Miguel Ponce de León

Content

• Working Papers
• Publications
  • Systems Biology and Cancer Modeling
  • Epidemiology, Mobility and Urban Health
  • HPC, Computational Infrastructure and Big Data
  • Bioinformatics, Genomics, and Sequence Analysis
• Research Projects
  • Soon

Working Papers

Coming soon

Publications

Systems Biology

• 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.
• Niarakis, A., et al. (2024). Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology.
• 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.
• 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.
• 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.
• 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.
• Ponce-de-León, M.✉︎, et al. (2017). Determinism and contingency shape metabolic complementation in an endosymbiotic consortium. Frontiers in Microbiology.
• Mori, M., Ponce-de-León, M., Peretó, J., & Montero, F. (2016). Metabolic complementation in bacterial communities: necessary conditions and optimality. Frontiers in Microbiology.
• 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.
• 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.
• 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.
• 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.

Epidemiology, Mobility and Urban Health

• Ponce-de-León, M.✉︎, Pontes, C., Arenas, A., & Valencia, A. (2025). Assessing the impact of interregional mobility on COVID19 spread in Spain using transfer entropy. Scientific Reports, 15(1), 31504.
• 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.
• Naidoo, M., Shephard, W., Mtshali, N., Kambewe, I., Muthien, B., Abuelezam, N. N., Ponce-de-León, M., Villela, D. A. M., Paes-Sousa, R., Pan-ngum, W., et al. (2025). How to incorporate social vulnerability into epidemic mathematical modelling: recommendations from an international Delphi. Social Science & Medicine, 118352.
• Noël, V., Carbonell, J., Ponce-de-León, M., Soliman, S., Niarakis, A., Calzone, L., Barillot, E., & Valencia, A., et al. (2020). PhysiBoSS-COVID: Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework.
• 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 COVID19 incidence. Scientific Reports, 12(1), 9132.
• 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.
• 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.

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.
• Streviniotis, E., Giatrakos, N., Kotidis, Y., Ntiniakou, T., & Ponce-de-León, M. (2023). Optimizing Resource Allocation for Tumor Simulations over HPC Infrastructures.
• Akasiadis, C., Ponce-de-León, M., et al. (2022). Parallel model exploration for tumor treatment simulations. Computational Intelligence.
• 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.
• Giatrakos, N., .... , Ponce-de-León, M., 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., .... , Ponce-de-León, M., et al. (2019). Interactive extreme-scale analytics: towards battling cancer. IEEE Technology and Society Magazine, 38(2), 54–61.

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, BBI–S24021.
• 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.
• 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.

Ressearch Projects

Coming soon