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Items: 1 to 50 of 51

1.

Mycobiome diversity: high-throughput sequencing and identification of fungi.

Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L.

Nat Rev Microbiol. 2019 Jan;17(2):95-109. doi: 10.1038/s41579-018-0116-y. Review.

PMID:
30442909
2.

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.

Ritter CD, Zizka A, Roger F, Tuomisto H, Barnes C, Nilsson RH, Antonelli A.

PeerJ. 2018 Sep 25;6:e5661. doi: 10.7717/peerj.5661. eCollection 2018.

3.

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.

Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Leho Tedersoo, Bahram M.

MycoKeys. 2018 Sep 11;(39):29-40. doi: 10.3897/mycokeys.39.28109. eCollection 2018.

4.

Introducing ribosomal tandem repeat barcoding for fungi.

Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH.

Mol Ecol Resour. 2018 Sep 21. doi: 10.1111/1755-0998.12944. [Epub ahead of print]

PMID:
30240145
5.

Protax-fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences.

Abarenkov K, Somervuo P, Nilsson RH, Kirk PM, Huotari T, Abrego N, Ovaskainen O.

New Phytol. 2018 Oct;220(2):517-525. doi: 10.1111/nph.15301. Epub 2018 Jul 23.

PMID:
30035303
6.

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.

Bioinformatics. 2018 Dec 1;34(23):4027-4033. doi: 10.1093/bioinformatics/bty482.

7.

New light on names and naming of dark taxa.

Ryberg M, Nilsson RH.

MycoKeys. 2018 Feb 23;(30):31-39. doi: 10.3897/mycokeys.30.24376. eCollection 2018.

8.

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

Nilsson RH, Taylor AFS, Adams RI, Baschien C, Johan Bengtsson-Palme, Cangren P, Coleine C, Heide-Marie Daniel, Glassman SI, Hirooka Y, Irinyi L, Reda Iršėnaitė, Pedro M Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M Visagie, Weiss M, Woudenberg JH, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K.

MycoKeys. 2018 Jan 8;(28):65-82. doi: 10.3897/mycokeys.28.20887. eCollection 2018.

9.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

Wurzbacher C, Nilsson RH, Rautio M, Peura S.

ISME J. 2017 Aug;11(8):1938-1941. doi: 10.1038/ismej.2017.54. Epub 2017 Apr 21.

10.

Novel soil-inhabiting clades fill gaps in the fungal tree of life.

Tedersoo L, Bahram M, Puusepp R, Nilsson RH, James TY.

Microbiome. 2017 Apr 8;5(1):42. doi: 10.1186/s40168-017-0259-5.

11.

Critical Issues in Mycobiota Analysis.

Halwachs B, Madhusudhan N, Krause R, Nilsson RH, Moissl-Eichinger C, Högenauer C, Thallinger GG, Gorkiewicz G.

Front Microbiol. 2017 Feb 14;8:180. doi: 10.3389/fmicb.2017.00180. eCollection 2017.

12.

Sequence-based classification and identification of Fungi.

Hibbett D, Abarenkov K, Kõljalg U, Öpik M, Chai B, Cole J, Wang Q, Crous P, Robert V, Helgason T, Herr JR, Kirk P, Lueschow S, O'Donnell K, Nilsson RH, Oono R, Schoch C, Smyth C, Walker DM, Porras-Alfaro A, Taylor JW, Geiser DM.

Mycologia. 2016 Nov/Dec;108(6):1049-1068. doi: 10.3852/16-130. Review.

PMID:
27760854
13.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA.

Syst Biol. 2017 Mar 1;66(2):152-166. doi: 10.1093/sysbio/syw066.

14.

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome-Picea glauca system at an arctic treeline ecotone.

Eusemann P, Schnittler M, Nilsson RH, Jumpponen A, Dahl MB, Würth DG, Buras A, Wilmking M, Unterseher M.

New Phytol. 2016 Sep;211(4):1221-31. doi: 10.1111/nph.13988. Epub 2016 May 4.

15.

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.

Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM.

Front Microbiol. 2015 Oct 30;6:1192. doi: 10.3389/fmicb.2015.01192. eCollection 2015.

16.

FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".

Tedersoo L, Bahram M, Põlme S, Anslan S, Riit T, Kõljalg U, Nilsson RH, Hildebrand F, Abarenkov K.

Science. 2015 Aug 28;349(6251):936. doi: 10.1126/science.aaa5594. Epub 2015 Aug 27.

17.

Standardizing metadata and taxonomic identification in metabarcoding studies.

Tedersoo L, Ramirez KS, Nilsson RH, Kaljuvee A, Kõljalg U, Abarenkov K.

Gigascience. 2015 Jul 31;4:34. doi: 10.1186/s13742-015-0074-5. eCollection 2015.

18.

Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation.

Elliott DR, Caporn SJ, Nwaishi F, Nilsson RH, Sen R.

PLoS One. 2015 May 13;10(5):e0124726. doi: 10.1371/journal.pone.0124726. eCollection 2015.

19.

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.

Microbes Environ. 2015;30(2):145-50. doi: 10.1264/jsme2.ME14121. Epub 2015 Mar 19.

20.

Fungal biogeography. Global diversity and geography of soil fungi.

Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Villarreal Ruiz L, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K.

Science. 2014 Nov 28;346(6213):1256688. doi: 10.1126/science.1256688.

21.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BT, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge ZW, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong SB, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, Krizsan K, Kurtzman CP, Larsson KH, Leavitt S, Letcher PM, Liimatainen K, Liu JK, Lodge DJ, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SS, Manamgoda D, Martín MP, Minnis AM, Moncalvo JM, Mulè G, Nakasone KK, Niskanen T, Olariaga I, Papp T, Petkovits T, Pino-Bodas R, Powell MJ, Raja HA, Redecker D, Sarmiento-Ramirez JM, Seifert KA, Shrestha B, Stenroos S, Stielow B, Suh SO, Tanaka K, Tedersoo L, Telleria MT, Udayanga D, Untereiner WA, Diéguez Uribeondo J, Subbarao KV, Vágvölgyi C, Visagie C, Voigt K, Walker DM, Weir BS, Weiß M, Wijayawardene NN, Wingfield MJ, Xu JP, Yang ZL, Zhang N, Zhuang WY, Federhen S.

Database (Oxford). 2014 Jun 30;2014. pii: bau061. doi: 10.1093/database/bau061. Print 2014.

22.

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.

Mol Ecol. 2013 Nov;22(21):5271-7. doi: 10.1111/mec.12481. Epub 2013 Sep 24.

PMID:
24112409
23.

Meeting report: fungal its workshop (october 2012).

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.

24.

Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest.

Kerekes J, Kaspari M, Stevenson B, Nilsson RH, Hartmann M, Amend A, Bruns TD.

Mol Ecol. 2013 May;22(10):2827-38. doi: 10.1111/mec.12259. Epub 2013 Apr 22.

PMID:
23601077
25.

Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.

Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H.

New Phytol. 2013 Jul;199(1):288-99. doi: 10.1111/nph.12243. Epub 2013 Mar 28. Review.

26.

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.

Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.

PMID:
22824070
27.

Unravelling soil fungal communities from different Mediterranean land-use backgrounds.

Orgiazzi A, Lumini E, Nilsson RH, Girlanda M, Vizzini A, Bonfante P, Bianciotto V.

PLoS One. 2012;7(4):e34847. doi: 10.1371/journal.pone.0034847. Epub 2012 Apr 20.

28.

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.

PLoS One. 2011;6(9):e24940. doi: 10.1371/journal.pone.0024940. Epub 2011 Sep 15.

29.

DivBayes and SubT: exploring species diversification using Bayesian statistics.

Ryberg M, Nilsson RH, Matheny PB.

Bioinformatics. 2011 Sep 1;27(17):2439-40. doi: 10.1093/bioinformatics/btr405. Epub 2011 Jul 7.

PMID:
21742635
30.

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.

Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15.

PMID:
21674231
31.

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP.

PLoS One. 2011 Apr 21;6(4):e19039. doi: 10.1371/journal.pone.0019039.

32.

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.

FEMS Microbiol Lett. 2011 Jun;319(2):140-5. doi: 10.1111/j.1574-6968.2011.02274.x. Epub 2011 Apr 27.

33.

V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.

Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH.

J Microbiol Methods. 2010 Nov;83(2):250-3. doi: 10.1016/j.mimet.2010.08.008. Epub 2010 Aug 27.

PMID:
20804791
34.

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.

Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U.

New Phytol. 2010 Oct;188(1):291-301. doi: 10.1111/j.1469-8137.2010.03373.x. Epub 2010 Jul 15.

35.
36.

A software pipeline for processing and identification of fungal ITS sequences.

Nilsson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N.

Source Code Biol Med. 2009 Jan 15;4:1. doi: 10.1186/1751-0473-4-1.

37.

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.

Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH.

New Phytol. 2009 Jan;181(2):471-477. doi: 10.1111/j.1469-8137.2008.02667.x.

38.

Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota).

Ryberg M, Nilsson RH, Kristiansson E, Töpel M, Jacobsson S, Larsson E.

BMC Evol Biol. 2008 Feb 18;8:50. doi: 10.1186/1471-2148-8-50.

39.

The Peniophorella praetermissa species complex (Basidiomycota).

Hallenberg N, Nilsson RH, Antonelli A, Wu SH, Maekawa N, Nordén B.

Mycol Res. 2007 Dec;111(Pt 12):1366-76. Epub 2007 Oct 7.

PMID:
18023990
40.

The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods.

Moncalvo JM, Nilsson RH, Koster B, Dunham SM, Bernauer T, Matheny PB, Porter TM, Margaritescu S, Weiss M, Garnica S, Danell E, Langer G, Langer E, Larsson E, Larsson KH, Vilgalys R.

Mycologia. 2006 Nov-Dec;98(6):937-48.

PMID:
17486970
41.

An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences.

Aime MC, Matheny PB, Henk DA, Frieders EM, Nilsson RH, Piepenbring M, McLaughlin DJ, Szabo LJ, Begerow D, Sampaio JP, Bauer R, Weiss M, Oberwinkler F, Hibbett D.

Mycologia. 2006 Nov-Dec;98(6):896-905.

PMID:
17486966
42.

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.

Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH, Kõljalg U.

PLoS One. 2006 Dec 20;1:e59.

43.
44.

Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi).

Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, McLaughlin DJ, Wilson AW, Frøslev T, Ge ZW, Kerrigan RW, Slot JC, Yang ZL, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS.

Mol Phylogenet Evol. 2007 May;43(2):430-51. Epub 2006 Sep 23.

PMID:
17081773
45.

Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi).

Hibbett DS, Nilsson RH, Snyder M, Fonseca M, Costanzo J, Shonfeld M.

Syst Biol. 2005 Aug;54(4):660-8. No abstract available.

PMID:
16126660
46.
47.

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.

New Phytol. 2005 Jun;166(3):1063-8.

48.

galaxieEST: addressing EST identity through automated phylogenetic analysis.

Nilsson RH, Rajashekar B, Larsson KH, Ursing BM.

BMC Bioinformatics. 2004 Jul 5;5:87.

49.

galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

Nilsson RH, Larsson KH, Ursing BM.

Bioinformatics. 2004 Jun 12;20(9):1447-52. Epub 2004 Feb 19.

PMID:
14976034
50.

Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere.

Nilsson RH, Hallenberg N, Nordén B, Maekawa N, Wu SH.

Mycol Res. 2003 Jun;107(Pt 6):645-52.

PMID:
12951791

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