Using Nets-Within-Nets for Modeling Differentiating Cells in the Epigenetic Landscape. - Roberta Bardini; Alfredo Benso; Stefano Di Carlo; Gianfranco Politano; Alessandro Savino (IWBBIO, 2016)

Using multi-level Petri nets models to simulate microbiota resistance to antibiotics. - Roberta Bardini; Gianfranco Politano; Alfredo Benso; Stefano Di Carlo (BIBM, 2017)

Modeling biological complexity using Biology System Description Language (BiSDL). - F. Muggianu; Alfredo Benso; Roberta Bardini; E. Hu; Gianfranco Politano; Stefano Di Carlo (BIBM, 2018)

A diversity-aware computational framework for systems biology. - Roberta Bardini (2019)

Meta-Analysis of cortical inhibitory interneurons markers landscape and their performances in scRNA-seq studies. - Lorenzo Martini; Roberta Bardini; Stefano Di Carlo (BIBM, 2021)

High-resolution sample size enrichment of single-cell multi-modal low-throughput Patch-seq datasets. - Lorenzo Martini; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (BIBM, 2022)

A Methodology for Co-simulation-Based Optimization of Biofabrication Protocols. - Leonardo Giannantoni; Roberta Bardini; Stefano Di Carlo (IWBBIO (2), 2022)

GAGAM: A Genomic Annotation-Based Enrichment of scATAC-seq Data for Gene Activity Matrix. - Lorenzo Martini; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (IWBBIO (2), 2022)

GRAIGH: Gene Regulation accessibility integrating GeneHancer database. - Lorenzo Martini; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (BIBM, 2023)

Meta-analysis of Gene Activity (MAGA) Contributions and Correlation with Gene Expression, Through GAGAM. - Lorenzo Martini; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (IWBBIO (2), 2023)

Fast and Accurate LSTM Meta-modeling of TNF-induced Tumor Resistance In Vitro. - Marco P. Abrate; Riccardo Smeriglio; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (BIBM, 2024)

Security Layers and Related Services within the Horizon Europe NEUROPULS Project. - Fabio Pavanello; Cédric Marchand 002; Paul Jiménez; Xavier Letartre; Ricardo Chaves; Niccolò Marastoni; Alberto Lovato; Mariano Ceccato; George Papadimitriou 001; Vasileios Karakostas; Dimitris Gizopoulos; Roberta Bardini; et al. (DATE, 2024)

A methodology combining reinforcement learning and simulation to optimize the in silico culture of epithelial sheets. - Alberto Castrignanò; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (J. Comput. Sci., 2024)

Neuronal Spike Shapes (NSS): A straightforward approach to investigate heterogeneity in neuronal excitability states. - Lorenzo Martini; Gianluca Amprimo; Stefano Di Carlo; Gabriella Olmo; Claudia Ferraris; Alessandro Savino; Roberta Bardini (Comput. Biol. Medicine, 2024)

Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems. - Leonardo Giannantoni; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (BMC Bioinform., 2024)

Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control. - Riccardo Smeriglio; Roberta Bardini; Alessandro Savino; Stefano Di Carlo (BMC Bioinform., 2025)