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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. Santamaria M, et al. Among authors: valiente g. Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Brief Bioinform. 2012. PMID: 22786784 Review.
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.
Fosso B, Santamaria M, Marzano M, Alonso-Alemany D, Valiente G, Donvito G, Monaco A, Notarangelo P, Pesole G. Fosso B, et al. Among authors: valiente g. BMC Bioinformatics. 2015 Jul 1;16:203. doi: 10.1186/s12859-015-0595-z. BMC Bioinformatics. 2015. PMID: 26130132 Free PMC article.
Unbiased Taxonomic Annotation of Metagenomic Samples.
Fosso B, Pesole G, Rosselló F, Valiente G. Fosso B, et al. Among authors: valiente g. J Comput Biol. 2018 Mar;25(3):348-360. doi: 10.1089/cmb.2017.0144. Epub 2017 Oct 13. J Comput Biol. 2018. PMID: 29028181 Free PMC article.
Further steps in TANGO: improved taxonomic assignment in metagenomics.
Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G. Alonso-Alemany D, et al. Among authors: valiente g. Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3. Bioinformatics. 2014. PMID: 23645816
Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space.
Marzano M, Fosso B, Manzari C, Grieco F, Intranuovo M, Cozzi G, Mulè G, Scioscia G, Valiente G, Tullo A, Sbisà E, Pesole G, Santamaria M. Marzano M, et al. Among authors: valiente g. PLoS One. 2016 Jun 14;11(6):e0157383. doi: 10.1371/journal.pone.0157383. eCollection 2016. PLoS One. 2016. PMID: 27299312 Free PMC article.
Flexible taxonomic assignment of ambiguous sequencing reads.
Clemente JC, Jansson J, Valiente G. Clemente JC, et al. Among authors: valiente g. BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8. BMC Bioinformatics. 2011. PMID: 21211059 Free PMC article.
An edit script for taxonomic classifications.
Page RD, Valiente G. Page RD, et al. Among authors: valiente g. BMC Bioinformatics. 2005 Aug 25;6:208. doi: 10.1186/1471-2105-6-208. BMC Bioinformatics. 2005. PMID: 16122379 Free PMC article.
53 results