Mora C, Tittensor DP, Adl S, Simpson AG, Worm B. How many species are there on earth and in the ocean? PLoS Biol. 2011;9(8):e1001127.
Article
CAS
PubMed Central
Google Scholar
Desprez-Loustau ML, Robin C, Buee M, Courtecuisse R, Garbaye J, Suffert F, Sache I, Rizzo DM. The fungal dimension of biological invasions. Trends Ecol Evol. 2007;22(9):472–80.
Article
Google Scholar
Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lucking R, et al. A higher-level phylogenetic classification of the fungi. Mycol Res. 2007;111(Pt 5):509–47.
Article
Google Scholar
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci. 2012;109(16):6241–6.
Article
CAS
PubMed Central
Google Scholar
Vilgalys D, Gonzalez D. Organization of ribosomal DNA in the basidiomycete thanatephorus praticola. Curr Genet. 1990;18(3):277–80.
Article
CAS
Google Scholar
Delhaes L, Monchy S, Frealle E, Hubans C, Salleron J, Leroy S, Prevotat A, Wallet F, Wallaert B, Dei-Cas E, et al. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community—implications for therapeutic management. PLoS ONE. 2012;7(4):e36313.
Article
CAS
PubMed Central
Google Scholar
Mello A, Napoli C, Murat C, Morin E, Marceddu G, Bonfante P. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia. 2011;103(6):1184–93.
Article
CAS
Google Scholar
Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1):e1000713.
Article
PubMed Central
Google Scholar
Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 2009;184(2):449–56.
Article
CAS
Google Scholar
Jumpponen A, Jones KL. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol. 2009;184(2):438–48.
Article
CAS
Google Scholar
Borman AM, Linton CJ, Miles SJ, Johnson EM. Molecular identification of pathogenic fungi. J Antimicrob Chemother. 2008;61(Suppl 1):i7–12.
Article
CAS
Google Scholar
Hillis DM, Dixon MT. Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991;66(4):411–53.
Article
CAS
Google Scholar
Narutaki S, Takatori K, Nishimura H, Terashima H, Sasaki T. Identification of fungi based on the nucleotide sequence homology of their internal transcribed spacer 1 (ITS1) region. PDA J Pharm Sci Technol. 2002;56(2):90–8.
CAS
Google Scholar
Hinrikson HP, Hurst SF, Lott TJ, Warnock DW, Morrison CJ. Assessment of ribosomal large-subunit D1-D2, internal transcribed spacer 1, and internal transcribed spacer 2 regions as targets for molecular identification of medically important Aspergillus species. J Clin Microbiol. 2005;43(5):2092–103.
Article
CAS
PubMed Central
Google Scholar
Domingos P, Pazzani M. On the optimality of the simple bayesian classifier under zero-one loss. Mach Learn. 1997;29:103–30.
Article
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–7.
Article
CAS
PubMed Central
Google Scholar
Nilsson RH, Ryberg M, Abarenkov K, Sjokvist E, Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett. 2009;296(1):97–101.
Article
CAS
Google Scholar
Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform. 2008;4:193–201.
Google Scholar
Ben-Hur A, Ong CS, Sonnenburg S, Scholkopf B, Ratsch G. Support vector machines and kernels for computational biology. PLoS Comput Biol. 2008;4(10):e1000173.
Article
PubMed Central
Google Scholar
Liu KL, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl Environ Microbiol. 2012;78(5):1523–33.
Article
CAS
PubMed Central
Google Scholar
Deshpande V, Wang Q, Greenfield P, Charleston M, Porras-Alfaro A, Kuske CR, Cole JR, Midgley DJ, Tran-Dinh N. Fungal identification using a bayesian classifier and the warcup training set of internal transcribed spacer sequences. Mycologia. 2016;108(1):1–5.
Article
Google Scholar
Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinform. 2010;11:538.
Article
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1.
Article
CAS
Google Scholar
Koljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Hoiland K, Kjoller R, Larsson E, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166(3):1063–8.
Article
CAS
PubMed
Google Scholar
Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson E, Ryberg M, Jumpponen A, Abarenkov K. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecol. 2010;3:284–7.
Article
Google Scholar
Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database 2014. 2014. doi:10.1093/database/bau061.
Google Scholar
Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using weka. Bioinformatics. 2004;20(15):2479–81.
Article
CAS
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.
Article
Google Scholar