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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: pesole g. BMC Ecol. 2016 Oct 20;16(1):49. doi: 10.1186/s12898-016-0103-y. BMC Ecol. 2016. PMID: 27765035 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. Among authors: pesole g. Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Brief Bioinform. 2012. PMID: 22786784 Review.
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
Fosso B, Santamaria M, D'Antonio M, Lovero D, Corrado G, Vizza E, Passaro N, Garbuglia AR, Capobianchi MR, Crescenzi M, Valiente G, Pesole G. Fosso B, et al. Among authors: pesole g. Bioinformatics. 2017 Jun 1;33(11):1730-1732. doi: 10.1093/bioinformatics/btx036. Bioinformatics. 2017. PMID: 28130230 Free PMC article.
However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to …
However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, …
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: pesole g. Gigascience. 2017 Aug 1;6(8):1-11. doi: 10.1093/gigascience/gix047. Gigascience. 2017. PMID: 28637310 Free PMC article.
Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.
Kissling WD, Ahumada JA, Bowser A, Fernandez M, Fernández N, García EA, Guralnick RP, Isaac NJB, Kelling S, Los W, McRae L, Mihoub JB, Obst M, Santamaria M, Skidmore AK, Williams KJ, Agosti D, Amariles D, Arvanitidis C, Bastin L, De Leo F, Egloff W, Elith J, Hobern D, Martin D, Pereira HM, Pesole G, Peterseil J, Saarenmaa H, Schigel D, Schmeller DS, Segata N, Turak E, Uhlir PF, Wee B, Hardisty AR. Kissling WD, et al. Among authors: pesole g. Biol Rev Camb Philos Soc. 2018 Feb;93(1):600-625. doi: 10.1111/brv.12359. Epub 2017 Aug 2. Biol Rev Camb Philos Soc. 2018. PMID: 28766908 Review.
Unbiased Taxonomic Annotation of Metagenomic Samples.
Fosso B, Pesole G, Rosselló F, Valiente G. Fosso B, et al. Among authors: pesole 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.
346 results