Publications

(2022). PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. bioRxiv, pp. 2022.01.06.468363, https://doi.org/10.1101/2022.01.06.468363.

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(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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(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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(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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(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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(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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(2021). Patient-specific Boolean models of signaling networks guide personalized treatments. eLife 11:e72626, https://doi.org/10.7554/eLife.72626.

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(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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(2020). INforE: Interactive Cross-platform Analytics for Everyone. NA, pp. 3389–3392, https://doi.org/10.1145/3340531.3417435.

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(2019). Framework for high-throughput personalization of logical models using multi-omics data. Chapman and Hall/CRC.

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(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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(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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(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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(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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(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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(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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(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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(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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(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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(2014). Herramienta para la optimización de flujos metabólicos en un sistema biológico. Investigación Operacional, (35), 2, pp. 96–103.

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

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(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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(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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(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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(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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(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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(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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(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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(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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(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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(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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(2010). El equipo Valencia-iGEM diseña y construye la primera pantalla biológica. Matematicalia, (6), 3, pp. 1–5.

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(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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(2009). Sins, Ethics and Biology. Valencia iGEM team.

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(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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(2009). Introduction to Synthetic Biology. PoliCLICK.

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(2007). Vanillin cell sensor. IET Synthetic Biology, (1), 1-2, pp. 74, https://doi.org/10.1049/iet-stb:20060003.

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