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Publication search results
found 94 matches
- 2023
- Claudio Lo Giudice, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole:
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. Nucleic Acids Res. 51(D1): 337-344 (2023) - 2022
- Bachir Balech, Anna Sandionigi, Marinella Marzano, Graziano Pesole, Monica Santamaria:
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. Database J. Biol. Databases Curation 2022(2022) (2022) - Marco Antonio Tangaro, Marica Antonacci, Pietro Mandreoli, Daniele Colombo, Nadina Foggetti, Giacinto Donvito, Graziano Pesole, Federico Zambelli:
The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. ICWE Workshops 2022: 179-191 - 2021
- 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:
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings Bioinform. 22(2): 616-630 (2021) - Matteo Chiara, Pietro Mandreoli, Marco Antonio Tangaro, Anna Maria D'Erchia, Sandro Sorrentino, Cinzia Forleo, David Stephen Horner, Federico Zambelli, Graziano Pesole:
VINYL: Variant prIoritizatioN bY survivaL analysis. Bioinform. 36(24): 5590-5599 (2021) - Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David Stephen Horner, Graziano Pesole:
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. Bioinform. 36(22-23): 5522-5523 (2021) - Marco Antonio Tangaro, Giuseppe Defazio, Bruno Fosso, Vito Flavio Licciulli, Giorgio Grillo, Giacinto Donvito, Enrico Lavezzo, Giacomo Baruzzo, Graziano Pesole, Monica Santamaria:
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy. Bioinform. 37(22): 4253-4254 (2021) - 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, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandrì, Elena Pedrini, Marina Mordenti, Emanuele Bonetti, Luca Sangiorgi, Graziano Pesole, Federico Zambelli:
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinform. 22-S(15): 544 (2021) - Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignanò, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi:
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. Nucleic Acids Res. 49(Database-Issue): D1012-D1019 (2021) - Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Le Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi, Monica Santamaria, Wouter Addink, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear:
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. F1000Research 10: 1238 (2021) - 2020
- Matteo Chiara, Federico Zambelli, Ernesto Picardi, David Stephen Horner, Graziano Pesole:
Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. Briefings Bioinform. 21(6): 1971-1986 (2020) - 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:
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. BMC Bioinform. 21-S(10): 352 (2020) - Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò:
HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis. BMC Bioinform. 21-S(10): 353 (2020) - 2019
- Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi:
Elucidating the editome: bioinformatics approaches for RNA editing detection. Briefings Bioinform. 20(2): 436-447 (2019) - 2018
- Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente:
Unbiased Taxonomic Annotation of Metagenomic Samples. J. Comput. Biol. 25(3): 348-360 (2018) - Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole:
ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. Nucleic Acids Res. 46(Database-Issue): D127-D132 (2018) - 2017
- Bruno Fosso, Monica Santamaria, Mattia D'Antonio, Domenica Lovero, Giacomo Corrado, Enrico Vizza, N. Pássaro, Anna Rosa Garbuglia, M. R. Capobianchi, Marco Crescenzi, Gabriel Valiente, Graziano Pesole:
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. Bioinform. 33(11): 1730-1732 (2017) - Ernesto Picardi, Anna Maria D'Erchia, Claudio Lo Giudice, Graziano Pesole:
REDIportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res. 45(Database-Issue): D750-D757 (2017) - Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente:
Unbiased Taxonomic Annotation of Metagenomic Samples. ISBRA 2017: 162-173 - 2015
- Bachir Balech, Saverio Vicario, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo, Graziano Pesole:
MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information. Bioinform. 31(15): 2571-2573 (2015) - Bruno Fosso, Monica Santamaria, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo, Graziano Pesole:
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinform. 16: 203:1-203:11 (2015) - 2014
- Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli:
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinform. 30(21): 3115-3117 (2014) - Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole, Ernesto Picardi:
EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. BMC Bioinform. 15(S-15): S7 (2014) - Mattia D'Antonio, Paolo D'Onorio De Meo, Tiziana Castrignanò, Giovanni Erbacci, Matteo Pallocca, Graziano Pesole:
ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data. HPCS 2014: 608-615 - 2013
- Federico Zambelli, Graziano Pesole, Giulio Pavesi:
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Briefings Bioinform. 14(2): 225-237 (2013) - Ernesto Picardi, Graziano Pesole:
REDItools: high-throughput RNA editing detection made easy. Bioinform. 29(14): 1813-1814 (2013) - Ilenia Boria, Lara Boatti, Graziano Pesole, Flavio Mignone:
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. BMC Bioinform. 14(S-7): S10 (2013) - Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Berardino Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò:
WEP: a high-performance analysis pipeline for whole-exome data. BMC Bioinform. 14(S-7): S11 (2013) - 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:
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res. 41(Database-Issue): 125-131 (2013) - Federico Zambelli, Graziano Pesole, Giulio Pavesi:
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 41(Webserver-Issue): 535-543 (2013)
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