Publications

Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noel, Gerard Pradas, Annika Meert, Emmanuel Barillot, Laurence Calzone, Alfonso Valencia (2023). PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. npj Systems Biology and Applications, 9, (1), pp. 1-12_, https://doi.org/10.1038/s41540-023-00314-4.

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Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, José Carbonell-Caballero, Alfonso Valencia (2023). Lessons learned from a performance analysis and optimization of a multiscale cellular simulation. Proceedings of the Platform for Advanced Scientific Computing Conference (PASC'23), pp. 1-10, https://doi.org/10.1145/3592979.3593403.

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Marco Ruscone, Arnau Montagud, Philippe Chavrier, Olivier Destaing, Isabelle Bonnet, Andrei Zinovyev, Emmanuel Barillot, Vincent Noel, Laurence Calzone (2023). Multiscale model of the different modes of cancer cell invasion. Bioinf, 39, (6), pp. btad374_, https://doi.org/10.1093/bioinformatics/btad374.

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Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras (2022). Parallel Model Exploration for Tumor Treatment Simulations. Computational Intelligence. 2022; pp. 1-23, https://doi.org/10.1111/coin.12515.

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Miguel Ponce-de-Leon, Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou, Alfonso Valencia (2022). Optimizing dosage-specific treatments in a multi-scale model of a tumor growth. Front. Mol. Biosci. 9:836794, https://doi.org/10.3389/fmolb.2022.836794.

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Arnau Montagud, Jonas Béal, Luis Tobalina, Pauline Traynard, Vigneshwari Subramanian, Bence Szalai, Robert Alfoldi, Laszlo Puskas, Alfonso Valencia, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone (2022). Patient-specific Boolean models of signaling networks guide personalized treatments. eLife 11:e72626, https://doi.org/10.7554/eLife.72626.

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

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Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce-de-Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Drager, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Bornigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. a. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology, (17), 10, pp. e10387, https://doi.org/10.15252/msb.202110387.

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Gaurav Saxena, Miguel Ponce-de-Leon, Arnau Montagud, David Vicente Dorca, Alfonso Valencia (2021). BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. Computational Methods in Systems Biology, pp. 266-279, https://doi.org/10.1007/978-3-030-85633-5_18.

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Enrico Santus, Nicola Marino, Davide Cirillo, Emmanuele Chersoni, Arnau Montagud, Antonella Santuccione Chadha, Alfonso Valencia, Kevin Hughes, Charlotta Lindvall (2021). Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development. Journal of Medical Internet Research, (23), 3, pp. e22453, https://doi.org/10.2196/22453.

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Nikos Giatrakos, David Arnu, Theodoros Bitsakis, Antonios Deligiannakis, Minos Garofalakis, Ralf Klinkenberg, Aris Konidaris, Antonis Kontaxakis, Yannis Kotidis, Vasilis Samoladas (2020). INforE: Interactive Cross-platform Analytics for Everyone. NA, pp. 3389–3392, https://doi.org/10.1145/3340531.3417435.

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Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone (2019). Framework for high-throughput personalization of logical models using multi-omics data. Chapman and Hall/CRC.

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

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Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev, Laurence Calzone (2019). PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling. Bioinformatics, 35 (7), pp. 1188–1196, https://doi.org/10.1093/bioinformatics/bty766.

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Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone (2019). Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients. Front. Physiol., (9), pp. 1965, https://doi.org/10.3389/fphys.2018.01965.

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Antoine Forget, Loredana Martignetti, Stéphanie Puget, Laurence Calzone, Sebastian Brabetz, Daniel Picard, Arnau Montagud, Stéphane Liva, Alexandre Sta, Florent Dingli, Guillaume Arras, Jaime Rivera, Damarys Loew, Aurore Besnard, Joëlle Lacombe, Mélanie Pagès, Pascale Varlet, Christelle Dufour, Hua Yu, Audrey L. Mercier, Emilie Indersie, Anaïs Chivet, Sophie Leboucher, Laura Sieber, Kevin Beccaria, Michael Gombert, Frauke D. Meyer, Nan Qin, Jasmin Bartl, Lukas Chavez, Konstantin Okonechnikov, Tanvi Sharma, Venu Thatikonda, Franck Bourdeaut, Celio Pouponnot, Vijay Ramaswamy, Andrey Korshunov, Arndt Borkhardt, Guido Reifenberger, Patrick Poullet, Michael D. Taylor, Marcel Kool, Stefan M. Pfister, Daisuke Kawauchi, Emmanuel Barillot, Marc Remke, Olivier Ayrault (2018). Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling. Cancer Cell, (34), 3, pp. 379–395.e7, https://doi.org/10.1016/j.ccell.2018.08.002.

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Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone (2017). Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings in Bioinformatics, bbx163, https://doi.org/10.1093/bib/bbx163.

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Filipe Pinto, Catarina C Pacheco, Paulo Oliveira, Arnau Montagud, Andrew Landels, Narciso Couto, Phillip C Wright, Javier F Urchueguía, Paula Tamagnini (2015). Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Research, (22), 6, pp. 425–437, https://doi.org/10.1093/dnares/dsv024.

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Arnau Montagud, Daniel Gamermann, Pedro Fernández de Córdoba, Javier F Urchueguía (2015). Synechocystis sp. PCC6803 metabolic models for the enhanced production of biofuels. Critical Reviews in Biotechnology, (35), 2, pp. 184–198, https://doi.org/10.3109/07388551.2013.829799.

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Daniel Gamermann, Arnau Montagud, RA Jaime-Infante, Julián Triana, Javier F Urchueguía, Pedro Fernández de Córdoba (2014). PyNetMet: Python tools for efficient work with networks and metabolic models. Computational and Mathematical Biology, (3), 5, pp. 1–19.

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Arnau Montagud (2014). Presente y futuro de los modelos matemáticos en la lucha contra el cáncer. NA.

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Daniel Gamermann, Arnau Montagud, Jose Alberto Conejero, Javier F. Urchueguía, Pedro Fernández de Córdoba (2014). New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks. Journal of Computational Biology, (21), 7, pp. 508–19, https://doi.org/10.1089/cmb.2013.0150.

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RA Jaime-Infante, Z Hernández-Martínez, J Triana-Dopico, O Fosado-Tellez, Arnau Montagud, Daniel Gamermann, Pedro Fernández de Córdoba, Javier F Urchueguía (2014). Herramienta para la optimización de flujos metabólicos en un sistema biológico. Investigación Operacional, (35), 2, pp. 96–103.

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Julián Triana, Arnau Montagud, Maria Siurana, David Fuente, Arantxa Urchueguía, Daniel Gamermann, Javier Torres, Jose Tena, Pedro Fernández de Córdoba, Javier F Urchueguía (2014). Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. Metabolites, (4), 3, pp. 680–698, https://doi.org/10.3390/metabo4030680.

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Arnau Montagud (2013). Modelling and analysis of biological systems to obtain biofuels. LAP Lambert Academic Publishing.

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Miguel Lopo, Arnau Montagud, Emilio Navarro, Isabel Cunha, Andrea Zille, Pedro Fernández de Córdoba, Pedro Moradas-Ferreira, Paula Tamagnini, Javier F Urchueguía (2012). Experimental and Modeling Analysis of Synechocystis sp. PCC6803 Growth. Journal of molecular microbiology and biotechnology, (22), 2, pp. 71–82, https://doi.org/10.1159/000336850.

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Filipe Pinto, Karin A Van Elburg, Catarina C Pacheco, Miguel Lopo, Josselin Noirel, Arnau Montagud, Javier F Urchueguía, Phillip C Wright, Paula Tamagnini (2012). Construction of a chassis for hydrogen production: physiological and molecular characterization of a Synechocystis sp. PCC6803 mutant lacking a functional bidirectional hydrogenase. Microbiology (Reading, England), (158), 2, pp. 448–464, https://doi.org/10.1099/mic.0.052282-0.

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Raymari Reyes, Daniel Gamermann, Arnau Montagud, David Fuente, Julián Triana, Javier F Urchueguía, Pedro Fernández de Córdoba (2012). Automation on the generation of genome-scale metabolic models. Journal of computational biology : a journal of computational molecular cell biology, (19), 12, pp. 1295–306, https://doi.org/10.1089/cmb.2012.0183.

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Daniel Gamermann, Arnau Montagud, Pablo Aparicio, Emilio Navarro, Julián Triana, Francisco R Villatoro, Javier F Urchueguía, Pedro Fernández de Córdoba (2012). A Modular Synthetic Device To Calibrate Promoters. Journal of Biological Systems, (20), 1, pp. 37, https://doi.org/10.1142/S0218339012500015.

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Eugeni Belda, Laia Pedrola, Juli Peretó, Juan F Martínez-Blanch, Arnau Montagud, Emilio Navarro, Javier F Urchueguía, Daniel Ramón, Andrés Moya, Manuel Porcar (2011). Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis. PLoS ONE, (6), 6, pp. e21751, https://doi.org/10.1371/journal.pone.0021751.

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Arnau Montagud, Aleksej Zelezniak, Emilio Navarro, Pedro Fernández de Córdoba, Javier F Urchueguía, Kiran Raosaheb Patil (2011). Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803. Biotechnology Journal, (6), 3, pp. 330–342, https://doi.org/10.1002/biot.201000109.

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Raymari Reyes, Jorge Garrido, Ramón A Jaime, Vinelia Vazquez, Julián Triana, Lizzael Villar, Juan C Castro, Pedro Fernández de Córdoba, Javier F Urchueguía, Emilio Navarro, Arnau Montagud (2011). Desarrollo de una plataforma computacional para el modelado metabólico de un microorganismo. Nereis. Revista Iberoamericana de Métodos, Modelización y Simulación Interdisciplinar., (3), pp. 25–31.

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Cristina Vilanova, Angeles Hueso, Carles Palanca, Guillem Marco, Miguel Pitarch, Eduardo Otero, Juny Crespo, Jerzy Szablowski, Sara Rivera, Laura Domínguez-Escribà, Emilio Navarro, Arnau Montagud, Pedro Fernández de Córdoba, Asier González, Joaquín Ariño, Andrés Moya, Javier F Urchueguía, Manuel Porcar (2011). Aequorin-expressing yeast emits light under electric control. Journal of Biotechnology, (152), pp. 93–5, https://doi.org/10.1016/j.jbiotec.2011.01.005.

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Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F Urchueguía, Kiran Raosaheb Patil (2010). Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Systems Biology, (4), 1, pp. 156, https://doi.org/10.1186/1752-0509-4-156.

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Miguel Pitarch, Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F Urchueguía (2010). iGEM: una experiencia educativa única de trabajo en grupos multidisciplinares en el campo de la biologia. Revista de la Facultad de Educación, (17), pp. 57–63.

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Miguel Pitarch, Juny Crespo, Angeles Hueso, Guillem Marco, Eduardo Otero, Carles Palanca, Sara Rivera, Cristina Vilanova, Jerzy Szablowski, Laura Domínguez-Escribà, Arnau Montagud, Emilio Navarro, Manuel Porcar, Juli Peretó, JJ Pérez, Javier F Urchueguía, Pedro Fernández de Córdoba (2010). El equipo Valencia-iGEM diseña y construye la primera pantalla biológica. Matematicalia, (6), 3, pp. 1–5.

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Joaquina Delás, Meritxell Notari, Jaume Forés, Joaquín Pechuan, Manuel Porcar, Emilio Navarro, Arnau Montagud, Minerva Baguena, Juli Peretó, Pedro Fernández de Córdoba, M Mar González-Barroso, Eduardo Rial, Andrés Moya, Javier F Urchueguía (2009). Yeast cultures with UCP1 uncoupling activity as a heating device. New Biotechnology, (26), 6, pp. 300–6, https://doi.org/10.1016/j.nbt.2009.09.005.

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Carles Palanca, Juny Crespo, Cristina Vilanova, Guillem Marco, Sara Rivera, Angeles Hueso, Miguel Pitarch, Eduardo Otero, Jerzy Szablowski, Arnau Montagud, Emilio Navarro, Manuel Porcar (2009). Sins, Ethics and Biology. Valencia iGEM team.

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

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Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F Urchueguía (2009). Introduction to Synthetic Biology. PoliCLICK.

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Guillermo Rodrigo, Arnau Montagud, Alberto Aparici, Maria Cristina Aroca, Minerva Baguena, Javier Carrera, Carlos Edo, Pedro Fernández de Córdoba, Albert Ferrando, Gustavo Fuertes, Diana Gimenez, Caterina Mata, Jose Vicente Medrano, Carlos Navarrete, Emilio Navarro, Jesús Salgado, Pablo Tortosa, Javier F Urchueguía, Alfonso Jaramillo (2007). Vanillin cell sensor. IET Synthetic Biology, (1), 1-2, pp. 74, https://doi.org/10.1049/iet-stb:20060003.

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