Data integration

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 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...

scientific paper May 27, 2026 | npj Systems Biology and Applications

Giampiccolo Stefano, Iacca Giovanni, Marchetti Luca

A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations

Abstract: Dynamical systems play a central role across the quantitative sciences, offering a powerful mathematical framework to describe, analyze, and...

scientific paper January 29, 2024 | Frontiers in genetics

Tomasoni Danilo, Lombardo Rosario, Lauria Mario

Strengths and limitations of non-disclosive data analysis: a comparison of breast cancer survival classifiers using VisualSHIELD

Abstract: Preserving data privacy is an important concern in the research use of patient data. The DataSHIELD suite enables privacy-aware advanced statistical...

scientific paper January 5, 2023 | Scientific Reports

Parolo Silvia, Mariotti Federica, Bora Pranami, Carboni Lucia, Domenici Enrico

Single-cell-led drug repurposing for Alzheimer’s disease

Abstract. Alzheimer's disease is the most common form of dementia. Notwithstanding the huge investments in drug development, only one disease-modifying...

scientific paper September 1, 2021 | CPT Pharmacometrics & Systems Pharmacology

Leonardelli Lorena, Lofano Giuseppe, Selvaggio Gianluca, Parolo Silvia, Giampiccolo Stefano, Tomasoni Danilo, Domenici Enrico, Priami Corrado, Song Haifeng, Medini Duccio, ...

Literature Mining and Mechanistic Graphical Modelling to Improve mRNA Vaccine Platforms

Abstract. RNA vaccines represent a milestone in the history of vaccinology. They provide several advantages over more traditional approaches to vaccine...

A new computational method for drug repurposing

Develop a systems pharmacology workflow that integrates different data types such as genomics, transcriptomics, and literature to identify in silico drug...

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

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Scientific publications