Ernesto Picardi

29 papers B 1Journal 25Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events.
Briefings Bioinform.
Adriano Fonzino, Pietro Luca Mazzacuva, Adam Handen, Domenico Alessandro Silvestris, Annette Arnold, Riccardo Pecori, Graziano Pesole, Ernesto Picardi
2023 J jnl
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions.
Nucleic Acids Res.
Claudio Lo Giudice, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole
2021 J jnl
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.
Briefings Bioinform.
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
2021 J jnl
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments.
Nucleic Acids Res.
Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignanò, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi
2020 J jnl
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data.
Briefings Bioinform.
Matteo Chiara, Federico Zambelli, Ernesto Picardi, David Stephen Horner, Graziano Pesole
2020 J jnl
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community.
BMC Bioinform.
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, Federico Zambelli
2020 J jnl
HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.
BMC Bioinform.
Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò
2019 J jnl
Elucidating the editome: bioinformatics approaches for RNA editing detection.
Briefings Bioinform.
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
2017 J jnl
REDIportal: a comprehensive database of A-to-I RNA editing events in humans.
Nucleic Acids Res.
Ernesto Picardi, Anna Maria D'Erchia, Claudio Lo Giudice, Graziano Pesole
2014 J jnl
EasyCluster2: an improved tool for clustering and assembling long transcriptome reads.
BMC Bioinform.
Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole, Ernesto Picardi
2014 J jnl
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.
Bioinform.
Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli
2013 — conf
Clustering and Assembling Large Transcriptome Datasets by EasyCluster2.
ICIC (3)
Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Graziano Pesole, Ernesto Picardi
2013 J jnl
REDItools: high-throughput RNA editing detection made easy.
Bioinform.
Ernesto Picardi, Graziano Pesole
2013 J jnl
SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
Nucleic Acids Res.
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
2013 J jnl
WEP: a high-performance analysis pipeline for whole-exome data.
BMC Bioinform.
Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Berardino Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò
2012 J jnl
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.
BMC Bioinform.
Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni
2011 — conf
A Novel Approach to Clustering and Assembly of Large-Scale Roche 454 Transcriptome Data for Gene Validation and Alternative Splicing Analysis.
ICIC (3)
Vitoantonio Bevilacqua, Fabio Stroppa, Stefano Saladino, Ernesto Picardi
2011 J jnl
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res.
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, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole
2011 J jnl
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
Bioinform.
Ernesto Picardi, Mattia D'Antonio, Danilo Carrabino, Tiziana Castrignanò, Graziano Pesole
2010 J jnl
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.
Briefings Bioinform.
David Stephen Horner, Giulio Pavesi, Tiziana Castrignanò, Paolo D'Onorio De Meo, Sabino Liuni, Michael Sammeth, Ernesto Picardi, Graziano Pesole
2010 — conf
New Tools for Expression Alternative Splicing Validation.
ICIC (3)
Vitoantonio Bevilacqua, Ernesto Picardi, Graziano Pesole, Daniele Ranieri, Vincenzo Stola, Vito Renò
2010 J jnl
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Nucleic Acids Res.
Giorgio Grillo, Antonio Turi, Flavio Licciulli, Flavio Mignone, Sabino Liuni, Sandro Banfi, Vincenzo Alessandro Gennarino, David Stephen Horner, Giulio Pavesi, Ernesto Picardi, Graziano Pesole
2009 J jnl
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach.
J. Comput. Biol.
Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi
2009 J jnl
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.
BMC Bioinform.
Ernesto Picardi, Flavio Mignone, Graziano Pesole
2008 J jnl
ASPicDB: A database resource for alternative splicing analysis.
Bioinform.
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, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole
2008 B conf
GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts.
APBC
Tyler S. Alioto, Roderic Guigó, Ernesto Picardi, Graziano Pesole
2008 J jnl
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from
BMC Bioinform.
Ernesto Picardi, Carla Quagliariello
2007 J jnl
REDIdb: the RNA editing database.
Nucleic Acids Res.
Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, Carla Quagliariello
2006 J jnl
EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing.
Comput. Biol. Chem.
Ernesto Picardi, Carla Quagliariello