Pathway analysis

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

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 July 14, 2023 | Nature Communications

Berquez Marine, Chen Zhiyong, Festa Beatrice Paola, Krohn Patrick, Keller Svenja Aline, Parolo Silvia, Korzinkin Mikhail, Gaponova Anna, Laczko Endre, Domenici Enrico, ...

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization

Abstract. Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb...

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...

Taking care of immune-beneficial infant gut bacteria

Hunting for foods to help infants build strong immune systems, a New Zealand National Science Challenge. These studies are traditionally conducted trialing...

scientific paper May 5, 2021 | International Journal of Molecular Sciences

Selvaggio Gianluca, Chaouiya Claudine, Janody Florence

In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer

Abstract. The multistep development of cancer involves the cooperation between multiple molecular lesions, as well as complex interactions between cancer...

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