M.✉︎, Pontes, C., Arenas, A., & Valencia, A. (2025). Assessing the impact of interregional mobility on COVID-19 spread in Spain using transfer entropy. Scientific Reports, 15(1), 31504. [DOI]
- Navarro-Martínez, A., Hajji, M., Armengol, J. M., Soret, A., Ponce-de-León, M.✉︎, & Valencia, A. (2025). The effect of recurrent mobility on air pollution exposure and mortality burden in Catalonia. International Journal of Health Geographics, 24(1), 19. [DOI]
- Naidoo, M., Shephard, W., Mtshali, N., Kambewe, I., Muthien, B., Abuelezam, N. N., Ponce-de-León, M., et al. (2025). How to incorporate social vulnerability into epidemic mathematical modelling: recommendations from an international Delphi. Social Science & Medicine, 383, 118352. [DOI]
- Andrienko, G., Andrienko, N., Akila, M., Kathirgamanathan, B., & Ponce-de-León, M. (2026). Detecting Stable Cross-Impact Patterns in Bivariate Time Series. IEEE Transactions on Visualization and Computer Graphics. [DOI]
- Andrienko, G., Andrienko, N., & Ponce-de-León, M. (2024). Mapping Time Lags in Epidemics. Abstracts of the ICA, 8, 2.
- Smith, M., Ponce-de-León, M., & Valencia, A. (2022). Evaluating the policy of closing bars and restaurants in Cataluña and its effects on mobility and COVID-19 incidence. Scientific Reports, 12(1), 9132. [DOI]
- Ponce-de-León, M.✉︎, Del Valle, J., et al. (2021). COVID-19 Flow-Maps: an open geographic information system on COVID-19 and human mobility for Spain. Scientific Data, 8(1), 310. [DOI]
- Ferrari, A., Santus, E., Cirillo, D., Ponce-de-León, M., et al. (2021). Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. NPJ Digital Medicine, 4(1), 9. [DOI]
- Noël, V., Carbonell, J., Ponce-de-León, M., et al. (2020). PhysiBoSS-COVID: Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework.
HPC, Computational Infrastructure and Big Data
- Streviniotis, E., Giatrakos, N., Kotidis, Y., Ntiniakou, T., & Ponce-de-León, M. (2025). RATS: A resource allocator for optimizing the execution of tumor simulations over HPC infrastructures. Information Systems, 132, 102538. [DOI]
- Streviniotis, E., Giatrakos, N., Kotidis, Y., Ntiniakou, T., & Ponce-de-León, M. (2023). Optimizing Resource Allocation for Tumor Simulations over HPC Infrastructures. In 2023 IEEE 10th International Conference on Data Science and Advanced Analytics (DSAA).
- Akasiadis, C., Ponce-de-León, M., et al. (2022). Parallel model exploration for tumor treatment simulations. Computational Intelligence. [DOI]
- Saxena, G., Ponce-de-León, M., Montagud, A., Vicente Dorca, D., & Valencia, A. (2021). BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. In Computational Methods in Systems Biology, 266–279. [DOI]
- Giatrakos, N., et al. (2020). Infore: Interactive cross-platform analytics for everyone. In Proceedings of the 29th ACM International Conference on Information & Knowledge Management, 3389–3392.
- Giatrakos, N., et al. (2019). Interactive extreme-scale analytics: towards battling cancer. IEEE Technology and Society Magazine, 38(2), 54–61. [DOI]
- Lloret-Llinares, M., Thomas-Lopez, D., Carbonell-Caballero, J., Calzone, L., Conejero, J., Harrison, J. P., Kratochvil, M., Montagud, A., Noël, V., Nortamo, H., Ponce-de-León, M., et al. (2026). Leveraging training expertise to build capacity in computational personalised medicine. Bioinformatics Advances, 6(1), vbag070. [DOI]
Bioinformatics, Genomics, and Sequence Analysis
- Carels, N., & Ponce-de-León, M. (2015). An interpretation of the ancestral codon from Miller's amino acids and nucleotide correlations in modern coding sequences. Bioinformatics and Biology Insights, 9. [DOI]
- Ponce-de-León, M., Basilio de Miranda, A., Alvarez-Valin, F., & Carels, N. (2014). The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins. Bioinformatics and Biology Insights, 8, 93–108. [DOI]
- Greif, G.*, Ponce-de-León, M.*, Lamolle, G., Rodriguez, M., Piñeyro, D., Tavares-Marques, L. M., Reyna-Bello, A., Robello, C., & Alvarez-Valin, F. (2013). Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax. BMC Genomics, 14(1), 149. [DOI]
Research Projects
2026–2029 · EU Horizon Europe (grant 101238943)
Health Assessment Refinement for Mitigation of Noise and Air Quality Effects. Reduces the health impacts of air and noise pollution in European cities by linking pollution monitoring with health outcomes, modelling urban interventions, and providing decision-support tools for climate strategies.
2023–2025 · PI · UNICO I+D Cloud / NextGenerationEU
Open cloud platform for health management in complex urban environments, integrating mobility, environmental, and epidemiological data with AI and simulation-based workflows for epidemic preparedness and decision-making.
2022–2025 · EU Horizon Europe
Platform for real-time critical situation management and adaptive decision-making over extreme-scale data. Led the Health Crisis use case, developing EpiSim.jl for large-scale epidemiological modelling, calibration, and intervention optimization.
2020–2023 · EU Horizon 2020 (grant 951773)
HPC and exascale entry point for personalized medicine, translating omics data into mechanistic models of cellular behaviour. Contributed multicellular simulation workflows for cancer research, including tumour dynamics and drug response analyses.
