UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002. - Graziano Pesole; Sabino Liuni; Giorgio Grillo; Flavio Licciulli; Flavio Mignone; Carmela Gissi; Cecilia Saccone (Nucleic Acids Res., 2002)

WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments. - Flavio Mignone; David Stephen Horner; Graziano Pesole (Bioinform., 2004)

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. - Tiziana Castrignanò; Alessandro Canali; Giorgio Grillo; Sabino Liuni; Flavio Mignone; Graziano Pesole (Nucleic Acids Res., 2004)

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. - Angelo Boccia; Mauro Petrillo; Diego di Bernardo; Alessandro Guffanti; Flavio Mignone; Stefano Confalonieri; Lucilla Luzi; Graziano Pesole; Giovanni Paolella; Andrea Ballabio; Sandro Banfi (Nucleic Acids Res., 2005)

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. - Flavio Mignone; Giorgio Grillo; Flavio Licciulli; Michele Iacono; Sabino Liuni; Paul J. Kersey; Jorge Duarte; Cecilia Saccone; Graziano Pesole (Nucleic Acids Res., 2005)

GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. - Tiziana Castrignanò; Paolo D'Onorio De Meo; Giorgio Grillo; Sabino Liuni; Flavio Mignone; Ivano Giuseppe Talamo; Graziano Pesole (Bioinform., 2006)

A high performance grid-web service framework for the identification of 'conserved sequence tags'. - Paolo D'Onorio De Meo; Danilo Carrabino; Nico Sanna; Tiziana Castrignanò; Giorgio Grillo; Flavio Licciulli; Sabino Liuni; Matteo Re; Flavio Mignone; Graziano Pesole (Future Gener. Comput. Syst., 2007)

HT-RLS: High-Throughput Web Tool for Analysis of DNA Microarray Data Using RLS classifiers. - Paolo D'Onorio De Meo; Danilo Carrabino; Mattia D'Antonio; Annarita D'Addabbo; Sabino Liuni; Flavio Mignone; Graziano Pesole; Nicola Ancona (CCGRID, 2008)

ASPicDB: A database resource for alternative splicing analysis. - Tiziana Castrignanò; Mattia D'Antonio; Anna Anselmo; Danilo Carrabino; A. D'Onorio De Meo; Anna Maria D'Erchia; Flavio Licciulli; Marina Mangiulli; Flavio Mignone; Giulio Pavesi; Ernesto Picardi; Alberto Riva; et al. (Bioinform., 2008)

Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements. - Teresa Maria Creanza; David Stephen Horner; Annarita D'Addabbo; Rosalia Maglietta; Flavio Mignone; Nicola Ancona; Graziano Pesole (BMC Bioinform., 2009)

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data. - Ernesto Picardi; Flavio Mignone; Graziano Pesole (BMC Bioinform., 2009)

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. - Giorgio Grillo; Antonio Turi; Flavio Licciulli; Flavio Mignone; Sabino Liuni; Sandro Banfi; Vincenzo Alessandro Gennarino; David Stephen Horner; Giulio Pavesi; Ernesto Picardi; Graziano Pesole (Nucleic Acids Res., 2010)

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. - Pier Luigi Martelli; Mattia D'Antonio; Paola Bonizzoni; Tiziana Castrignanò; Anna Maria D'Erchia; Paolo D'Onorio De Meo; Piero Fariselli; Michele Finelli; Flavio Licciulli; Marina Mangiulli; Flavio Mignone; Giulio Pavesi; et al. (Nucleic Acids Res., 2011)

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. - Ilenia Boria; Lara Boatti; Graziano Pesole; Flavio Mignone (BMC Bioinform., 2013)

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow. - Igor Saggese; Elisa Bona; Maxwell Conway; Francesco Favero; Marco Ladetto; Pietro Liò; Giovanni Manzini; Flavio Mignone (BMC Bioinform., 2018)

Graph Neural Networks for Gut Microbiome Metaomic data: A preliminary work. - Christopher Irwin; Flavio Mignone; Stefania Montani; Luigi Portinale (CoRR, 2024)

Graph Representation Learning for IBD Diagnosis Based on Microbiome Metaomic Data. - Christopher Irwin; Flavio Mignone; Stefania Montani; Luigi Portinale (AIME (1), 2025)