EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing. - Ernesto Picardi; Carla Quagliariello (Comput. Biol. Chem., 2006)

REDIdb: the RNA editing database. - Ernesto Picardi; Teresa Maria Rosaria Regina; Axel Brennicke; Carla Quagliariello (Nucleic Acids Res., 2007)

GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts. - Tyler S. Alioto; Roderic Guigó; Ernesto Picardi; Graziano Pesole (APBC, 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)

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets. - Ernesto Picardi; Carla Quagliariello (BMC Bioinform., 2008)

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

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. - Paola Bonizzoni; Giancarlo Mauri; Graziano Pesole; Ernesto Picardi; Yuri Pirola; Raffaella Rizzi (J. Comput. Biol., 2009)

New Tools for Expression Alternative Splicing Validation. - Vitoantonio Bevilacqua; Ernesto Picardi; Graziano Pesole; Daniele Ranieri; Vincenzo Stola; Vito Renò (ICIC (3), 2010)

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. - David Stephen Horner; Giulio Pavesi; Tiziana Castrignanò; Paolo D'Onorio De Meo; Sabino Liuni; Michael Sammeth; Ernesto Picardi; Graziano Pesole (Briefings Bioinform., 2010)

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)

A Novel Approach to Clustering and Assembly of Large-Scale Roche 454 Transcriptome Data for Gene Validation and Alternative Splicing Analysis. - Vitoantonio Bevilacqua; Fabio Stroppa; Stefano Saladino; Ernesto Picardi (ICIC (3), 2011)

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments. - Ernesto Picardi; Mattia D'Antonio; Danilo Carrabino; Tiziana Castrignanò; Graziano Pesole (Bioinform., 2011)

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)

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. - Yuri Pirola; Raffaella Rizzi; Ernesto Picardi; Graziano Pesole; Gianluca Della Vedova; Paola Bonizzoni (BMC Bioinform., 2012)

Clustering and Assembling Large Transcriptome Datasets by EasyCluster2. - Vitoantonio Bevilacqua; Nicola Pietroleonardo; Ely Ignazio Giannino; Fabio Stroppa; Graziano Pesole; Ernesto Picardi (ICIC (3), 2013)

REDItools: high-throughput RNA editing detection made easy. - Ernesto Picardi; Graziano Pesole (Bioinform., 2013)

WEP: a high-performance analysis pipeline for whole-exome data. - Mattia D'Antonio; Paolo D'Onorio De Meo; Daniele Paoletti; Berardino Elmi; Matteo Pallocca; Nico Sanna; Ernesto Picardi; Graziano Pesole; Tiziana Castrignanò (BMC Bioinform., 2013)

SpliceAid-F: a database of human splicing factors and their RNA-binding sites. - Matteo Giulietti; Francesco Piva; Mattia D'Antonio; Paolo D'Onorio De Meo; Daniele Paoletti; Tiziana Castrignanò; Anna Maria D'Erchia; Ernesto Picardi; Federico Zambelli; Giovanni Principato; Giulio Pavesi; Graziano Pesole (Nucleic Acids Res., 2013)

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. - Claudia Calabrese; Domenico Simone; Maria Angela Diroma; Mariangela Santorsola; Cristiano Guttà; Giuseppe Gasparre; Ernesto Picardi; Graziano Pesole; Marcella Attimonelli (Bioinform., 2014)

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. - Vitoantonio Bevilacqua; Nicola Pietroleonardo; Ely Ignazio Giannino; Fabio Stroppa; Domenico Simone; Graziano Pesole; Ernesto Picardi (BMC Bioinform., 2014)

REDIportal: a comprehensive database of A-to-I RNA editing events in humans. - Ernesto Picardi; Anna Maria D'Erchia; Claudio Lo Giudice; Graziano Pesole (Nucleic Acids Res., 2017)

Elucidating the editome: bioinformatics approaches for RNA editing detection. - Maria Angela Diroma; Loredana Ciaccia; Graziano Pesole; Ernesto Picardi (Briefings Bioinform., 2019)

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)

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis. - Tiziano Flati; Silvia Gioiosa; Nicola Spallanzani; Ilario Tagliaferri; Maria Angela Diroma; Graziano Pesole; Giovanni Chillemi; Ernesto Picardi; Tiziana Castrignanò (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)

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. - Luigi Mansi; Marco Antonio Tangaro; Claudio Lo Giudice; Tiziano Flati; Eli Kopel; Amos Avraham Schaffer; Tiziana Castrignanò; Giovanni Chillemi; Graziano Pesole; Ernesto Picardi (Nucleic Acids Res., 2021)

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)

REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events. - Adriano Fonzino; Pietro Luca Mazzacuva; Adam Handen; Domenico Alessandro Silvestris; Annette Arnold; Riccardo Pecori; Graziano Pesole; Ernesto Picardi (Briefings Bioinform., 2025)