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 December 22, 2021 | ACL Anthology

Ramponi Alan, van der Goot Rob, Lombardo Rosario, Plank Barbara

Biomedical Event Extraction as Sequence Labeling

Abstract. We introduce Biomedical Event Extraction as Sequence Labeling (BeeSL), a joint end-to-end neural information extraction model. BeeSL recasts...

scientific paper December 15, 2021 | CPT Pharmacometrics & Systems Pharmacology

Abrams Ruth, Kaddi Chanchala, Tao Mengdi, Leiser Randolph J, Simoni Giulia, Reali Federico, Tolsma John, Jasper Paul, van Rijn Zachary, Li Jing, ...

A Quantitative Systems Pharmacology Model of Gaucher Disease Type 1 Provides Mechanistic Insight Into the Response to Substrate Reduction Therapy With Eliglustat

Abstract. Gaucher's disease type 1 (GD1) leads to significant morbidity and mortality through clinical manifestations, such as splenomegaly, hematological...

scientific paper December 15, 2021 | Bioinformatics

Simoni Giulia, Kaddi Chanchala, Tao Mengdi, Reali Federico, Tomasoni Danilo, Priami Corrado, Azer Karim, Neves-Zaph Susana, Marchetti Luca

A robust computational pipeline for model-based and data-driven phenotype clustering

Abstract. Motivation: Precision medicine is a promising field that proposes, in contrast to a one-size-fits-all approach, the tailoring of medical decisions...

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

Selvaggio Gianluca, Leonardelli Lorena, Lofano Giuseppe, Fresnay Stephanie, Parolo Silvia, Medini Duccio, Siena Emilio, Marchetti Luca

A quantitative systems pharmacology approach to support mRNA vaccine development and optimization

Abstract. This commentary presents a Quantitative Systems Pharmacology (QSP) framework designed to support the development and optimization of mRNA vaccines...

scientific paper September 1, 2021 | Communications Biology

Tomasoni Danilo, Paris Alessio, Giampiccolo Stefano, Reali Federico, Simoni Giulia, Marchetti Luca, Kaddi Chanchala, Neves-Zaph Susana, Priami Corrado, Azer Karim, ...

QSPcc reduces bottlenecks in computational model simulations

Abstract. Mathematical models have grown in size and complexity becoming often computationally intractable. In sensitivity analysis and optimization phases...

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...

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