Arnau Montagud

Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative

This paper presents a community-driven benchmarking initiative for cell-based multiscale models, highlighting variations in tool implementations and advocating for standardized benchmarks and interoperability.

Explainable Generative AI Uncovers a Molecular Continuum in Medulloblastoma with Implications for Rare Cancer Subtyping and Treatment Equity

This study uses synthetic data generation and explainable AI to uncover an intermediate subgroup in medulloblastoma, highlighting treatment disparities and supporting the continuum hypothesis between Groups 3 and 4.

PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

PhysiBoSS 2.0 integrates stochastic Boolean and agent-based models for multiscale cancer simulations, improving modularity and functionality.

Multiscale model of the different modes of cancer cell invasion

The paper presents a multiscale model of cancer cell invasion using PhysiBoSS, integrating spatial and intracellular processes to study migration modes and validate against experimental data.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

Optimizing dosage-specific treatments in a multi-scale model of a tumor growth

The paper develops an HPC-optimized workflow to explore treatment strategies for tumor growth using a multi-scale model, finding that spatial geometry and population variability affect treatment effectiveness.

Patient-specific Boolean models of signaling networks guide personalized treatments

The paper develops patient-specific Boolean models of prostate cancer signaling networks to identify actionable targets for personalized treatment, finding dose-dependent effects of inhibitors on key targets.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

PhysiBoSS integrates multi-scale agent-based modelling with Boolean networks to study cell population dynamics and treatment responses in 2D and 3D environments.