Systems Pharmacology

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 January 8, 2025 | Frontiers in Pharmacology

Visintainer Roberto, Fochesato Anna, Boaretti Daniele, Levi Micha, Reali Federico, Marchetti Luca

stormTB: a web-based simulator of a murine minimal-PBPK model for anti-tuberculosis treatments

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

scientific paper November 29, 2024 | npj Systems Biology and Applications

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

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

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

scientific paper January 24, 2024 | Frontiers in Pharmacology

Reali Federico, Fochesato Anna, Kaddi Chanchala, Visintainer Roberto, Watson Shayne, Levi Micha, Dartois Veronique, Azer Karim

A minimal PBPK model to accelerate preclinical development of drugs against tuberculosis

Abstract. Introduction: Understanding drug exposure at disease target sites is pivotal to profiling new drug candidates in terms of tolerability and...

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 December 22, 2021 | IEEE

Ramponi Alan, Giampiccolo Stefano, Tomasoni Danilo, Priami Corrado, Lombardo Rosario

High-Precision Biomedical Relation Extraction for Reducing Human Curation Efforts in Industrial Applications

Abstract. The body of biomedical literature is growing at an unprecedented rate, exceeding the ability of researchers to make effective use of this knowledge...

scientific paper December 22, 2021 | ACL Anthology

Ramponi Alan, Plank Barbara, Lombardo Rosario

Cross-Domain Evaluation of Edge Detection for Biomedical Event Extraction

Abstract. Biomedical event extraction is a crucial task in order to automatically extract information from the increasingly growing body of biomedical...

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