Three-dimensional computation of atom depth in complex molecular structures. - Daniele Varrazzo; Andrea Bernini; Ottavia Spiga; Arianna Ciutti; Stefano Chiellini; Vincenzo Venditti; Luisa Bracci; Neri Niccolai (Bioinform., 2005)

ProCoCoA: A quantitative approach for analyzing protein core composition. - Silvia Bottini; Andrea Bernini; Matteo De Chiara; Diego Garlaschelli; Ottavia Spiga; Marco Dioguardi; Elisa Vannuccini; Anna Tramontano; Neri Niccolai (Comput. Biol. Chem., 2013)

Toward a generalized computational workflow for exploiting transient pockets as new targets for small molecule stabilizers: Application to the homogentisate 1, 2-dioxygenase mutants at the base of rare disease Alkaptonuria. - Andrea Bernini; Silvia Galderisi; Ottavia Spiga; Giulia Bernardini 003; Neri Niccolai; Fabrizio Manetti; Annalisa Santucci (Comput. Biol. Chem., 2017)

ApreciseKUre: an approach of Precision Medicine in a Rare Disease. - Ottavia Spiga; Vittoria Cicaloni; Andrea Bernini; Andrea Zatkova; Annalisa Santucci (BMC Medical Informatics Decis. Mak., 2017)

A new integrated and interactive tool applicable to inborn errors of metabolism: Application to alkaptonuria. - Ottavia Spiga; Vittoria Cicaloni; Andrea Zatkova; Lia Millucci; Giulia Bernardini 003; Andrea Bernini; Barbara Marzocchi; Monica Bianchini; Andrea Zugarini; Alberto Rossi; Matteo Zazzeri; Alfonso Trezza; et al. (Comput. Biol. Medicine, 2018)

Process calculi for biological processes. - Andrea Bernini; Linda Brodo; Pierpaolo Degano; Moreno Falaschi; Diana Hermith (Nat. Comput., 2018)

Transient pockets as mediators of gas molecules routes inside proteins: The case study of dioxygen pathway in homogentisate 1, 2-dioxygenase and its implication in Alkaptonuria development. - Andrea Bernini; Silvia Galderisi; Ottavia Spiga; Chukwudi Onyekachi Amarabom; Annalisa Santucci (Comput. Biol. Chem., 2020)

AKUImg: A database of cartilage images of Alkaptonuria patients. - Alberto Rossi; Giorgia Giacomini; Vittoria Cicaloni; Silvia Galderisi; Maria Serena Milella; Andrea Bernini; Lia Millucci; Ottavia Spiga; Monica Bianchini; Annalisa Santucci (Comput. Biol. Medicine, 2020)

Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease. - Ottavia Spiga; Vittoria Cicaloni; Giovanna Maria Dimitri; Francesco Pettini; Daniela Braconi; Andrea Bernini; Annalisa Santucci (Briefings Bioinform., 2021)

Contrastive Learning with 3D Shapes. - Andrea Bernini (Tiny Papers @ ICLR, 2023)

Community Membership Hiding as Counterfactual Graph Search via Deep Reinforcement Learning. - Andrea Bernini; Fabrizio Silvestri; Gabriele Tolomei (CoRR, 2023)

Evading Community Detection via Counterfactual Neighborhood Search. - Andrea Bernini; Fabrizio Silvestri; Gabriele Tolomei (KDD, 2024)