Large Scale Prediction of Protein Interactions by a SVM-Based Method. - Francesco Marangoni; Matteo Barberis; Marco Botta (WIRN, 2003)

Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network. - Matteo Barberis; Edda Klipp; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2007)

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. - Roberta Alfieri; Matteo Barberis; Ferdinando Chiaradonna; Daniela Gaglio; Luciano Milanesi; Marco Vanoni; Edda Klipp; Lilia Alberghina (BMC Bioinform., 2009)

GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. - Thierry D. G. A. Mondeel; Frédéric Crémazy; Matteo Barberis (Bioinform., 2018)

Coupling Cell Division to Metabolic Pathways Through Transcription. - Petter Holland; Jens Nielsen; Thierry D. G. A. Mondeel; Matteo Barberis (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Andreas Dräger; Tomás Helikar; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar (Bioinform., 2021)

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections. - Kenneth Y. Wertheim; Bhanwar Lal Puniya; Alyssa La Fleur; Ab Rauf Shah; Matteo Barberis; Tomás Helikar (PLoS Comput. Biol., 2021)

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. - Anna Niarakis; Juilee Thakar; Matteo Barberis; María Rodríguez Martínez; Tomás Helikar; Marc R. Birtwistle; Claudine Chaouiya; Laurence Calzone; Andreas Dräger (Bioinform., 2022)