Ponce-de-Leon, M., Montagud, A., Noel, V., Pradas, G., Meert, A., Barillot, E., Calzone, L., & Valencia, A. (2022). PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. https://doi.org/10.1101/2022.01.06.468363

Montagud, A., Béal, J., Tobalina, L., Traynard, P., Subramanian, V., Szalai, B., Alföldi, R., Puskás, L., Valencia, A., Barillot, E., Saez-Rodriguez, J., & Calzone, L. (2022). Patient-specific Boolean models of signalling networks guide personalised treatments. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.72626

Akasiadis, C., Ponce‐de‐Leon, M., Montagud, A., Michelioudakis, E., Atsidakou, A., Alevizos, E., Artikis, A., Valencia, A., & Paliouras, G. (2022). Parallel model exploration for tumor treatment simulations. Computational Intelligence, 38(4), 1379–1401. Portico. https://doi.org/10.1111/coin.12515

Ruscone, M., Montagud, A., Chavrier, P., Destaing, O., Bonnet, I., Zinovyev, A., Barillot, E., Noël, V., & Calzone, L. (2022). Multiscale model of the different modes of cancer cell invasion. https://doi.org/10.1101/2022.10.07.511296

Santus, E., Marino, N., Cirillo, D., Chersoni, E., Montagud, A., Santuccione Chadha, A., Valencia, A., Hughes, K., & Lindvall, C. (2021). Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development. Journal of Medical Internet Research, 23(3), e22453. https://doi.org/10.2196/22453

Saxena, G., Ponce-de-Leon, M., Montagud, A., Vicente Dorca, D., & Valencia, A. (2021). BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. Computational Methods in Systems Biology, 266–279. https://doi.org/10.1007/978-3-030-85633-5_18

Montagud, A., Ponce-de-Leon, M., & Valencia, A. (2021). Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology, 28, 100385. https://doi.org/10.1016/j.coisb.2021.100385

Ponce-de-Leon, M., Montagud, A., Akasiadis, C., Schreiber, J., Ntiniakou, T., & Valencia, A. (2021). Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth. https://doi.org/10.1101/2021.12.17.473136

Giatrakos, N., Arnu, D., Bitsakis, T., Deligiannakis, A., Garofalakis, M., Klinkenberg, R., Konidaris, A., Kontaxakis, A., Kotidis, Y., Samoladas, V., Simitsis, A., Stamatakis, G., Temme, F., Torok, M., Yaqub, E., Montagud, A., Ponce de León, M., Arndt, H., & Burkard, S. (2020). INforE. Proceedings of the 29th ACM International Conference on Information & Knowledge Management, 3389–3392. https://doi.org/10.1145/3340531.3417435

Béal, J., Montagud, A., Traynard, P., Barillot, E., & Calzone, L. (2019). Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients. Frontiers in Physiology, 9. https://doi.org/10.3389/fphys.2018.01965

Gamermann, D., Montagud, A., Conejero, J. A., Fernández de Córdoba, P., & Urchueguía, J. F. (2019). Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction. PLOS ONE, 14(9), e0221631. https://doi.org/10.1371/journal.pone.0221631

Forget, A., Martignetti, L., Puget, S., Calzone, L., Brabetz, S., Picard, D., Montagud, A., Liva, S., Sta, A., Dingli, F., Arras, G., Rivera, J., Loew, D., Besnard, A., Lacombe, J., Pagès, M., Varlet, P., Dufour, C., Yu, H., … Ayrault, O. (2018). Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling. Cancer Cell, 34(3), 379-395.e7. https://doi.org/10.1016/j.ccell.2018.08.002

Letort, G., Montagud, A., Stoll, G., Heiland, R., Barillot, E., Macklin, P., Zinovyev, A., & Calzone, L. (2018). PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics, 35(7), 1188–1196. https://doi.org/10.1093/bioinformatics/bty766

Montagud, A., Traynard, P., Martignetti, L., Bonnet, E., Barillot, E., Zinovyev, A., & Calzone, L. (2017). Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings in Bioinformatics, 20(4), 1238–1249. https://doi.org/10.1093/bib/bbx163

Pinto, F., Pacheco, C. C., Oliveira, P., Montagud, A., Landels, A., Couto, N., Wright, P. C., Urchueguía, J. F., & Tamagnini, P. (2015). Improving aSynechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Research, 22(6), 425–437. https://doi.org/10.1093/dnares/dsv024

Gamermann, D., Montagud, A., Conejero, J. A., Urchueguía, J. F., & de Córdoba, P. F. (2014). New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks. Journal of Computational Biology, 21(7), 508–519. https://doi.org/10.1089/cmb.2013.0150

Triana, J., Montagud, A., Siurana, M., Fuente, D., Urchueguía, A., Gamermann, D., Torres, J., Tena, J., De Córdoba, P., & Urchueguía, J. (2014). Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. Metabolites, 4(3), 680–698. https://doi.org/10.3390/metabo4030680

Montagud, A., Gamermann, D., Fernández de Córdoba, P., & Urchueguía, J. F. (2013). Synechocystissp. PCC6803 metabolic models for the enhanced production of hydrogen. Critical Reviews in Biotechnology, 35(2), 184–198. https://doi.org/10.3109/07388551.2013.829799

GAMERMANN, D., MONTAGUD, A., APARICIO, P., NAVARRO, E., TRIANA, J., VILLATORO, F. R., URCHUEGUÍA, J. F., & DE CÓRDOBA, P. F. (2012). A MODULAR SYNTHETIC DEVICE TO CALIBRATE PROMOTERS. Journal of Biological Systems, 20(01), 37–55. https://doi.org/10.1142/s0218339012500015

Lopo, M., Montagud, A., Navarro, E., Cunha, I., Zille, A., de Córdoba, P. F., Moradas-Ferreira, P., Tamagnini, P., & Urchueguía, J. F. (2012). Experimental and Modeling Analysis of <i> Synechocystis </i>sp. PCC 6803 Growth. Microbial Physiology, 22(2), 71–82. Portico. https://doi.org/10.1159/000336850

Pinto, F., van Elburg, K. A., Pacheco, C. C., Lopo, M., Noirel, J., Montagud, A., Urchueguía, J. F., Wright, P. C., & Tamagnini, P. (2012). Construction of a chassis for hydrogen production: physiological and molecular characterization of a Synechocystis sp. PCC 6803 mutant lacking a functional bidirectional hydrogenase. Microbiology, 158(2), 448–464. https://doi.org/10.1099/mic.0.052282-0

Reyes, R., Gamermann, D., Montagud, A., Fuente, D., Triana, J., Urchueguía, J. F., & de Córdoba, P. F. (2012). Automation on the Generation of Genome-Scale Metabolic Models. Journal of Computational Biology, 19(12), 1295–1306. https://doi.org/10.1089/cmb.2012.0183

Belda, E., Pedrola, L., Peretó, J., Martínez-Blanch, J. F., Montagud, A., Navarro, E., Urchueguía, J., Ramón, D., Moya, A., & Porcar, M. (2011). Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis. PLoS ONE, 6(6), e21751. https://doi.org/10.1371/journal.pone.0021751

Montagud, A., Zelezniak, A., Navarro, E., de Córdoba, P. F., Urchueguía, J. F., & Patil, K. R. (2011). Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803. Biotechnology Journal, 6(3), 330–342. Portico. https://doi.org/10.1002/biot.201000109

Vilanova, C., Hueso, Á., Palanca, C., Marco, G., Pitarch, M., Otero, E., Crespo, J., Szablowski, J., Rivera, S., Domínguez-Escribà, L., Navarro, E., Montagud, A., de Córdoba, P. F., González, A., Ariño, J., Moya, A., Urchueguía, J., & Porcar, M. (2011). Aequorin-expressing yeast emits light under electric control. Journal of Biotechnology, 152(3), 93–95. https://doi.org/10.1016/j.jbiotec.2011.01.005

Montagud, A., Navarro, E., Fernández de Córdoba, P., Urchueguía, J. F., & Patil, K. R. (2010). Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Systems Biology, 4(1). https://doi.org/10.1186/1752-0509-4-156

Delás, J., Notari, M., Forés, J., Pechuan, J., Porcar, M., Navarro, E., Montagud, A., Baguena, M., Peretó, J., Córdoba, P. F. de, González-Barroso, M. M., Rial, E., Moya, A., & Urchueguía, J. (2009). Yeast cultures with UCP1 uncoupling activity as a heating device. New Biotechnology, 26(6), 300–306. https://doi.org/10.1016/j.nbt.2009.09.005

Navarro, E., Montagud, A., Fernández de Córdoba, P., & Urchueguía, J. F. (2009). Metabolic flux analysis of the hydrogen production potential in Synechocystis sp. PCC6803. International Journal of Hydrogen Energy, 34(21), 8828–8838. https://doi.org/10.1016/j.ijhydene.2009.08.036