Publications

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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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

2021

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

Despite the great progress in the techniques, the retrieved evidence still needs to undergo a time-consuming manual curation process to be truly useful...

2021

Cross-Domain Evaluation of Edge Detection for Biomedical Event Extraction

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

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2021

Biomedical Event Extraction as Sequence Labeling

Biomedical Event Extraction as Sequence Labeling (BEESL) is a joint end-to-end neural information extraction model.BEESL recasts the task as sequence...

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2021

Gaucher Disease Type 1

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

2021

Phenotype clustering

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

2021

QSP Modeling and Its Applications

History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications

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