Daniele Santoni

20 papers Journal 18Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Comprehensive Review of Transformer-based language models for Protein Sequence Analysis and Design.
CoRR
Nimisha Ghosh, Daniele Santoni, Debaleena Nawn, Eleonora Ottaviani, Giovanni Felici
2025 J jnl
TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites.
CoRR
Nimisha Ghosh, Pratik Dutta, Daniele Santoni
2025 J jnl
Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients.
Frontiers Bioinform.
Nicolina Sciaraffa, Daniele Santoni, Andrea Li Greci, Swonild Ilenia Genovese, Claudia Coronnello, Walter Arancio
2024 J jnl
A Review on the Applications of Transformer-based language models for Nucleotide Sequence Analysis.
CoRR
Nimisha Ghosh, Daniele Santoni, Indrajit Saha, Giovanni Felici
2024 J jnl
An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators.
J. Comput. Biol.
Claudio Arbib, Andrea D'Ascenzo, Fabrizio Rossi, Daniele Santoni
2023 J jnl
Evaluating homophily in networks via
Bioinform.
Nicola Apollonio, Daniel J. Blankenberg, Fabio Cumbo, Paolo Giulio Franciosa, Daniele Santoni
2023 — conf
Homophily of Large Weighted Networks in a Data Streaming Setting.
CIBB
Nicola Apollonio, Paolo Giulio Franciosa, Daniele Santoni
2023 J jnl
Predicting Transcription Factor Binding Sites using Transformer based Capsule Network.
CoRR
Nimisha Ghosh, Daniele Santoni, Indrajit Saha, Giovanni Felici
2023 J jnl
TRANSPARENT: a Python tool for designing transcription factor regulatory networks.
Soft Comput.
Carlo Derelitto, Daniele Santoni
2021 J jnl
On function homophily of microbial Protein-Protein Interaction Networks.
CoRR
Nicola Apollonio, Paolo Giulio Franciosa, Daniele Santoni
2021 J jnl
The impact of flanking sequence features on DNA CpG methylation.
Comput. Biol. Chem.
Daniele Santoni
2018 J jnl
A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples.
J. Integr. Bioinform.
Duygu Dede Sener, Daniele Santoni, Giovanni Felici, Hasan Ogul
2016 J jnl
Automatic Detection of Words Associations in Texts Based on Joint Distribution of Words Occurrences.
Comput. Intell.
Daniele Santoni, Elaheh Pourabbas
2016 J jnl
Optimal discretization and selection of features by association rates of joint distributions.
RAIRO Oper. Res.
Daniele Santoni, Emanuel Weitschek, Giovanni Felici
2014 J jnl
Correction to Modules Identification in Protein Structures: The Topological and Geometrical Solutions.
J. Chem. Inf. Model.
Setareh Tasdighian, Luisa Di Paola, Micol De Ruvo, Paola Paci, Daniele Santoni, Pasquale Palumbo, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani
2014 J jnl
Modules Identification in Protein Structures: The Topological and Geometrical Solutions.
J. Chem. Inf. Model.
Setareh Tasdighian, Luisa Di Paola, Micol De Ruvo, Paola Paci, Daniele Santoni, Pasquale Palumbo, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani
2014 — conf
Multi-scale Simulation of T Helper Lymphocyte Differentiation.
BSB
Paolo Tieri, Vinca Prana, Teresa Colombo, Daniele Santoni, Filippo Castiglione
2012 J jnl
Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles.
J. Chem. Inf. Model.
Luisa Di Paola, Paola Paci, Daniele Santoni, Micol De Ruvo, Alessandro Giuliani
2010 J jnl
Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation.
PLoS Comput. Biol.
Marco Pedicini, Fredrik Barrenäs, Trevor Clancy, Filippo Castiglione, Eivind Hovig, Kartiek Kanduri, Daniele Santoni, Mikael Benson
2008 J jnl
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions.
Bioinform.
Daniele Santoni, Marco Pedicini, Filippo Castiglione