Modeling & simulation

We target specialized journals dedicated to the development of computational tools, and broader audience journals where state-of-the art technologies are applied to the investigation and elucidation of biological processes in key and emerging research areas.

The value of our research

publications-infographic

poster June 24, 2026 | ENCALS 2026

De Nardi Alex, Paris Alessio, Lauria Mario, Martinelli Ilaria, Zucchi Elisabetta, Mesini Nicolò, Mandrioli Jessica, Marchetti Luca

A Multi-Linear Model For Predicting ALSFRS-R Score Progression Using Heterogeneous Longitudinal Data From Clinical Studies

This work presents a computational model to predict the progression of Amyotrophic Lateral Sclerosis (ALS) by integrating longitudinal clinical data,...

poster June 16, 2026 | Biomath 2026

Bozza Marco, Giampiccolo Stefano, Marchetti Luca

Surrogate-Assisted Virtual Population Generation in QSP Models

Abstract. Background: Quantitative Systems Pharmacology (QSP) models are increasingly used to investigate drug effects in complex biological systems....

poster June 15, 2026 | PAGE 2026 - Dubrovnik

Righetti Elena, D’Agaro Niccolò, Bozza Marco, Giampiccolo Stefano, Pezzuto Simone, Reali Federico

No One-Size-Fits-All: A Multi-Model Evaluation of Optimization-Based and Surrogate-Assisted Virtual Population Generation in QSP

Background Quantitative systems pharmacology (QSP) models increasingly support clinical decision-making by integrating mechanistic knowledge with heterogeneous...

poster June 11, 2026

De Nardi Alex, Paris Alessio, Lauria Mario, Marchetti Luca

A minimal mechanistic QSP-ready model to bridge aggrephagy and mTOR signaling in ALS

Objectives: Develop a parsimonious model of aggrephagy in ALS that can be incorporated as a selective autophagy module within published mTOR QSP models...

poster June 10, 2026 | PAGE 2026 - Dubrovnik

Boaretti Daniele, Levi Micha, Dartois Veronique, Reali Federico

A lesion-centric extension of a minimal PBPK model to predict anti-tuberculosis drug target attainment in rabbits

Tuberculosis (TB), one of the deadliest infectious diseases worldwide [1], still requires therapy optimization to eradicate Mycobacterium tuberculosis...

poster June 9, 2026 | PAGE 2026 - Dubrovnik

Chiesa Martina, Righetti Elena, Domenici Enrico, Reali Federico

Toward a Quantitative Systems Pharmacology framework of cell-level alpha-synuclein dynamics

Introduction: Parkinson’s disease (PD) – the second most prevalent neurodegenerative disorder worldwide [1] – is characterized by the progressive...

Our books

Analysis Of Biological Systems

Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science.

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2015

Simulation Algorithms for Computational Systems Biology

This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies. This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.

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2018

Check out COSBI publications on PubMed

Scientific publications