+390805442179

+390805443317

algorithms,biological data integration,comparative genomics,sequence analysis

- Epitrascriptomics
- RNA Editing in animals and plants
- Gene prediction and annotation
- Biological Databases
- Next Generation Sequencing (transcriptomics by short and long reads)

Monaco A, Pantaleo E, Amoroso N, Lacalamita A, Lo Giudice C, Fonzino A, Fosso B, Picardi E, Tangaro S, Pesole G, Bellotti R. A primer on machine learning techniques for genomic applications. Comput Struct Biotechnol J. 2021 Jul 31;19:4345-4359. doi: 10.1016/j.csbj.2021.07.021. PMID: 34429852; PMCID: PMC8365460.

Mansi L, Tangaro MA, Lo Giudice C, Flati T, Kopel E, Schaffer AA, Castrignanò T, Chillemi G, Pesole G, Picardi E. REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. Nucleic Acids Res. 2021 Jan 8;49(D1):D1012-D1019. doi: 10.1093/nar/gkaa916. PMID: 33104797; PMCID: PMC7778987.

Lo Giudice C, Tangaro MA, Pesole G, Picardi E. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat Protoc. 2020 Mar;15(3):1098-1131. doi: 10.1038/s41596-019-0279-7. Epub 2020 Jan 29. PMID: 31996844.

Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing. Genome Res. 2019 Sep;29(9):1453-1463. doi: 10.1101/gr.242636.118. Epub 2019 Aug 19. PMID: 31427386; PMCID: PMC6724681.

Silvestris DA, Picardi E, Cesarini V, Fosso B, Mangraviti N, Massimi L, Martini M, Pesole G, Locatelli F, Gallo A. Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma. Genome Biol. 2019 Feb 13;20(1):33. doi: 10.1186/s13059-019-1647-x. PMID: 30760294; PMCID: PMC6373152.

Annese A, Manzari C, Lionetti C, Picardi E, Horner DS, Chiara M, Caratozzolo MF, Tullo A, Fosso B, Pesole G, D'Erchia AM. Whole transcriptome profiling of Late-Onset Alzheimer's Disease patients provides insights into the molecular changes involved in the disease. Sci Rep. 2018 Mar 9;8(1):4282. doi: 10.1038/s41598-018-22701-2. PMID: 29523845; PMCID: PMC5844946.

Picardi E, Horner DS, Pesole G. Single cell transcriptomics reveals specific
RNA editing signatures in the human brain. RNA. 2017 Mar 3. pii: rna.058271.116.
doi: 10.1261/rna.058271.116. PubMed PMID: 28258159

Picardi E, D'Erchia AM, Lo Giudice C, Pesole G. REDIportal: a comprehensive
database of A-to-I RNA editing events in humans. Nucleic Acids Res. 2017 Jan
4;45(D1):D750-D757. doi: 10.1093/nar/gkw767. Epub 2016 Sep 1. PubMed PMID:
27587585; PubMed Central PMCID: PMC5210607

Khermesh K, D'Erchia AM, Barak M, Annese A, Wachtel C, Levanon EY, Picardi E,
Eisenberg E. Reduced levels of protein recoding by A-to-I RNA editing in
Alzheimer's disease. RNA. 2016 Feb;22(2):290-302. doi: 10.1261/rna.054627.115.
Epub 2015 Dec 11. PubMed PMID: 26655226; PubMed Central PMCID: PMC4712678.

Picardi E, Manzari C, Mastropasqua F, Aiello I, D'Erchia AM, Pesole G.
Profiling RNA editing in human tissues: towards the inosinome Atlas. Sci Rep.
2015 Oct 9;5:14941. doi: 10.1038/srep14941. PubMed PMID: 26449202; PubMed Central
PMCID: PMC4598827.

D'Antonio M, D'Onorio De Meo P, Pallocca M, Picardi E, D'Erchia AM, Calogero
RA, Castrignanò T, Pesole G. RAP: RNA-Seq Analysis Pipeline, a new cloud-based
NGS web application. BMC Genomics. 2015;16:S3. doi: 10.1186/1471-2164-16-S6-S3.
Epub 2015 Jun 1. PubMed PMID: 26046471; PubMed Central PMCID: PMC4461013.

Mechelli R, Manzari C, Policano C, Annese A, Picardi E, Umeton R, Fornasiero
A, D'Erchia AM, Buscarinu MC, Agliardi C, Annibali V, Serafini B, Rosicarelli B,
Romano S, Angelini DF, Ricigliano VA, Buttari F, Battistini L, Centonze D,
Guerini FR, D'Alfonso S, Pesole G, Salvetti M, Ristori G. Epstein-Barr virus
genetic variants are associated with multiple sclerosis. Neurology. 2015 Mar
31;84(13):1362-8. doi: 10.1212/WNL.0000000000001420. Epub 2015 Mar 4. PubMed
PMID: 25740864; PubMed Central PMCID: PMC4388746.

D'Erchia AM, Atlante A, Gadaleta G, Pavesi G, Chiara M, De Virgilio C, Manzari
C, Mastropasqua F, Prazzoli GM, Picardi E, Gissi C, Horner D, Reyes A, Sbisà E,
Tullo A, Pesole G. Tissue-specific mtDNA abundance from exome data and its
correlation with mitochondrial transcription, mass and respiratory activity.
Mitochondrion. 2015 Jan;20:13-21. doi: 10.1016/j.mito.2014.10.005. Epub 2014 Nov
1. PubMed PMID: 25446395.

Calabrese C, Simone D, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi
E, Pesole G, Attimonelli M. MToolBox: a highly automated pipeline for
heteroplasmy annotation and prioritization analysis of human mitochondrial
variants in high-throughput sequencing. Bioinformatics. 2014 Nov 1;30(21):3115-7.
doi: 10.1093/bioinformatics/btu483. Epub 2014 Jul 14. PubMed PMID: 25028726;
PubMed Central PMCID: PMC4201154.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N,
Picardi E, Pesole G, Castrignanò T. WEP: a high-performance analysis pipeline for
whole-exome data. BMC Bioinformatics. 2013;14 Suppl 7:S11. doi:
10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22. PubMed PMID: 23815231; PubMed
Central PMCID: PMC3633005.

Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made
easy. Bioinformatics. 2013 Jul 15;29(14):1813-4. doi:
10.1093/bioinformatics/btt287. Epub 2013 Jun 5. PubMed PMID: 23742983.

Picardi E, Pesole G. Mitochondrial genomes gleaned from human whole-exome
sequencing. Nat Methods. 2012 May 30;9(6):523-4. doi: 10.1038/nmeth.2029. PubMed
PMID: 22669646.

Picardi E, D'Antonio M, Carrabino D, Castrignanò T, Pesole G. ExpEdit: a
webserver to explore human RNA editing in RNA-Seq experiments. Bioinformatics.
2011 May 1;27(9):1311-2. doi: 10.1093/bioinformatics/btr117. Epub 2011 Mar 22.
PubMed PMID: 21427194.

Picardi E, Regina TM, Verbitskiy D, Brennicke A, Quagliariello C. REDIdb: an
upgraded bioinformatics resource for organellar RNA editing sites. Mitochondrion.
2011 Mar;11(2):360-5. doi: 10.1016/j.mito.2010.10.005. Epub 2010 Nov 6. PubMed
PMID: 21059409.

Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio
De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G,
Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole
G. ASPicDB: a database of annotated transcript and protein variants generated by
alternative splicing. Nucleic Acids Res. 2011 Jan;39(Database issue):D80-5. doi:
10.1093/nar/gkq1073. Epub 2010 Nov 4. PubMed PMID: 21051348; PubMed Central
PMCID: PMC3013677.

Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. Large-scale
detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Nucleic Acids Res. 2010 Aug;38(14):4755-67. doi: 10.1093/nar/gkq202. Epub 2010
Apr 12. PubMed PMID: 20385587; PubMed Central PMCID: PMC2919710.

ISCB
BITS

Biomed Research International
International Journal of Genomics
BMC Genomics

Bioinformatica ed analisi del genoma - Corso di Laurea Magistrale in Biotecnologie Industriali ed Farmaceutiche - Università degli Studi di Bari "Aldo Moro"
Scienze Omiche: Genomica e Trascrittomica - Corso di Laurea Magistrale in Bioinformatica - Università degli Studi di Bari "Aldo Moro"