BioSystems Modelling Group

  • Systems Biology
  • Signalling and metabolic pathways, gene regulation networks
  • Epidemic and population models
  • Modelling and simulation
  • ODEs and stochastic modelling
  • Formal methods
  • Model checking and static analyses

Members

Roberta Gori

Roberta Gori

Associate Professor

Francesca Levi

Associate Professor

Paolo Milazzo

Associate Professor

Lucia Nasti

PostDoc

Projects

MEDICA: Modelling and vErification of alkaptonuria and multiple sclerosis Driven by biomedICAl data

PRIN 2022 Project, 2023.

(Abstract | Links)

Abstract: The goal of this project is to bridge the gap between data, models and validation, integrating the data-driven and model-driven research directions, so that to develop next generation modelling and analysis approaches for biomedical investigations. We are tackling open research questions for Multiple Sclerosis (MS) and Alkaptonuria (AKU), for which we have world-leading experts in our consortium.

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PreMed2

Funder: Regione Toscana, Bando Salute, 2020.

(Abstract)

The main purpose of this project is to identify the population of subjects at risk of developing type 2 diabetes based on eating habits (using validated questionnaires), physical activity (using wearable devices) and metabolic profile.

The BioSystems Modeling group is involved in data analysis with the application of systems biology approaches.

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Metodi Informatici Integrati per la Biomedica

PRA – Progetti di Ricerca di Ateneo (Institutional Research Grants) - Project no. PRA_2020-2021_26 , 2020.

(Abstract)

This project aims at integrating different computer methodologies that contribute to interdisciplinary research in bioinformatics and, in particular, to its applications in the biomedical field. This in order to experiment the co-existence of algorithmic, modeling, and machine learning methods in the analysis of biomedical data and, at the same time, to refine the synergy of the many research groups that have been active in the Department of Computer Science for decades.

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Selected Publications

2020

Bove, Pasquale; Micheli, Alessio; Milazzo, Paolo; Podda, Marco

Prediction of Dynamical Properties of Biochemical Pathways with Graph Neural Networks Proceedings Article

In: Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies, SCITEPRESS - Science and Technology Publications, 2020.

Links | BibTeX

Barbuti, Roberto; Gori, Roberta; Milazzo, Paolo

Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation Journal Article

In: Theoretical Computer Science, 2020.

Links | BibTeX

2016

Barbuti, Roberto; Gori, Roberta; Levi, Francesca; Milazzo, Paolo

Investigating dynamic causalities in reaction systems Journal Article

In: Theoretical Computer Science, vol. 623, pp. 114–145, 2016.

Links | BibTeX

Sameen, Sheema; Barbuti, Roberto; Milazzo, Paolo; Cerone, Antonio; Re, Marzia Del; Danesi, Romano

Mathematical modeling of drug resistance due to KRAS mutation in colorectal cancer Journal Article

In: Journal of Theoretical Biology, vol. 389, pp. 263–273, 2016.

Links | BibTeX

2012

Barbuti, Roberto; Levi, Francesca; Milazzo, Paolo; Scatena, Guido

Probabilistic model checking of biological systems with uncertain kinetic rates Journal Article

In: Theoretical Computer Science, vol. 419, pp. 2–16, 2012.

Links | BibTeX