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

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Scientific Publications

poster | QSPC 2026 Leiden

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

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

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scientific paper | The AAPS Journal

Danilo Tomasoni, Alessio Paris, Roberto Visintainer

Predicting Aberrant Fc-fusion Protein Pharmacokinetics from In Silico Structural Properties and Physiologically Based Pharmacokinetic (PBPK) Modeling

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scientific paper | bioRxiv

Elio Campanile, Elisa Pettinà, Stefano Giampiccolo, Lorena Leonardelli, Luca Marchetti

Physiologically Based Pharmacokinetic Modeling of mRNA-Encoded Therapeutics: A Multiscale Framework for LNP and Antibody Trafficking in Mice.

Antibody-based therapeutics have revolutionized disease treatment, and recent advances in messenger RNA (mRNA) technologies have opened new opportunities...

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scientific paper

Giada Fiandaca, Elio Campanile, Lorena Leonardelli, Elisa Pettinà, Stefano Giampiccolo, Elizabeth J. Carstens, Lorenzo Dasti, Natascia Zangani, Luca Marchetti

A multiscale physiologically based pharmacokinetic model to support mRNA-encoded BiTE therapy in cancer treatment

In the field of cancer therapy, bispecific T cell engagers (BiTEs) have demonstrated significant potential. However, their clinical application is constrained...

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scientific paper

Roberto Visintainer, Anna Fochesato, Daniele Boaretti, Stefano Giampiccolo, Shayne Watson, Micha Levi, Federico Reali, Luca Marchetti

stormTB: a web-based simulator of a murine minimal-PBPK model for anti-tuberculosis treatments —– National Library of Medicine

Tuberculosis (TB) poses a significant threat to global health, with millions of new infections and approximately one million deaths annually. Various...

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scientific paper | npj Systems Biology and Applications

Stefano Giampiccolo, Federico Reali, Anna Fochesato, Giovanni Iacca, Luca Marchetti

Robust parameter estimation and identifiability analysis with hybrid neural ordinary differential equations in computational biology

Parameter estimation is one of the central challenges in computational biology. In this paper, we present an approach to estimate model parameters and...

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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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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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Scientific publications

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