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Towards a unified paradigm for sequence-based identification of fungi.
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH. Kõljalg U, et al. Among authors: hartmann m. Mol Ecol. 2013 Nov;22(21):5271-7. doi: 10.1111/mec.12481. Epub 2013 Sep 24. Mol Ecol. 2013. PMID: 24112409
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.
Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K. Nilsson RH, et al. Among authors: hartmann m. Microbes Environ. 2015;30(2):145-50. doi: 10.1264/jsme2.ME14121. Epub 2015 Mar 19. Microbes Environ. 2015. PMID: 25786896 Free PMC article.
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.
Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ÉD, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH. Bengtsson-Palme J, et al. Among authors: hartmann m. Bioinformatics. 2018 Dec 1;34(23):4027-4033. doi: 10.1093/bioinformatics/bty482. Bioinformatics. 2018. PMID: 29912385 Free PMC article.
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: hartmann m. 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
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. 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
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: hartmann m. 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.
1,962 results