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V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets.
Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH. Hartmann M, et al. Among authors: abarenkov k. FEMS Microbiol Lett. 2011 Jun;319(2):140-5. doi: 10.1111/j.1574-6968.2011.02274.x. Epub 2011 Apr 27. FEMS Microbiol Lett. 2011. PMID: 21453324
UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.
Kõljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AF, Tedersoo L, Vrålstad T, Ursing BM. Kõljalg U, et al. Among authors: abarenkov k. New Phytol. 2005 Jun;166(3):1063-8. doi: 10.1111/j.1469-8137.2005.01376.x. New Phytol. 2005. PMID: 15869663 Free article.
An open source chimera checker for the fungal ITS region.
Nilsson RH, Abarenkov K, Veldre V, Nylinder S, DE Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E. Nilsson RH, et al. Among authors: abarenkov k. Mol Ecol Resour. 2010 Nov;10(6):1076-81. doi: 10.1111/j.1755-0998.2010.02850.x. Mol Ecol Resour. 2010. PMID: 21565119
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH. Bengtsson J, et al. Among authors: abarenkov k. Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15. Antonie Van Leeuwenhoek. 2011. PMID: 21674231
Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.
Tedersoo L, Abarenkov K, Nilsson RH, Schüssler A, Grelet GA, Kohout P, Oja J, Bonito GM, Veldre V, Jairus T, Ryberg M, Larsson KH, Kõljalg U. Tedersoo L, et al. Among authors: abarenkov k. PLoS One. 2011;6(9):e24940. doi: 10.1371/journal.pone.0024940. Epub 2011 Sep 15. PLoS One. 2011. PMID: 21949797 Free PMC article.
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. Bengtsson J, et al. Among authors: abarenkov k. Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21. Res Microbiol. 2012. PMID: 22824070 Free article.
ITS1 versus ITS2 as DNA metabarcodes for fungi.
Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H. Blaalid R, et al. Among authors: abarenkov k. Mol Ecol Resour. 2013 Mar;13(2):218-24. doi: 10.1111/1755-0998.12065. Epub 2013 Jan 25. Mol Ecol Resour. 2013. PMID: 23350562
49 results