Publications by authors named "Marco Beccuti"

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Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node.
Sandro Gepiro Contaldo, Antonio d'Acierno, Lorenzo Bosio, Francesco Venice, Elisa Li Perottino, Marco Beccuti

Front Bioinform· June 2025

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UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.
Riccardo Aucello, Simone Pernice, Dora Tortarolo, Raffaele A Calogero, Celia Herrera-Rincon, Marco Beccuti

Bioinformatics· March 2025

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CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.
Simone Alessandri, Maria L Ratto, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Marco Beccuti

BMC Bioinformatics· March 2024

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A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity.
Maddalena Arigoni, Maria Luisa Ratto, Federica Riccardo, Elisa Balmas, Lorenzo Calogero, Marco Beccuti

Sci Data· February 2024

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A new computational workflow to guide personalized drug therapy.
Simone Pernice, Alessandro Maglione, Dora Tortarolo, Roberta Sirovich, Marinella Clerico, Marco Beccuti

J Biomed Inform· December 2023

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Tamoxifen Activates Transcription Factor EB and Triggers Protective Autophagy in Breast Cancer Cells by Inducing Lysosomal Calcium Release: A Gateway to the Onset of Endocrine Resistance.
Cecilia Boretto, Chiara Actis, Pawan Faris, Francesca Cordero, Marco Beccuti

Int J Mol Sci· December 2023

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CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system.
Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Marco Beccuti

Bioinformatics· May 2023

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Single-Cell RNAseq Clustering.
Marco Beccuti, Raffaele A Calogero

Methods Mol Biol· December 2022

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Bringing Cell Subpopulation Discovery on a Cloud-HPC Using rCASC and StreamFlow.
Sandro G Contaldo, Luca Alessandri, Iacopo Colonnelli, Marco Beccuti, Marco Aldinucci

Methods Mol Biol· December 2022

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Stardust: improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering.
Simone Avesani, Eva Viesi, Luca Alessandrì, Giovanni Motterle, Vincenzo Bonnici, Marco Beccuti

Gigascience· August 2022

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Sparsely Connected Autoencoders: A Multi-Purpose Tool for Single Cell omics Analysis.
Luca Alessandri, Maria Luisa Ratto, Sandro Gepiro Contaldo, Marco Beccuti, Francesca Cordero

Int J Mol Sci· November 2021

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Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial.
Elisa Genuardi, Greta Romano, Marco Beccuti, Beatrice Alessandria, Donato Mannina

Br J Haematol· July 2021

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Computational Analysis of circRNA Expression Data.
Giulio Ferrero, Nicola Licheri, Michele De Bortoli, Raffaele A Calogero, Marco Beccuti

Methods Mol Biol· June 2021

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Computational Analysis of Single-Cell RNA-Seq Data.
Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Raffaele A Calogero

Methods Mol Biol· June 2021

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GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases.
Nicola Licheri, Vincenzo Bonnici, Marco Beccuti, Rosalba Giugno

BMC Bioinformatics· April 2021

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MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning.
Vladimir Nosi, Alessandrì Luca, Melissa Milan, Maddalena Arigoni, Silvia Benvenuti, Marco Beccuti

Int J Mol Sci· April 2021

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Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining.
Luca Alessandri, Francesca Cordero, Marco Beccuti, Nicola Licheri, Maddalena Arigoni

NPJ Syst Biol Appl· January 2021

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Computational modeling of the immune response in multiple sclerosis using epimod framework.
Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Marco Beccuti

BMC Bioinformatics· December 2020

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Impacts of reopening strategies for COVID-19 epidemic: a modeling study in Piedmont region.
Simone Pernice, Paolo Castagno, Linda Marcotulli, Milena Maria Maule, Lorenzo Richiardi, Marco Beccuti

BMC Infect Dis· October 2020

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A computational framework for modeling and studying pertussis epidemiology and vaccination.
Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Marco Beccuti

BMC Bioinformatics· September 2020

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A computational approach based on the colored Petri net formalism for studying multiple sclerosis.
Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Marco Beccuti

BMC Bioinformatics· December 2019

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Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data.
Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Marco Beccuti

Int J Mol Sci· December 2019

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rCASC: reproducible classification analysis of single-cell sequencing data.
Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Martina Olivero

Gigascience· September 2019

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Integrative Analysis of Novel Metabolic Subtypes in Pancreatic Cancer Fosters New Prognostic Biomarkers.
Laura Follia, Giulio Ferrero, Giorgia Mandili, Marco Beccuti, Daniele Giordano

Front Oncol· February 2019

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Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.
Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Marco Beccuti

BMC Bioinformatics· October 2018

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