A Discrete/Continuous Model of Anti-HIV Response and Therapy. - Paola Paci; Filippo Castiglione; Massimo Bernaschi; Valentina Baldazzi (UKSim, 2008)

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. - Francesco Pappalardo 001; Mark D. Halling-Brown; Nicolas Rapin; Ping Zhang 008; Davide Alemani; Andrew P. J. Emerson; Paola Paci; Patrice Duroux; Marzio Pennisi; Arianna Palladini; Olivo Miotto; Daniel Churchill; et al. (Briefings Bioinform., 2009)

Modeling lymphocyte homing and encounters in lymph nodes. - Valentina Baldazzi; Paola Paci; Massimo Bernaschi; Filippo Castiglione (BMC Bioinform., 2009)

Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles. - Luisa Di Paola; Paola Paci; Daniele Santoni; Micol De Ruvo; Alessandro Giuliani (J. Chem. Inf. Model., 2012)

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. - Filippo Cacace; Paola Paci; Valerio Cusimano; Alfredo Germani; Lorenzo Farina (PLoS Comput. Biol., 2012)

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. - Paola Paci; Teresa Colombo; Lorenzo Farina (BMC Syst. Biol., 2014)

Modules Identification in Protein Structures: The Topological and Geometrical Solutions. - Setareh Tasdighian; Luisa Di Paola; Micol De Ruvo; Paola Paci; Daniele Santoni; Pasquale Palumbo; Giampiero Mei; Almerinda Di Venere; Alessandro Giuliani (J. Chem. Inf. Model., 2014)

Correction to Modules Identification in Protein Structures: The Topological and Geometrical Solutions. - Setareh Tasdighian; Luisa Di Paola; Micol De Ruvo; Paola Paci; Daniele Santoni; Pasquale Palumbo; Giampiero Mei; Almerinda Di Venere; Alessandro Giuliani (J. Chem. Inf. Model., 2014)

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. - Valerio Licursi; Federica Conte; Giulia Fiscon; Paola Paci (BMC Bioinform., 2019)

Network Inference and Reconstruction in Bioinformatics. - Paolo Tieri; Lorenzo Farina; Manuela Petti; Laura Astolfi; Paola Paci; Filippo Castiglione (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

SAveRUNNER: an R-based tool for drug repurposing. - Giulia Fiscon; Paola Paci (BMC Bioinform., 2021)

Assessing the impact of data-driven limitations on tracing and forecasting the outbreak dynamics of COVID-19. - Giulia Fiscon; Francesco Salvadore; Valerio Guarrasi; Anna Rosa Garbuglia; Paola Paci (Comput. Biol. Medicine, 2021)

SEaCorAl: Identifying and contrasting the regulation-correlation bias in RNA-Seq paired expression data of patient groups. - Manuela Petti; Antonella Verrienti; Paola Paci; Lorenzo Farina (Comput. Biol. Medicine, 2021)

Integro-differential approach for modeling the COVID-19 dynamics - Impact of confinement measures in Italy. - Francesco Salvadore; Giulia Fiscon; Paola Paci (Comput. Biol. Medicine, 2021)

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19. - Giulia Fiscon; Federica Conte; Lorenzo Farina; Paola Paci (PLoS Comput. Biol., 2021)

SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks. - Paola Paci; Giulia Fiscon (Bioinform., 2022)

StaRTrEK: in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition. - Federica Conte; Federico Papa; Paola Paci; Lorenzo Farina (BMC Bioinform., 2022)

SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks. - Paola Paci; Giulia Fiscon (BMC Bioinform., 2022)

Mining sponge phenomena in RNA expression data. - Fabrizio Angiulli; Teresa Colombo; Fabio Fassetti; Angelo Furfaro; Paola Paci (J. Bioinform. Comput. Biol., 2022)

A Transcriptome- and Interactome-Based Analysis Identifies Repurposable Drugs for Human Breast Cancer Subtypes. - Federica Conte; Pasquale Sibilio; Giulia Fiscon; Paola Paci (Symmetry, 2022)

A network-based bioinformatic analysis for identifying potential repurposable active molecules in different types of human cancers. - Martina Brunetti; Paola Paci; Giulia Fiscon (BIBM, 2023)

Network-based analysis to uncover drug-induced adverse side-effects. - Alessio Funari; Paola Paci; Federica Conte (BIBM, 2023)

A single-cell transcriptomic analysis of Neuroblastomas revealed a selective cGAS-STING pathway suppression in malignant cells. - Pasquale Sibilio; Stefano Di Giulio; Alessio Funari; Paola Paci; Veronica Veschi; Giuseppe Giannini (BIBM, 2023)

Overview of bioinformatic tools to study viral infections. - Verdiana Zulian; Anna Rosa Garbuglia; Giulia Fiscon; Paola Paci (BIBM, 2023)

A network-based bioinformatic analysis for identifying potential repurposable drugs for obesity avoiding hepatic steatosis side-effect. - Martina Brunetti; Giulia Fiscon; Alessia Di Costanzo; Marcello Arca; Paola Paci (BIBM, 2024)

Differential gene correlation analysis to investigate evolutionary divergence between Cardamine hirsuta and Arabidopsis thaliana. - Federica D'Annunzio; Giulia Fiscon; Gaia Bertolotti; Raffaele Dello Ioio; Paola Paci (BIBM, 2024)

Unveiling drug-induced side effects through network-based analysis: an update. - Alessio Funari; Federica Conte; Paola Paci (BIBM, 2024)

Beyond the network-based multi-omics data integration in COPD: a pathway-centric analysis. - Pasquale Sibilio; Federica Conte; Paola Paci (BIBM, 2024)