Publications by authors named "Daniele Santoni"

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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

Front Bioinform· April 2025

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A review on the applications of Transformer-based language models for nucleotide sequence analysis.
Nimisha Ghosh, Daniele Santoni, Indrajit Saha, Giovanni Felici

Comput Struct Biotechnol J· March 2025

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An entropy-based study on the mutational landscape of SARS-CoV-2 in USA: Comparing different variants and revealing co-mutational behavior of proteins.
Daniele Santoni

Gene· September 2024

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HDAC6 inhibition disrupts HDAC6-P300 interaction reshaping the cancer chromatin landscape.
Michela Gottardi Zamperla, Barbara Illi, Veronica Barbi, Chiara Cencioni, Daniele Santoni

Clin Epigenetics· August 2024

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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· May 2024

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Predicting Transcription Factor Binding Sites with Deep Learning.
Nimisha Ghosh, Daniele Santoni, Indrajit Saha, Giovanni Felici

Int J Mol Sci· May 2024

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Network homophily via tail inequalities.
Nicola Apollonio, Paolo G Franciosa, Daniele Santoni

Phys Rev E· November 2023

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Peptide Hamming Graphs: A network representation of peptides presented through specific HLAs to identify potential epitope clusters.
Daniele Santoni

J Immunol Methods· June 2023

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Transcription Factor Driven Gene Regulation in COVID-19 Patients.
Daniele Santoni, Nimisha Ghosh, Carlo Derelitto, Indrajit Saha

Viruses· May 2023

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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

Bioinformatics· January 2023

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An immunological glimpse of human virus peptides: Distance from self, MHC class I binding, proteasome cleveage, TAP transport and sequence composition entropy.
Daniele Santoni, Giovanni Felici

Virus Res· August 2022

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Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches.
Davide Vergni, Daniele Santoni, Yagai Bouba, Saverio Lemme, Lavinia Fabeni

Infect Genet Evol· July 2022

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A novel method for assessing and measuring homophily in networks through second-order statistics.
Nicola Apollonio, Paolo G Franciosa, Daniele Santoni

Sci Rep· June 2022

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An entropy-based study on mutational trajectory of SARS-CoV-2 in India.
Daniele Santoni, Nimisha Ghosh, Indrajit Saha

Infect Genet Evol· January 2022

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The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure.
Daniele Santoni

J Theor Biol· October 2021

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The impact of flanking sequence features on DNA CpG methylation.
Daniele Santoni

Comput Biol Chem· June 2021

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The farther the better: Investigating how distance from human self affects the propensity of a peptide to be presented on cell surface by MHC class I molecules, the case of Trypanosoma cruzi.
Davide Vergni, Rosanna Gaudio, Daniele Santoni

PLoS One· January 2021

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In the search of potential epitopes for Wuhan seafood market pneumonia virus using high order nullomers.
Daniele Santoni, Davide Vergni

J Immunol Methods· June 2020

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A study of the impact of DNA helical rise on protein-DNA interaction.
Francesco Pedone, Filomena Mazzei, Daniele Santoni

Genomics· December 2019

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A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples.
Duygu Dede Şener, Daniele Santoni, Giovanni Felici, Hasan Oğul

J Integr Bioinform· October 2018

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Viral peptides-MHC interaction: Binding probability and distance from human peptides.
Daniele Santoni

J Immunol Methods· August 2018

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Investigating transcription factor synergism in humans.
Fabio Cumbo, Davide Vergni, Daniele Santoni

DNA Res· February 2018

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Nullomers and High Order Nullomers in Genomic Sequences.
Davide Vergni, Daniele Santoni

PLoS One· July 2017

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Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175.
Federica Valeriani, Tommaso Biagini, Saverio Giampaoli, Silvia Crognale, Daniele Santoni

Genome Announc· September 2016

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Natural vs. random protein sequences: Discovering combinatorics properties on amino acid words.
Daniele Santoni, Giovanni Felici, Davide Vergni

J Theor Biol· February 2016

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