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Results: 1 to 20 of 183

1.

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

Calabrese C, Simone D, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi E, Pesole G, Attimonelli M.

Bioinformatics. 2014 Jul 14. pii: btu483. [Epub ahead of print]

PMID:
25028726
[PubMed - as supplied by publisher]
Free Article
2.

VDR primary targets by genome-wide transcriptional profiling.

Goeman F, De Nicola F, D'Onorio De Meo P, Pallocca M, Elmi B, Castrignanò T, Pesole G, Strano S, Blandino G, Fanciulli M, Muti P.

J Steroid Biochem Mol Biol. 2014 Apr 13;143C:348-356. doi: 10.1016/j.jsbmb.2014.03.007. [Epub ahead of print]

PMID:
24726990
[PubMed - as supplied by publisher]
3.

Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy Products from a Processing Plant in Southern Italy.

Chiara M, D'Erchia AM, Manzari C, Minotto A, Montagna C, Addante N, Santagada G, Latorre L, Pesole G, Horner DS, Parisi A.

Genome Announc. 2014 Apr 10;2(2). pii: e00282-14. doi: 10.1128/genomeA.00282-14.

PMID:
24723720
[PubMed]
Free PMC Article
4.

Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events.

Griggio F, Voskoboynik A, Iannelli F, Justy F, Tilak MK, Turon X, Pesole G, Douzery EJ, Mastrototaro F, Gissi C.

Genome Biol Evol. 2014 Mar;6(3):591-605. doi: 10.1093/gbe/evu041. Erratum in: Genome Biol Evol. 2014 Apr;6(4):931. Xavier, Turon [corrected to Turon, Xavier].

PMID:
24572017
[PubMed - in process]
Free PMC Article
5.

A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

Calabrese C, Mangiulli M, Manzari C, Paluscio AM, Caratozzolo MF, Marzano F, Kurelac I, D'Erchia AM, D'Elia D, Licciulli F, Liuni S, Picardi E, Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, Tullo A.

BMC Genomics. 2013 Dec 5;14:855. doi: 10.1186/1471-2164-14-855.

PMID:
24308330
[PubMed - in process]
Free PMC Article
6.

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

Alioto T, Picardi E, Guigó R, Pesole G.

Biomed Res Int. 2013;2013:502827. doi: 10.1155/2013/502827. Epub 2013 Nov 7.

PMID:
24308000
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell renal cell carcinoma.

Valletti A, Gigante M, Palumbo O, Carella M, Divella C, Sbisà E, Tullo A, Picardi E, D'Erchia AM, Battaglia M, Gesualdo L, Pesole G, Ranieri E.

PLoS One. 2013 Oct 23;8(10):e78452. doi: 10.1371/journal.pone.0078452. eCollection 2013.

PMID:
24194935
[PubMed - in process]
Free PMC Article
8.

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

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.

PMID:
23815231
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.

Boria I, Boatti L, Pesole G, Mignone F.

BMC Bioinformatics. 2013;14 Suppl 7:S10. doi: 10.1186/1471-2105-14-S7-S10. Epub 2013 Apr 22.

PMID:
23815181
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

PMID:
23748563
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

REDItools: high-throughput RNA editing detection made easy.

Picardi E, Pesole G.

Bioinformatics. 2013 Jul 15;29(14):1813-4. doi: 10.1093/bioinformatics/btt287. Epub 2013 Jun 5.

PMID:
23742983
[PubMed - indexed for MEDLINE]
Free Article
12.

Regulation of the expression of CLU isoforms in endometrial proliferative diseases.

Fuzio P, Valletti A, Napoli A, Napoli G, Cormio G, Selvaggi L, Liuni S, Pesole G, Maiorano E, Perlino E.

Int J Oncol. 2013 Jun;42(6):1929-44. doi: 10.3892/ijo.2013.1894. Epub 2013 Apr 11.

PMID:
23589125
[PubMed - indexed for MEDLINE]
13.

Differences in gene expression and cytokine release profiles highlight the heterogeneity of distinct subsets of adipose tissue-derived stem cells in the subcutaneous and visceral adipose tissue in humans.

Perrini S, Ficarella R, Picardi E, Cignarelli A, Barbaro M, Nigro P, Peschechera A, Palumbo O, Carella M, De Fazio M, Natalicchio A, Laviola L, Pesole G, Giorgino F.

PLoS One. 2013;8(3):e57892. doi: 10.1371/journal.pone.0057892. Epub 2013 Mar 5.

PMID:
23526958
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Bioinformatics approaches and tools for metagenomic analysis. Editorial.

Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):645. doi: 10.1093/bib/bbs079. No abstract available.

PMID:
23175747
[PubMed - indexed for MEDLINE]
15.

SpliceAid-F: a database of human splicing factors and their RNA-binding sites.

Giulietti M, Piva F, D'Antonio M, D'Onorio De Meo P, Paoletti D, Castrignanò T, D'Erchia AM, Picardi E, Zambelli F, Principato G, Pavesi G, Pesole G.

Nucleic Acids Res. 2013 Jan;41(Database issue):D125-31. doi: 10.1093/nar/gks997. Epub 2012 Oct 30.

PMID:
23118479
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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

Picardi E, Gallo A, Galeano F, Tomaselli S, Pesole G.

PLoS One. 2012;7(9):e44184. doi: 10.1371/journal.pone.0044184. Epub 2012 Sep 5.

PMID:
22957051
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Reference databases for taxonomic assignment in metagenomics.

Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Review.

PMID:
22786784
[PubMed - indexed for MEDLINE]
18.

SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data.

Chiara M, Pesole G, Horner DS.

Nucleic Acids Res. 2012 Oct;40(18):e145. doi: 10.1093/nar/gks606. Epub 2012 Jun 25.

PMID:
22735696
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets.

Zambelli F, Prazzoli GM, Pesole G, Pavesi G.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W510-5. doi: 10.1093/nar/gks483. Epub 2012 Jun 4.

PMID:
22669907
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Mitochondrial genomes gleaned from human whole-exome sequencing.

Picardi E, Pesole G.

Nat Methods. 2012 May 30;9(6):523-4. doi: 10.1038/nmeth.2029. No abstract available.

PMID:
22669646
[PubMed - indexed for MEDLINE]

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