Arnau Montagud Aquino
Systems Biology Modeling · I2SYSBIO
Biography
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My goal as a researcher is to understand the mechanisms behind diseases by using personalised models in biomedical and biotechnological projects. To do this, I lean on tools from mathematics and computer science to solve interesting problems in biology. I am interested in combining multi-omics patient data to build multiscale models of cellular behaviours that merge intracellular models, agents for cells and a complex environment. Once built, these models need to be optimised to run efficiently in high-performance computers to have real-sized simulations, scaling-up the scope of projects. If these subjects resonate with your interests, feel free to reach out! Download my resumé Interests
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Profile
| Institution | I2SYSBIO |
| Position | PI, Tenured Researcher |
| Home page | https://arnaumontagud.netlify.app/ |
| Contact email | arnau.montagud@csic.es |
| ORCID | 0000-0002-7696-1241 |
BCB Hub
| BCB Committee | Expertise mapping, Future Plan |
| BCB Tools | PhysiBoSS, PROFILE |
| BCB Services |
Research
Research topics
Computational MethodsResourcesBioinformatics Software and ToolsAnalysis packages (R, Python, etc.)Applications of Computational BiologyModel organismsBioinformatics enabling techniquesBenchmarkingFunctional genomicsComputational models and simulationsBiosystems ModelingGene regulatory networks
View all (9 more)
Metabolic modellingComputational TechniquesHigh-performance ComputingParallel ComputingDesktop applicationPersonal medicineSystems BiologyRegulatory biologyPathway analysis
Research lines
None
Projects, networks, transfer & teaching
Funded projects 2
Publications 40 entries
- Systems biology at the body scale: Toward adaptive digital twins in precision medicine Article · Jun 2026
- Experimentally calibrated multiscale model predicts schedule dependent drug combination effects Article · 3 Mar 2026
- Leveraging training expertise to build capacity in computational personalised medicine Article · 2026
- PhysiBoSS-Models: A database for multiscale models Conference paper · 29 Sep 2025
- Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative Preprint · 18 Jul 2025
View all (35 more)
- Immune digital twins for complex human pathologies: applications, limitations, and challenges Article · 30 Nov 2024
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches Article · 13 Feb 2024
- PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks Software · 30 Oct 2023
- Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation Conference paper · 26 Jun 2023
- Multiscale model of the different modes of cancer cell invasion Article · 1 Jun 2023
- Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth Article · 6 Apr 2022
- Parallel model exploration for tumor treatment simulations Article · 3 Mar 2022
- Patient-specific Boolean models of signalling networks guide personalised treatments Article · 15 Feb 2022
- Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems Article · Dec 2021
- COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms Article · 1 Oct 2021
- Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development Article · 12 Mar 2021
- BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems Book / chapter · 2021
- INforE: Interactive Cross-platform Analytics for Everyone Conference paper · 19 Oct 2020
- Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction Article · 5 Sep 2019
- Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients Software · 24 Jan 2019
- Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling Article · Sep 2018
- PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling Software · 30 Aug 2018
- Conceptual and computational framework for logical modelling of biological networks deregulated in diseases Article · 8 Dec 2017
- Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites Article · 21 Oct 2015
- Sins, Ethics and Biology Article · 16 Oct 2014
- Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. Article · 20 Aug 2014
- New approach for phylogenetic tree recovery based on genome-scale metabolic networks Article · Jul 2014
- Synechocystis sp. PCC6803 metabolic models for the enhanced production of hydrogen Article · 3 Oct 2013
- Automation on the generation of genome-scale metabolic models Article · Dec 2012
- A modular synthetic device to calibrate promoters Article · Mar 2012
- Construction of a chassis for hydrogen production: physiological and molecular characterization of a Synechocystis sp PCC 6803 mutant lacking a functional bidirectional hydrogenase Article · 1 Feb 2012
- Experimental and Modeling Analysis of Synechocystis sp. PCC 6803 Growth Article · 2012
- Microbial diversity in the midguts of field and lab-reared populations of the European Corn Borer Ostrinia nubilalis Article · 30 Jun 2011
- Aequorin-expressing yeast emits light under electric control Article · Mar 2011
- Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp PCC6803 Article · 11 Jan 2011
- Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium Article · 17 Nov 2010
- Yeast cultures with UCP1 uncoupling activity as a heating device Article · Dec 2009
- Metabolic flux analysis of the hydrogen production potential in Synechocystis sp. PCC6803 Article · Nov 2009
- Vanillin cell sensor Article · 1 Jun 2007
- Modelling and analysis of biological systems to obtain biofuels Thesis