This study examines the CSF virome in people with HIV, finding associations between viral composition and neuroinflammation, cognition, and depressive symptoms.

Frontiers in Microbiology · Nov 4, 2025Peer-reviewedMicrobiology

UnifiedGreatMod: A New Holistic Modeling Paradigm for Studying Biological Systems on a Complete and Harmonious Scale

Riccardo Aucello, Simone Pernice, Dora Tortarolo, Raffaele Calogero, Celia Herrera‐Rincon, Giulia Ronchi, Stefano Geuna, Francesca Cordero, Píetro Lió, Marco Beccuti

The paper introduces a new modeling paradigm, UnifiedGreatMod, that integrates fine-grained and coarse-grained biological information to study system behavior, demonstrating its application in simulating E. coli metabolism and analyzing cell responses to infection.

Bioinformatics · Mar 1, 2025Peer-reviewedSystems Biology

OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data.

Dora Tortarolo, Simone Pernice, Fabiana Clapero, Donatella Valdembri, Guido Serini, Federica Riccardo, Lidia Tarone, Chiara Enrico Bena, Carla Bosia, Sandro Gepiro Contaldo, Marco Beccuti, Marzio Alfio Pennisi, Francesca Cordero

The paper introduces ORCA, an open-source Shiny application for semi-automated analysis of cellular biology experiments, promoting reproducibility and open science practices.

IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · Dec 5, 2023Peer-reviewedBioinformatics

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system.

Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Paolo Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero

CONNECTOR analyzes longitudinal tumor growth data to identify clusters and reveal new molecular associations with therapy response.

Bioinformatics · Apr 20, 2023Peer-reviewedBioinformatics