Publications by authors named "Ernesto Picardi"

72Publications

Evaluation of the Interplay between the ADAR Editome and Immunotherapy in Melanoma.

Noncoding RNA 2021 Jan 12;7(1). Epub 2021 Jan 12.

Department of Dermatology, University Hospital of Zürich, Gloriastrasse 31, 8091 Zürich, Switzerland.

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January 2021

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.

Brief Bioinform 2020 Dec 7. Epub 2020 Dec 7.

molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari.

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December 2020

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments.

Nucleic Acids Res 2021 01;49(D1):D1012-D1019

Department of Biosciences, Biotechnologies and Biopharmaceutics (DBBB), University of Bari, Via Orabona 4, 70125 Bari, Italy.

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January 2021

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community.

BMC Bioinformatics 2020 Aug 21;21(Suppl 10):352. Epub 2020 Aug 21.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy.

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August 2020

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

BMC Bioinformatics 2020 Aug 21;21(Suppl 10):353. Epub 2020 Aug 21.

Department of Ecological and Biological Sciences (DEB), University of Tuscia, Via S. Camillo de Lellis, 44, Viterbo, 01100, Italy.

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August 2020

High-Throughput Sequencing to Detect DNA-RNA Changes.

Methods Mol Biol 2021 ;2181:193-212

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.

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January 2021

Bioinformatics Resources for RNA Editing.

Methods Mol Biol 2021 ;2181:177-191

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.

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January 2021

Investigating Human Mitochondrial Genomes in Single Cells.

Genes (Basel) 2020 05 11;11(5). Epub 2020 May 11.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy.

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May 2020

The cell line A-to-I RNA editing catalogue.

Nucleic Acids Res 2020 06;48(11):5849-5858

Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.

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June 2020

Quantifying RNA Editing in Deep Transcriptome Datasets.

Front Genet 2020 6;11:194. Epub 2020 Mar 6.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.

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March 2020

Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal.

Nat Protoc 2020 03 29;15(3):1098-1131. Epub 2020 Jan 29.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy.

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March 2020

Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data.

Brief Bioinform 2020 Dec;21(6):1971-1986

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy.

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December 2020

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.

Genome Res 2019 09 19;29(9):1453-1463. Epub 2019 Aug 19.

Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria.

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September 2019

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma.

Genome Biol 2019 02 13;20(1):33. Epub 2019 Feb 13.

RNA Editing Lab., Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo, 15 00146, Rome, Italy.

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February 2019

RNA editing in plants: A comprehensive survey of bioinformatics tools and databases.

Plant Physiol Biochem 2019 Apr 2;137:53-61. Epub 2019 Feb 2.

IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A. Moro, Bari, Italy. Electronic address:

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April 2019

REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes.

Front Plant Sci 2018 11;9:482. Epub 2018 Apr 11.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy.

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April 2018

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

BMC Genomics 2018 01 12;19(1):44. Epub 2018 Jan 12.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.

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January 2018

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain.

RNA 2017 06 3;23(6):860-865. Epub 2017 Mar 3.

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy.

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June 2017

REDIportal: a comprehensive database of A-to-I RNA editing events in humans.

Nucleic Acids Res 2017 01 1;45(D1):D750-D757. Epub 2016 Sep 1.

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy

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January 2017

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease.

RNA 2016 Feb 11;22(2):290-302. Epub 2015 Dec 11.

Sagol School of Neuroscience and Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, 69978, Israel.

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February 2016

Profiling RNA editing in human tissues: towards the inosinome Atlas.

Sci Rep 2015 Oct 9;5:14941. Epub 2015 Oct 9.

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy.

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October 2015

Using REDItools to Detect RNA Editing Events in NGS Datasets.

Curr Protoc Bioinformatics 2015 Mar 9;49:12.12.1-12.12.15. Epub 2015 Mar 9.

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.

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March 2015

Epstein-Barr virus genetic variants are associated with multiple sclerosis.

Neurology 2015 Mar 4;84(13):1362-8. Epub 2015 Mar 4.

From the Centre for Experimental Neurological Therapies (R.M., C.P., R.U., V.A.G.R., A.F., V.A., M.C.B., S.R., M.S., G.R.), S. Andrea Hospital-site, Department of Neuroscience, Mental Health and Sensory Organs, Faculty of Medicine and Psychology, Sapienza University, Rome; Don C. Gnocchi Foundation IRCCS (F.R.G., C.A.), S. Maria Nascente, Milan; Department of Health Sciences (S.D.), Interdisciplinary Research Center of Autoimmune Diseases, Eastern Piedmont University, Novara; Clinica Neurologica (F.B., D.C.), Dipartimento di Medicina dei Sistemi, University of Tor Vergata, Rome; Department of Cell Biology and Neuroscience (B.S., B.R.), Istituto Superiore di Sanità, Rome; Department of Bioscience, Biotechnology and Biopharmaceutics (C.M., A.A., A.M.D., E.P., G.P.) University of Bari "Aldo Moro"; Institute of Biomembranes and Bioenergetics (G.P.), CNR, Bari; and Neuroimmunology Unit (D.F.A., L.B.), Fondazione Santa Lucia (I.R.C.C.S.), Rome, Italy.

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March 2015

Exploring the RNA editing potential of RNA-Seq data by ExpEdit.

Methods Mol Biol 2015 ;1269:327-38

Consorzio Interuniversitario CINECA, 00185, Rome, Italy.

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September 2015

Detection of post-transcriptional RNA editing events.

Methods Mol Biol 2015 ;1269:189-205

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126, Bari, Italy,

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September 2015

Transcriptome assembly and alternative splicing analysis.

Methods Mol Biol 2015 ;1269:173-88

Department of Informatics, Systems and Communication (DISCo), University of Milano-Bicocca, Viale Sarca 336, Milano, 20126, Italy,

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September 2015

Uncovering RNA Editing Sites in Long Non-Coding RNAs.

Front Bioeng Biotechnol 2014 5;2:64. Epub 2014 Dec 5.

Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Bari , Italy ; Institute of Biomembranes and Bioenergetics , Bari , Italy.

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December 2014

Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity.

Mitochondrion 2015 Jan 1;20:13-21. Epub 2014 Nov 1.

Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy; Istituto di Biomembrane e Bioenergetica, CNR, via Amendola 165/A, Bari 70126, Italy. Electronic address:

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January 2015

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.

Bioinformatics 2014 Nov 14;30(21):3115-7. Epub 2014 Jul 14.

Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Department of Biosciences, University of Milan, 20133 Milan, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70126 Bari, Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, National Institute of Biostructures and Biosystems, 00136 Rome and Center of Excellence in Genomics for Biomedicine and Agri-food (CEGBA), University of Bari, 70126 Bari, Italy.

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November 2014

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.

Biomed Res Int 2013 7;2013:502827. Epub 2013 Nov 7.

Centre Nacional d'Anàlisi Genòmica (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain.

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June 2014

WEP: a high-performance analysis pipeline for whole-exome data.

BMC Bioinformatics 2013 22;14 Suppl 7:S11. Epub 2013 Apr 22.

Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università degli Studi di Bari, Bari, Italy.

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December 2013

REDItools: high-throughput RNA editing detection made easy.

Bioinformatics 2013 Jul 5;29(14):1813-4. Epub 2013 Jun 5.

Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy.

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July 2013

A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue.

PLoS One 2012 5;7(9):e44184. Epub 2012 Sep 5.

Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, Italy.

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February 2013

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.

BMC Bioinformatics 2012 Apr 12;13 Suppl 5:S2. Epub 2012 Apr 12.

Dipartimento di Informatica Sistemistica e Comunicazione, Univ, degli Studi di Milano-Bicocca, Milano, 20126, Italy.

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April 2012

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.

Bioinformatics 2011 May 22;27(9):1311-2. Epub 2011 Mar 22.

Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università di Bari, Bari, Italy.

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May 2011

REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

Mitochondrion 2011 Mar 6;11(2):360-5. Epub 2010 Nov 6.

Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università di Bari, Bari, Italy.

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March 2011

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.

Nucleic Acids Res 2010 Aug 12;38(14):4755-67. Epub 2010 Apr 12.

Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università degli Studi di Bari, Bari, Italy.

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August 2010

Computational methods for ab initio and comparative gene finding.

Methods Mol Biol 2010 ;609:269-84

Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, University of Bari, Bari, Italy.

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May 2010

MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies.

Mitochondrion 2010 Mar 18;10(2):192-9. Epub 2010 Jan 18.

Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Italy.

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March 2010

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.

BMC Bioinformatics 2009 Jun 16;10 Suppl 6:S10. Epub 2009 Jun 16.

Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Università degli Studi di Bari, 70126 Bari, Italy.

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June 2009

Detecting alternative gene structures from spliced ESTs: a computational approach.

J Comput Biol 2009 Jan;16(1):43-66

Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy.

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January 2009

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets.

BMC Bioinformatics 2008 Mar 26;9 Suppl 2:S14. Epub 2008 Mar 26.

Dipartimento di Biologia Cellulare, Università della Calabria, Arcavacata di Rende, (87036), Italy.

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March 2008

Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin.

Mol Biol Evol 2008 Feb 28;25(2):330-8. Epub 2007 Nov 28.

Department of Pharmacological Sciences, University of Milan, Milano, Italy.

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February 2008

REDIdb: the RNA editing database.

Nucleic Acids Res 2007 Jan 14;35(Database issue):D173-7. Epub 2006 Dec 14.

Dipartimento di Biologia Cellulare, Università della Calabria, 87030 Arcavacata di Rende (CS), Italy.

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January 2007

EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing.

Comput Biol Chem 2006 Feb;30(1):77-80

Dipartimento di Biologia Cellulare, Università della Calabria, 87030 Arcavacata di Rende (CS), Italy.

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February 2006

A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms.

J Mol Evol 2005 Feb;60(2):196-206

Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, 87036 Arcavacata di Rende, Italy.

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February 2005

Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria.

Gene 2002 Mar;286(1):33-41

Dipartimento di Biologia Cellulare, Università degli Studi della Calabria, 87030 Arcavacata di Rende, Italy.

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March 2002