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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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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Featured publications

stormTB: a web-based simulator of a murine minimal-PBPK model for anti-tuberculosis treatments —– National Library of Medicine

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

View on Frontiers in pharmacology
Storm TB

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

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

Robust

Strengths and limitations of non-disclosive data analysis: a comparison of breast cancer survival classifiers using VisualSHIELD

Preserving data privacy is an important concern in the research use of patient data. The DataSHIELD suite enables privacy-aware advanced statistical analysis...

View on Frontiers in genetics
Strenghts new

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

Understanding drug exposure at disease target sites is pivotal to profiling new drug candidates in terms of tolerability and efficacy. Such quantification...

View on Frontiers in pharmacology
mPBPK

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

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

View on Nature Communications
Lycosomal

Single-cell-led drug repurposing for Alzheimer’s disease

Alzheimer's disease is the most common form of dementia. Notwithstanding the huge investments in drug development, only one disease-modifying treatment...

View on Scientific Reports
Single cell
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