Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. - Matteo Chiara; Federico Zambelli; Ernesto Picardi; David Stephen Horner; Graziano Pesole (Briefings Bioinform., 2020)

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. - Tiziana Castrignanò; Silvia Gioiosa; Tiziano Flati; Mirko Cestari; Ernesto Picardi; Matteo Chiara; Maddalena Fratelli; Stefano Amente; Marco Cirilli; Marco Antonio Tangaro; Giovanni Chillemi; Graziano Pesole; et al. (BMC Bioinform., 2020)

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. - Matteo Chiara; Anna Maria D'Erchia; Carmela Gissi; Caterina Manzari; Antonio Parisi; Nicoletta Resta; Federico Zambelli; Ernesto Picardi; Giulio Pavesi; David Stephen Horner; Graziano Pesole (Briefings Bioinform., 2021)

VINYL: Variant prIoritizatioN bY survivaL analysis. - Matteo Chiara; Pietro Mandreoli; Marco Antonio Tangaro; Anna Maria D'Erchia; Sandro Sorrentino; Cinzia Forleo; David Stephen Horner; Federico Zambelli; Graziano Pesole (Bioinform., 2021)

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. - Matteo Chiara; Federico Zambelli; Marco Antonio Tangaro; Pietro Mandreoli; David Stephen Horner; Graziano Pesole (Bioinform., 2021)

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. - Marco Antonio Tangaro; Pietro Mandreoli; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Manila Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; et al. (BMC Bioinform., 2021)

ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time. - Luca Cilibrasi; Pietro Pinoli; Anna Bernasconi 002; Arif Canakoglu; Matteo Chiara; Stefano Ceri (Bioinform., 2022)

VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants. - Pietro Pinoli; Arif Canakoglu; Stefano Ceri; Matteo Chiara; Erika Ferrandi; Luca Minotti; Anna Bernasconi 002 (Database J. Biol. Databases Curation, 2023)

UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. - Claudio Lo Giudice; Federico Zambelli; Matteo Chiara; Giulio Pavesi; Marco Antonio Tangaro; Ernesto Picardi; Graziano Pesole (Nucleic Acids Res., 2023)

Supporting data and code for "Data-driven recombination detection in viral genomes". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2023)

Supporting data and code for "Data-driven recombination detection in viral genomes". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2023)

SENSIBLE: Implementing Data-Driven Early Warning Systems for Future Viral Epidemics. - Anna Bernasconi 002; Matteo Chiara; Tommaso Alfonsi; Stefano Ceri (CAiSE Research Projects Exhibition, 2024)

Supporting data and code for "Data-driven recombination detection in viral genomes". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2024)

Supporting data and code for "Data-driven recombination detection in viral genomes". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2024)

Supporting data and code for "Data-driven recombination detection in viral genomes". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2024)

Supporting data and code for "Multi-scale early spillover warnings for influenza A viruses". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2025)

Supporting data and code for "Multi-scale early spillover warnings for influenza A viruses". - Tommaso Alfonsi; Anna Bernasconi 002; Matteo Chiara; Stefano Ceri (Zenodo, 2025)