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The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. Ten Hoopen P, et al. Among authors: santamaria m. Gigascience. 2017 Aug 1;6(8):1-11. doi: 10.1093/gigascience/gix047. Gigascience. 2017. PMID: 28637310 Free PMC article.
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: santamaria m. BMC Bioinformatics. 2015 Jul 1;16:203. doi: 10.1186/s12859-015-0595-z. BMC Bioinformatics. 2015. PMID: 26130132 Free PMC article.
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. Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Brief Bioinform. 2012. PMID: 22786784 Review.
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.
Tangaro MA, Defazio G, Fosso B, Licciulli VF, Grillo G, Donvito G, Lavezzo E, Baruzzo G, Pesole G, Santamaria M. Tangaro MA, et al. Among authors: santamaria m. Bioinformatics. 2021 Nov 18;37(22):4253-4254. doi: 10.1093/bioinformatics/btab431. Bioinformatics. 2021. PMID: 34117876 Free PMC article.
BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.
Hardisty AR, Bacall F, Beard N, Balcázar-Vargas MP, Balech B, Barcza Z, Bourlat SJ, De Giovanni R, de Jong Y, De Leo F, Dobor L, Donvito G, Fellows D, Guerra AF, Ferreira N, Fetyukova Y, Fosso B, Giddy J, Goble C, Güntsch A, Haines R, Ernst VH, Hettling H, Hidy D, Horváth F, Ittzés D, Ittzés P, Jones A, Kottmann R, Kulawik R, Leidenberger S, Lyytikäinen-Saarenmaa P, Mathew C, Morrison N, Nenadic A, de la Hidalga AN, Obst M, Oostermeijer G, Paymal E, Pesole G, Pinto S, Poigné A, Fernandez FQ, Santamaria M, Saarenmaa H, Sipos G, Sylla KH, Tähtinen M, Vicario S, Vos RA, Williams AR, Yilmaz P. Hardisty AR, et al. Among authors: santamaria m. BMC Ecol. 2016 Oct 20;16(1):49. doi: 10.1186/s12898-016-0103-y. BMC Ecol. 2016. PMID: 27765035 Free PMC article.
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: santamaria m. PLoS One. 2016 Jun 14;11(6):e0157383. doi: 10.1371/journal.pone.0157383. eCollection 2016. PLoS One. 2016. PMID: 27299312 Free PMC article.
605 results