Peer-Reviewed Scientific Publications in International Journals

Peer-Reviewed Scientific Publications in International Journals

CV (HENRIK NILSSON, 760115)

Peer-reviewed scientific publications in international journals

2012 / accepted / in press

  • Hyde KD, Udayanga D, Manamgoda DS, Liu J-K, Tedersoo L, Larsson E, Abarenkov K, Bertrand Y, Oxelman B, Hartmann M, Kauserud H, Ryberg M, Kristiansson E, Nilsson RH. 2013.Incorporating molecular data in fungal systematics: a guide for aspiring researchers. (in preparation)
  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. 2012.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.Research in Microbiology 163: 407-412. (Number of citations: 1) open access
  • Hallenberg N, Nilsson RH, Robledo G. 2012/3.Species complexes in Hericium (Russulales, Agaricomycota) and a new species – Hericium rajchenbergii – from southern South America.Mycological Progress (in press). DOI 10.1007/s11557-012-0848-4
  • Hartmann M, Howes CG, VanInsberghe D, Yu H, Bachar D, Christen R, Nilsson RH, Hallam SJ, Mohn WW. 2012.Significant and persistent impact of timber harvesting on soil microbial communities in northern coniferous forests.The ISME Journal 6: 2199-2218. (Number of citations: 4)
  • La Duc MT, Vaishampayan P, Nilsson RH, Torok T, Venkateswaran K. 2012.Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.Applied and Environmental Microbiology 78: 5912-5922. (Number of citations: 3)
  • Münzenberger B, Schneider B, Nilsson RH, Bubner B, Larsson K-H, Hüttl RF. 2012. Morphology, anatomy, and molecular studies of the ectomycorrhiza formed axenically by a fungus of the Sistotrema/Hydnum group.Mycological Progress11: 817-826. (Number of citations: 1)
  • Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson J, Eriksson M, Larsson K-H, Larsson E, and Kõljalg U. 2012.Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.MycoKeys4: 37-63. (Number of citations: 0) open access
  • Orgiazzi A, Lumini E, Nilsson RH, Girlanda M, Vizzini A, Bonfante P, Bianciotto V. 2012.Unravelling soil fungal communities from different Mediterranean land-use backgrounds.PLoS ONE 7: e34847. (Number of citations: 2) open access
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, ..., Nilsson RH, ..., Schindel D. 2012.Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.Proceedings of the National Academy of Sciences USA 109: 6241-6246. (Number of citations: 61) open access
  • Xu L, Ravnskov S, Larsen J, Nilsson RH, Nicolaisen M. 2012. Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing.Soil Biology and Biochemistry 46: 26-32. (Number of citations: 7)

2011

  • Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G-A, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH. 2011.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.Antonie van Leeuwenhoek100: 471-475. (Number of citations: 8)
  • Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Mohn WW, Nilsson RH. 2011.V-RevComp: Automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets.FEMS Microbiology Letters 319: 140-145. (Number of citations: 4)
  • Nilsson RH, Ryberg M, Sjökvist E, Abarenkov K. 2011.Rethinking taxon sampling in the light of environmental sequencing.Cladistics 27: 197-203. (Number of citations: 10)
  • Nilsson RH, Tedersoo L, Lindahl B, Kjøller R, Carlsen T, Quince C, Abarenkov K, Pennanen T, Stenlid J, Bruns T, Larsson K-H, Kõljalg U, Kauserud H. 2011.Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.New Phytologist191: 314-318. (Number of citations: 9)
  • Nilsson RH, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Bertrand Y, Alfredsson JF, Larsson K-H, Kõljalg U, Abarenkov K. 2011.A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation.Mycoscience52: 278-282. (Number of citations: 6)
  • Ryberg M, NilssonRH, Matheny B. 2011. DivBayes and SubT: exploring species diversification using Bayesian statistics.Bioinformatics 27: 2439-2440. (Number of citations: 1)
  • Tedersoo L, Abarenkov K, Nilsson RH, Schussler A, Grelet G-A, Kohout P, Oja J, Bonito GM, Veldre V, Jairus T, Ryberg M, Larsson K-H, Kõljalg U. 2011. Tidying up International Nucleotide Sequence Databases: ecological, geographical, and sequence quality annotation of ITS sequences of mycorrhizal fungi.PLoS ONE 6: e24940. (Number of citations: 5) open access
  • Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang W-Y, Dai Y-C, Johnston PR, Townsend JP. 2011. Tasting soil fungal diversity with earth tongues: Phylogenetic test of SATé alignments for environmental ITS data.PLoS ONE 6: e19039. (Number of citations: 5) open access

2010

  • Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Ursing BM, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U. 2010.The UNITE database for molecular identification of fungi - recent updates and future perspectives.New Phytologist 186: 281-285. (Number of citations: 60)
  • Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, Veldre V, Parmasto E, Prous M, Aan A, Ots M, Kurina O, Ostonen I, Jõgeva J, Halapuu S, Põldmaa K, Toots M, Truu J, Larsson K-H, Kõljalg U. 2010.PlutoF - a web-based workbench for ecological and taxonomical research, with an online implementation for fungal ITS sequences.Evolutionary Bioinformatics6: 189-196 (Number of citations: 25) open access
  • Ghobad-Nejhad M, Nilsson RH, Hallenberg N. 2010. Phylogeny and taxonomy of the genus Vuilleminia (Basidiomycota) based on molecular and morphological evidence, with new insights into Corticiales.Taxon 59: 1519-1534. (Number of citations: 6)
  • Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH. 2010.V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.Journal of Microbiological Methods 83: 250-253. (Number of citations: 14)
  • Nilsson RH, Abarenkov K, Veldre V, Nylinder S, De Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E. 2010.An open source chimera checker for the fungal ITS region.Molecular Ecology Resources10: 1076-1081. (Number of citations: 29)
  • Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson E, Ryberg M, Jumpponen A, Abarenkov K. 2010.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 Ecology3: 284-287. (Number of citations:30)
  • Tedersoo L§, Nilsson RH§, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. 2010.454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist188: 291-301. § = equal contribution (Number of citations: 87)
  • Wu S-H, Nilsson RH, Chen C-T, Yu S-Y, Hallenberg N. 2010.The white-rotting genus Phanerochaete is polyphyletic and distributed throughout the phleboid clade of the Polyporales (Basidiomycota).Fungal Diversity42: 107-118. (Number of citations: 3)

2009

  • Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009.454 pyrosequencing analyses of forest soil reveal an unexpectedly high fungal diversity. New Phytologist 184: 449-456. (Number of citations: 180)
  • Eriksson KM, Antonelli A, Nilsson RH, Clarke AK, Blanck H. 2009. A phylogenetic approach to detect selection on the target site of the antifouling compound irgarol in tolerant periphyton communities.Environmental Microbiology 11: 2065-2077. (Number of citations: 1)
  • Nilsson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N. 2009. A software pipeline for processing and identification of fungal ITS sequences.Source Code in Biology and Medicine 4: 1. (Number of citations: 31) open access
  • Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. 2009. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.FEMS Microbiology Letters 296: 97-101. (Number of citations: 61)
  • Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH.2009. An outlook on the fungal ITS sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytologist 181: 471-477. (Number of citations: 49)

2008

  • Bidartondo M, ..., Nilsson RHet al. 2008. Preserving accuracy in GenBank.Science 319: 1616. (Number of citations: 69) [Letter to Science]
  • Bienert GP, Thorsen M, Schuessler MD, Nilsson RH, Wagner A, Tamas MJ, Jahn TP. 2008. A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)3 and Sb(OH)3 across membranes.BMC Biology 6: 26. (Number of citations: 92) open access
  • Hallenberg N, Ryberg M, Nilsson RH, Wood AR, Wu S-H. 2008. Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi.Botany 86: 1319-1325. (Number of citations: 3)
  • Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. 2008. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification.Evolutionary Bioinformatics 4: 193-201. (Number of citations: 193) open access
  • Ryberg M, Nilsson RH, Kristiansson E, Töpel M, Jacobsson S, Larsson E. 2008. Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota).BMC Evolutionary Biology 8:50. (Number of citations: 47) open access

2007

  • Hallenberg N, Nilsson RH, Antonelli A, Wu S-H, Maekawa N, Nordén B. 2007. The Peniophorella praetermissa species complex (Basidiomycota).Mycological Research 111: 1366-1376. (Number of citations: 12)
  • Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch C, Langer E, Langer G, McLaughlin DJ, Wilson AW, Froslev T, Ge ZW, Kerrigan RW, Kerrigan R, Slot J, Yang Z-L, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl M, Vauras J, Hibbett DS. 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics and Evolution 43: 430-451. (Number of citations: 83)
  • Paulus B, Nilsson RH, Hallenberg N. 2007.Phylogenetic studies in Hypochnicium (Basidiomycota), with special emphasis on species from New Zealand.New Zealand Journal of Botany 45: 139-150. (Number of citations: 11)

2006

  • 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 DS. 2006. An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences.Mycologia 98: 896-905. (Number of citations: 53)
  • Moncalvo J-M, Nilsson RH, Koster B, Dunham SM, Bernauer T, Matheny PB, McLenon T, Margaritescu S, Weiss M, Garnica S, Danell E, Langer E, Langer G, Larsson E, Larsson K-H, Vilgalys R. 2006. The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods.Mycologia 98: 937-948. (Number of citations: 62)
  • Nilsson RH, Larsson K-H, Larsson E, Kõljalg U. 2006. Fruiting-body guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota).Mycological Research 110: 1426-1432. (Number of citations: 18)
  • Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K-H, Kõljalg U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.PLoS ONE 1: e59. (Number of citations: 171) open access

2005

  • Hibbett DS, Nilsson RH, Snyder M, Fonseca M, Costanzo J, Shonfeld M. 2005. Automated phylogenetic taxonomy: an example in the homobasidiomycetes.Systematic Biology 54: 660-668. (Number of citations: 45; highlighted in Science 309 p. 374.)
  • Kõljalg U§, Larsson K-H§, Abarenkov K§, Nilsson RH§, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Vrålstad T, Ursing BM. 2005. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.New Phytologist 166: 1063-1068. § = equal contribution (Number of citations: 240)
  • Nilsson RH, Kristiansson E, Ryberg M, Larsson K-H. 2005. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi. BMC Bioinformatics 6: 178. (Number of citations: 52) open access

2004

  • Nilsson RH, Larsson K-H, Ursing B. 2004. galaxie - CGI scripts for sequence identification through automated phylogenetic analysis.Bioinformatics 20: 1447-1452. (Number of citations: 24)
  • Nilsson RH, Rajashekar B, Larsson K-H, Ursing BM. 2004. galaxieEST: addressing EST identity through automated phylogenetic analysis.BMC Bioinformatics 5: 87. (Number of citations: 7) open access
  • Parmasto E, Nilsson RH, Larsson K-H. 2004. Cortbase version 2 - extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes).Phyloinformatics 1: 5. (Number of citations: 26; highlighted in Science 310 p. 753) open access

2003

  • Nilsson RH, Hallenberg N. 2003. Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data.Mycologia 95: 54-60. (Number of citations: 11)
  • Nilsson RH, Hallenberg N, Norden B, Maekawa N, Wu S.-H. 2003. Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere.Mycological Research 107: 645-652. (Number of citations: 21)

Peer-reviewed review articles

  • Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, Nilsson RH. 2011.Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences.Fungal Biology Reviews 25: 38-47. (Number of citations: 41)
  • Nilsson RH, Abarenkov K, Larsson K-H, Kõljalg U. 2011.Molecular identification of fungi: rationale, philosophical concerns, and the UNITE database.Open Applied Informatics Journal 5: 81-86 (Number of citations: 1) open access
  • Begerow D, Nilsson RH, Unterseher M, Maier W. 2010.Current state and perspectives of fungal DNA barcoding and rapid identification procedures.Applied Microbiology and Biotechnology87: 99-108. (Number of citations: 71)

Peer-reviewed book chapters

Hartmann M, Bengtsson J, Nilsson RH. 2013.High-throughput quality control of next-generation sequencing datasets from environmental studies using Hidden Markov Models.Protein and Nucletide Sequence Analysis(Academy Publish, in press).open access

Thesis

Nilsson RH (2007) Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota). Department of Plant and Environmental Sciences, University of Gothenburg. ISBN 978-91-85529-10-0.

Supervisor: Prof. Nils Hallenberg (completed on time)

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