Systems Biology

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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poster September 4, 2026 | CIBB 2026

Zardo Marco, Lauria Mario, Tomasoni Danilo

Benchmarking LLMs for automated systems biology model replication

Automated LLM reproducibility score was defined as the percentage of reproduced models for which agreement with published results was achieved, where...

scientific paper June 26, 2026 | npj Systems Biology and Applications

Marchetti Luca, et al.

A mathematical model of folate-mediated one-carbon metabolism in Down syndrome

Abstract: Following the Lejeune work, researchers focused on a potential anomaly within the folate-mediated one-carbon metabolism (FOCM). Here, we present...

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,...

scientific paper June 17, 2026 | Biomedicines

Siragusa Silvia, Tantillo Elena, Parolo Silvia, Pitozzi Vanessa, Domenici Enrico, Pontis Silvia, et al.

From Airways to Arteries: Dissecting the Inflammatory Mechanisms of Pulmonary Vascular Remodeling in a Murine Model of Chronic Airway Inflammation

Abstract. Background: Chronic Obstructive Pulmonary Disease (COPD) is a progressive, incurable condition marked by irreversible airflow limitation and...

scientific paper April 25, 2025 | Frontiers in Pediatrics

Boggi Carlotta, Casiraghi Nicola, Murgia Xabier, Parolo Silvia, Scalera Enrica, et al.

Longitudinal transcriptomic analysis of the hyperoxia-exposed preterm rabbit as a model of BPD

Abstract. Bronchopulmonary dysplasia (BPD) is a multifactorial chronic lung disease of premature neonates. BPD development depends on prenatal and postnatal...

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...

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