Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. - Daniele Santoni; Marco Pedicini; Filippo Castiglione (Bioinform., 2008)

Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation. - Marco Pedicini; Fredrik Barrenäs; Trevor Clancy; Filippo Castiglione; Eivind Hovig; Kartiek Kanduri; Daniele Santoni; Mikael Benson (PLoS Comput. Biol., 2010)

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)

Multi-scale Simulation of T Helper Lymphocyte Differentiation. - Paolo Tieri; Vinca Prana; Teresa Colombo; Daniele Santoni; Filippo Castiglione (BSB, 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)

Automatic Detection of Words Associations in Texts Based on Joint Distribution of Words Occurrences. - Daniele Santoni; Elaheh Pourabbas (Comput. Intell., 2016)

Optimal discretization and selection of features by association rates of joint distributions. - Daniele Santoni; Emanuel Weitschek; Giovanni Felici (RAIRO Oper. Res., 2016)

A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples. - Duygu Dede Sener; Daniele Santoni; Giovanni Felici; Hasan Ogul (J. Integr. Bioinform., 2018)

The impact of flanking sequence features on DNA CpG methylation. - Daniele Santoni (Comput. Biol. Chem., 2021)

On function homophily of microbial Protein-Protein Interaction Networks. - Nicola Apollonio; Paolo Giulio Franciosa; Daniele Santoni (CoRR, 2021)

Homophily of Large Weighted Networks in a Data Streaming Setting. - Nicola Apollonio; Paolo Giulio Franciosa; Daniele Santoni (CIBB, 2023)

Predicting Transcription Factor Binding Sites using Transformer based Capsule Network. - Nimisha Ghosh; Daniele Santoni; Indrajit Saha; Giovanni Felici (CoRR, 2023)

Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks. - Nicola Apollonio; Daniel Blankenberg; Fabio Cumbo; Paolo Giulio Franciosa; Daniele Santoni (Bioinform., 2023)

TRANSPARENT: a Python tool for designing transcription factor regulatory networks. - Carlo Derelitto; Daniele Santoni (Soft Comput., 2023)

A Review on the Applications of Transformer-based language models for Nucleotide Sequence Analysis. - Nimisha Ghosh; Daniele Santoni; Indrajit Saha; Giovanni Felici (CoRR, 2024)

An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators. - Claudio Arbib; Andrea D'Ascenzo; Fabrizio Rossi; Daniele Santoni (J. Comput. Biol., 2024)

Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients. - Nicolina Sciaraffa; Daniele Santoni; Andrea Li Greci; Swonild Ilenia Genovese; Claudia Coronnello; Walter Arancio (Frontiers Bioinform., 2025)

TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites. - Nimisha Ghosh; Pratik Dutta; Daniele Santoni (CoRR, 2025)

A Comprehensive Review of Transformer-based language models for Protein Sequence Analysis and Design. - Nimisha Ghosh; Daniele Santoni; Debaleena Nawn; Eleonora Ottaviani; Giovanni Felici (CoRR, 2025)