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Rolf Henrik Nilsson. Works in the area(s) of Natural sciences with emphasis on Biological Sciences.
Identification

Personal identification

Full name
Rolf Henrik Nilsson

Citation names

  • Nilsson, Rolf

Author identifiers

Ciência ID
9315-4E8E-DAD4
ORCID iD
0000-0002-8052-0107

Addresses

  • University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, 405 30, Göteborg, Västra Götaland, Sweden (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2002/01/15 - 2007/06/19
Concluded
 Henrik Nilsson (Doktor (PhD))
Göteborgs Universitet, Sweden
Affiliation

Science

Category
Host institution 		Employer
2011/01/01 - Current Researcher (Research) Göteborgs Universitet, Sweden
Göteborgs Universitet, Sweden
Projects

Grant

Designation Funders
2012/01/01 - 2019/12/31 A bioinformatics platform to reconcile environmental sampling of fungi with fungal systematics and ecology: conceptual, methodological, and software-related solutions
FORMAS 2011-00498
Principal investigator
Göteborgs Universitet, Sweden
Concluded
Outputs

Publications

Book chapter
  1. Nilsson, Rolf. "Molecular Techniques in Mycological Studies and Sequence Data Curating: Quality Control and Challenges". 2016.
    10.1007/978-3-319-29137-6_4
  2. Nilsson, Rolf. "Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data". 2016.
    10.1007/978-3-319-29137-6_3
  3. Nilsson, Rolf. "Agaricomycetes". 2014.
    10.1007/978-3-642-55318-9_14
Conference paper
  1. Bok, G.; Nilsson, H.R.. "Identification of mould fungi by combining blast-based similarity searches and phylogenetic analysis". 2011.
Journal article
  1. Nilsson, Rolf. "The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia". Scientific Reports (2019): http://dx.doi.org/10.1038/s41598-019-55490-3.
    10.1038/s41598-019-55490-3
  2. Nilsson, Rolf. "Notes, outline and divergence times of Basidiomycota". Fungal Diversity (2019): http://dx.doi.org/10.1007/s13225-019-00435-4.
    10.1007/s13225-019-00435-4
  3. Alice Retter; R. Henrik Nilsson; Sarah J. Bourlat. "Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding". Biodiversity Data Journal 7 (2019): https://doi.org/10.3897/BDJ.7.e35332.
    10.3897/BDJ.7.e35332
  4. Urmas Kõljalg; Kessy Abarenkov; R. Henrik Nilsson; Karl-Henrik Larsson; Andy F.S. Taylor. "The UNITE Database for Molecular Identification and for Communicating Fungal Species". Biodiversity Information Science and Standards (2019): https://doi.org/10.3897/biss.3.37402.
    10.3897/biss.3.37402
  5. Sten Svantesson; Karl-Henrik Larsson; Urmas Kõljalg; Tom W. May; Patrik Cangren; R. Henrik Nilsson; Ellen Larsson. "Solving the taxonomic identity of Pseudotomentella tristis s.l. (Thelephorales, Basidiomycota) – a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data". MycoKeys (2019): https://doi.org/10.3897/mycokeys.50.32432.
    10.3897/mycokeys.50.32432
  6. Christian Wurzbacher; Ellen Larsson; Johan Bengtsson-Palme; Silke Van den Wyngaert; Sten Svantesson; Erik Kristiansson; Maiko Kagami; R. Henrik Nilsson. "Introducing ribosomal tandem repeat barcoding for fungi". Molecular Ecology Resources 19 1 (2019): 118-127. https://doi.org/10.1111/1755-0998.12944.
    10.1111/1755-0998.12944
  7. Nilsson, Rolf. "Large expert-curated database for benchmarking document similarity detection in biomedical literature search". Database (2019): http://dx.doi.org/10.1093/database/baz085.
    10.1093/database/baz085
  8. Nilsson, Rolf. "Mycobiome diversity: high-throughput sequencing and identification of fungi". Nature Reviews Microbiology (2018): https://www.nature.com/articles/s41579-018-0116-y.
    10.1038/s41579-018-0116-y
  9. Sten Anslan; R. Henrik Nilsson; Christian Wurzbacher; Petr Baldrian; Leho Tedersoo; Mohammad Bahram. "Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding". MycoKeys (2018): https://doi.org/10.3897/mycokeys.39.28109.
    10.3897/mycokeys.39.28109
  10. Nilsson, Rolf. "High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia". PeerJ 6 (2018): e5661-e5661. https://doi.org/10.7717/peerj.5661.
    10.7717/peerj.5661
  11. Martin Ryberg; R. Henrik Nilsson. "New light on names and naming of dark taxa". MycoKeys (2018): https://doi.org/10.3897/mycokeys.30.24376.
    10.3897/mycokeys.30.24376
  12. R. Henrik Nilsson; Andy F.S. Taylor; Rachel I. Adams; Christiane Baschien; Johan Bengtsson-Palme; Patrik Cangren; Claudia Coleine; et al. "Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)". MycoKeys 28 (2018): 65-82. https://doi.org/10.3897/mycokeys.28.20887.
    10.3897/mycokeys.28.20887
  13. Nilsson, Rolf. "Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) -- a case study reveals clear tissue preferences and differences in diversity and composition". Mycological Progress 17 4 (2018): 489-500. https://doi.org/10.1007/s11557-018-1375-8.
    10.1007/s11557-018-1375-8
  14. Nilsson, Rolf. "Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker". Bioinformatics (2018): bty482-bty482. http://dx.doi.org/10.1093/bioinformatics/bty482.
    10.1093/bioinformatics/bty482
  15. Nilsson, Rolf. "The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications". Nucleic Acids Research (2018): gky1022-gky1022. http://dx.doi.org/10.1093/nar/gky1022.
    10.1093/nar/gky1022
  16. Nilsson, Rolf. "Relationships within Capitotricha bicolor (Lachnaceae, Ascomycota) as inferred from ITS rDNA sequences, including some notes on the Brunnipila and Erioscyphella clades". Mycological Progress (2018): https://doi.org/10.1007/s11557-017-1346-5.
    10.1007/s11557-017-1346-5
  17. Nilsson, Rolf. "Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory". MycoKeys 26 (2017): 13-13. https://mycokeys.pensoft.net/article/14591/.
    10.3897/mycokeys.26.14591
  18. Nilsson, Rolf. "Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota". MycoKeys 25 (2017): 31-50. https://doi.org/10.3897/mycokeys.25.12446.
    10.3897/mycokeys.25.12446
  19. Nilsson, Rolf. "Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma (Agaricales)". MycoKeys 21 (2017): 33-88. https://doi.org/10.3897/mycokeys.21.12176.
    10.3897/mycokeys.21.12176
  20. Nilsson, Rolf. "Novel soil-inhabiting clades fill gaps in the fungal tree of life". Microbiome 5 1 (2017): 42-42. https://doi.org/10.1186/s40168-017-0259-5.
    10.1186/s40168-017-0259-5
  21. Ritter, C.D.; McCrate, G.; Nilsson, R.H.; Fearnside, P.M.; Palme, U.; Antonelli, A.. "Environmental impact assessment in Brazilian Amazonia: Challenges and prospects to assess biodiversity". Biological Conservation 206 (2017): 161-168. http://www.scopus.com/inward/record.url?eid=2-s2.0-85008951224&partnerID=MN8TOARS.
    10.1016/j.biocon.2016.12.031
  22. Nilsson, Rolf. "Critical Issues in Mycobiota Analysis". Frontiers in Microbiology (2017): http://journal.frontiersin.org/article/10.3389/fmicb.2017.00180.
    10.3389/fmicb.2017.00180
  23. Nilsson, Rolf. "Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds". The ISME Journal (2017):
    10.1038/ismej.2017.54
  24. Somervuo P; Koskela S; Pennanen J; Henrik Nilsson R; Ovaskainen O. "Unbiased probabilistic taxonomic classification for DNA barcoding.". (2016): http://europepmc.org/abstract/med/27296980.
    10.1093/bioinformatics/btw346
  25. Hibbett D; Abarenkov K; Koljalg U; Opik M; Chai B; Cole JR; Wang Q; et al. "Sequence-based classification and identification of Fungi.". (2016): http://europepmc.org/abstract/med/27760854.
  26. Antonelli A; Hettling H; Condamine FL; Vos K; Nilsson RH; Sanderson MJ; Sauquet H; et al. "Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.". (2016): http://europepmc.org/abstract/med/27616324.
  27. Eusemann P; Schnittler M; Nilsson RH; Jumpponen A; Dahl MB; Würth DG; Buras A; Wilmking M; Unterseher M. "Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome-Picea glauca system at an arctic treeline ecotone.". (2016): http://europepmc.org/abstract/med/27144386.
    10.1111/nph.13988
  28. Kõljalg U; Tedersoo L; Nilsson RH; Abarenkov K. "Digital identifiers for fungal species.". (2016): http://europepmc.org/abstract/med/27257249.
    10.1126/science.aaf7115
  29. Martin Ryberg; Erik Kristiansson; Christian Wurzbacher; R. Henrik Nilsson. "New Ph.D. students in the empirical sciences should be recruited into ongoing scientific studies right from the start". Zenodo (2016):
    10.5281/ZENODO.48179
  30. Nilsson, R.H.; Wurzbacher, C.; Bahram, M.; Coimbra, V.R.M.; Larsson, E.; Tedersoo, L.; Eriksson, J.; et al. "Top 50 most wanted fungi". MycoKeys 12 (2016): 29-40. http://www.scopus.com/inward/record.url?eid=2-s2.0-84963656253&partnerID=MN8TOARS.
    10.3897/mycokeys.12.7553
  31. Abarenkov, K.; Adams, R.I.; Irinyi, L.; Agan, A.; Ambrosio, E.; Antonelli, A.; Bahram, M.; et al. "Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - A report from a May 23-24, 2016 workshop (Gothenburg, Sweden)". MycoKeys 16 (2016): 1-15. http://www.scopus.com/inward/record.url?eid=2-s2.0-85006986456&partnerID=MN8TOARS.
    10.3897/mycokeys.16.10000
  32. Hembrom, M.E.; Das, K.; Nilsson, R.H.; Parihar, A.; Baghela, A.; Mehta, N.; Singh, S.K.; Hallenberg, N.. "Morphology and phylogeny reveal a novel hydnoid taxon from India: Mycorrhaphoides stalpersii gen. and sp. nov". Nordic Journal of Botany (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84990913782&partnerID=MN8TOARS.
    10.1111/njb.01256
  33. Rosenblad, M.A.; Martín, M.P.; Tedersoo, L.; Ryberg, M.; Larsson, E.; Wurzbacher, C.; Abarenkov, K.; Henrik Nilsson, R.. "Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer I (ITSI) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)". MycoKeys 13 (2016): 21-33. http://www.scopus.com/inward/record.url?eid=2-s2.0-84971385333&partnerID=MN8TOARS.
    10.3897/mycokeys.13.8579
  34. Bengtsson-Palme, J.; Thorell, K.; Wurzbacher, C.; Sjöling, Å.; Nilsson, R.H.. "Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2". Ecological Informatics 33 (2016): 45-50. http://www.scopus.com/inward/record.url?eid=2-s2.0-84963983890&partnerID=MN8TOARS.
    10.1016/j.ecoinf.2016.04.004
  35. Tedersoo L; Bahram M; Põlme S; Anslan S; Riit T; Kõljalg U; Nilsson RH; Hildebrand F; Abarenkov K. "FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".". (2015): http://europepmc.org/abstract/med/26315429.
    10.1126/science.aaa5594
  36. Bengtsson-Palme J; Hartmann M; Eriksson KM; Pal C; Thorell K; Larsson DG; Nilsson RH. "Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.". (2015): http://europepmc.org/abstract/med/25732605.
    10.1111/1755-0998.12399
  37. Nilsson, R.H.; Tedersoo, L.; Ryberg, M.; Kristiansson, E.; Hartmann, M.; Unterseher, M.; Porter, T.M.; et al. "A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts". Microbes and Environments 30 2 (2015): 145-150. http://www.scopus.com/inward/record.url?eid=2-s2.0-84931464569&partnerID=MN8TOARS.
    10.1264/jsme2.ME14121
  38. Tedersoo, L.; Anslan, S.; Bahram, M.; Põlme, S.; Riit, T.; Liiv, I.; Kõljalg, U.; et al. "Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi". MycoKeys 10 (2015): 1-43. http://www.scopus.com/inward/record.url?eid=2-s2.0-84940567255&partnerID=MN8TOARS.
    10.3897/mycokeys.10.4852
  39. Jayasiri, S.C.; Hyde, K.D.; Ariyawansa, H.A.; Bhat, J.; Buyck, B.; Cai, L.; Dai, Y.-C.; et al. "The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts". Fungal Diversity 74 1 (2015): 3-18. http://www.scopus.com/inward/record.url?eid=2-s2.0-84944592190&partnerID=MN8TOARS.
    10.1007/s13225-015-0351-8
  40. Elliott DR; Caporn SJ; Nwaishi F; Nilsson RH; Sen R. "Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation.". (2015): http://europepmc.org/abstract/med/25969988.
    10.1371/journal.pone.0124726
  41. Checinska A; Probst AJ; Vaishampayan P; White JR; Kumar D; Stepanov VG; Fox GE; et al. "Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.". (2015): http://europepmc.org/abstract/med/26502721.
    10.1186/s40168-015-0116-3
  42. Sanli K; Bengtsson-Palme J; Nilsson RH; Kristiansson E; Alm Rosenblad M; Blanck H; Eriksson KM. "Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.". (2015): http://europepmc.org/abstract/med/26579098.
    10.3389/fmicb.2015.01192
  43. Tedersoo L; Ramirez KS; Nilsson RH; Kaljuvee A; Kõljalg U; Abarenkov K. "Standardizing metadata and taxonomic identification in metabarcoding studies.". (2015): http://europepmc.org/abstract/med/26236474.
    10.1186/s13742-015-0074-5
  44. Tedersoo L; Bahram M; Põlme S; Kõljalg U; Yorou NS; Wijesundera R; Villarreal Ruiz L; et al. "Fungal biogeography. Global diversity and geography of soil fungi.". (2014): http://europepmc.org/abstract/med/25430773.
    10.1126/science.1256688
  45. Schoch CL; Robbertse B; Robert V; Vu D; Cardinali G; Irinyi L; Meyer W; et al. "Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.". (2014): http://europepmc.org/abstract/med/24980130.
    10.1093/database/bau061
  46. Tedersoo, L.; Bahram, M.; Põlme, S.; Kõljalg, U.; Yorou, N.S.; Wijesundera, R.; Ruiz, L.V.; et al. "Global diversity and geography of soil fungi". Science 346 6213 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84914142313&partnerID=MN8TOARS.
  47. Nilsson, R.H.; Hyde, K.D.; Pawlowska, J.; Ryberg, M.; Tedersoo, L.; Aas, A.B.; Alias, S.A.; et al. "Improving ITS sequence data for identification of plant pathogenic fungi". Fungal Diversity 67 1 (2014): 11-19. http://www.scopus.com/inward/record.url?eid=2-s2.0-84916234886&partnerID=MN8TOARS.
    10.1007/s13225-014-0291-8
  48. Hyde, K.D.; Nilsson, R.H.; Alias, S.A.; Ariyawansa, H.A.; Blair, J.E.; Cai, L.; de Cock, A.W.A.M.; et al. "One stop shop: backbones trees for important phytopathogenic genera: I (2014)". Fungal Diversity 67 1 (2014): 21-125. http://www.scopus.com/inward/record.url?eid=2-s2.0-84916221630&partnerID=MN8TOARS.
    10.1007/s13225-014-0298-1
  49. Kõljalg U; Nilsson RH; Abarenkov K; Tedersoo L; Taylor AF; Bahram M; Bates ST; et al. "Towards a unified paradigm for sequence-based identification of fungi.". (2013): http://europepmc.org/abstract/med/24112409.
    10.1111/mec.12481
  50. Lindahl BD; Nilsson RH; Tedersoo L; Abarenkov K; Carlsen T; Kjøller R; Kõljalg U; et al. "Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.". (2013): http://europepmc.org/abstract/med/23534863.
    10.1111/nph.12243
  51. Lindner DL; Carlsen T; Henrik Nilsson R; Davey M; Schumacher T; Kauserud H. "Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.". (2013): http://europepmc.org/abstract/med/23789083.
    10.1002/ece3.586
  52. Kerekes J; Kaspari M; Stevenson B; Nilsson RH; Hartmann M; Amend A; Bruns TD. "Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest.". (2013): http://europepmc.org/abstract/med/23601077.
    10.1111/mec.12259
  53. Bates ST; Ahrendt S; Bik HM; Bruns TD; Caporaso JG; Cole J; Dwan M; et al. "Meeting report: fungal its workshop (october 2012).". (2013): http://europepmc.org/abstract/med/23961317.
    10.4056/sigs.3737409
  54. Blaalid R; Kumar S; Nilsson RH; Abarenkov K; Kirk PM; Kauserud H. "ITS1 versus ITS2 as DNA metabarcodes for fungi.". (2013): http://europepmc.org/abstract/med/23350562.
    10.1111/1755-0998.12065
  55. Jeppson, M.; Nilsson, R.H.; Larsson, E.. "European earthstars in geastraceae (geastrales, Phallomycetidae)-a systematic approach using morphology and molecular sequence data". Systematics and Biodiversity 11 4 (2013): 437-465. http://www.scopus.com/inward/record.url?eid=2-s2.0-84892530076&partnerID=MN8TOARS.
    10.1080/14772000.2013.857367
  56. Hallenberg, N.; Nilsson, R.H.; Robledo, G.. "Species complexes in Hericium (Russulales, Agaricomycota) and a new species - Hericium rajchenbergii - from southern South America". Mycological Progress 12 2 (2013): 413-420. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876436912&partnerID=MN8TOARS.
    10.1007/s11557-012-0848-4
  57. Bengtsson-Palme, J.; Ryberg, M.; Hartmann, M.; Branco, S.; Wang, Z.; Godhe, A.; De Wit, P.; et al. "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data". Methods in Ecology and Evolution 4 10 (2013): 914-919. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885611996&partnerID=MN8TOARS.
    10.1111/2041-210X.12073
  58. Hartmann M; Howes CG; VanInsberghe D; Yu H; Bachar D; Christen R; Henrik Nilsson R; Hallam SJ; Mohn WW. "Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests.". (2012): http://europepmc.org/abstract/PMC/PMC3504964.
  59. Nilsson, Rolf. "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences". MycoKeys (2012): https://mycokeys.pensoft.net/articles.php?id=1186&element_type=13.
    10.3897/mycokeys.4.3606
  60. La Duc MT; Vaishampayan P; Nilsson HR; Torok T; Venkateswaran K. "Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.". (2012): http://europepmc.org/abstract/med/22729532.
    10.1128/AEM.01435-12
  61. Bengtsson J; Hartmann M; Unterseher M; Vaishampayan P; Abarenkov K; Durso L; Bik EM; et al. "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.". (2012): http://europepmc.org/abstract/med/22824070.
    10.1016/j.resmic.2012.07.001
  62. Schoch CL; Seifert KA; Huhndorf S; Robert V; Spouge JL; Levesque CA; Chen W; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List. "Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.". (2012): http://europepmc.org/abstract/med/22454494.
    10.1073/pnas.1117018109
  63. Orgiazzi A; Lumini E; Nilsson RH; Girlanda M; Vizzini A; Bonfante P; Bianciotto V. "Unravelling soil fungal communities from different Mediterranean land-use backgrounds.". (2012): http://europepmc.org/abstract/med/22536336.
    10.1371/journal.pone.0034847
  64. Münzenberger, B.; Schneider, B.; Nilsson, R.H.; Bubner, B.; Larsson, K.-H.; Hüttl, R.F.. "Morphology, anatomy, and molecular studies of the ectomycorrhiza formed axenically by the fungus Sistotrema sp. (Basidiomycota)". Mycological Progress 11 3 (2012): 817-826. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864139386&partnerID=MN8TOARS.
    10.1007/s11557-011-0797-3
  65. Bengtsson J; Eriksson KM; Hartmann M; Wang Z; Shenoy BD; Grelet GA; Abarenkov K; et al. "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.". (2011): http://europepmc.org/abstract/med/21674231.
    10.1007/s10482-011-9598-6
  66. Ryberg M; Nilsson RH; Matheny PB. "DivBayes and SubT: exploring species diversification using Bayesian statistics.". (2011): http://europepmc.org/abstract/med/21742635.
    10.1093/bioinformatics/btr405
  67. Nilsson, Rolf. "Molecular Identification of Fungi: Rationale, Philosophical Concerns, and the UNITE Database". The Open Applied Informatics Journal (2011): https://benthamopen.com/ABSTRACT/TOAINFOJ-5-81.
    10.2174/1874136301005010081
  68. Henrik Nilsson R; Tedersoo L; Lindahl BD; Kjøller R; Carlsen T; Quince C; Abarenkov K; et al. "Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.". (2011): http://europepmc.org/abstract/med/21557749.
    10.1111/j.1469-8137.2011.03755.x
  69. Hartmann M; Howes CG; Veldre V; Schneider S; Vaishampayan PA; Yannarell AC; Quince C; et al. "V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets.". (2011): http://europepmc.org/abstract/med/21453324.
    10.1111/j.1574-6968.2011.02274.x
  70. Tedersoo L; Abarenkov K; Nilsson RH; Schüssler A; Grelet GA; Kohout P; Oja J; et al. "Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.". (2011): http://europepmc.org/abstract/med/21949797.
    10.1371/journal.pone.0024940
  71. Wang Z; Nilsson RH; Lopez-Giraldez F; Zhuang WY; Dai YC; Johnston PR; Townsend JP. "Tasting soil fungal diversity with earth tongues: phylogenetic test of SATe alignments for environmental ITS data.". (2011): http://europepmc.org/abstract/med/21533038.
    10.1371/journal.pone.0019039
  72. Henrik Nilsson, R.; Ryberg, M.; Sjökvist, E.; Abarenkov, K.. "Rethinking taxon sampling in the light of environmental sequencing". Cladistics 27 2 (2011): 197-203. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952428465&partnerID=MN8TOARS.
    10.1111/j.1096-0031.2010.00336.x
  73. Nilsson, R.H.; Veldre, V.; Wang, Z.; Eckart, M.; Branco, S.; Hartmann, M.; Quince, C.; et al. "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". Mycoscience 52 4 (2011): 278-282. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959633458&partnerID=MN8TOARS.
    10.1007/s10267-010-0086-z
  74. Hibbett, D.S.; Ohman, A.; Glotzer, D.; Nuhn, M.; Kirk, P.; Nilsson, R.H.. "Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences". Fungal Biology Reviews 25 1 (2011): 38-47. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952447866&partnerID=MN8TOARS.
    10.1016/j.fbr.2011.01.001
  75. Hartmann M; Howes CG; Abarenkov K; Mohn WW; Nilsson RH. "V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.". (2010): http://europepmc.org/abstract/med/20804791.
    10.1016/j.mimet.2010.08.008
  76. Nilsson RH; Abarenkov K; Veldre V; Nylinder S; DE Wit P; Brosché S; Alfredsson JF; Ryberg M; Kristiansson E. "An open source chimera checker for the fungal ITS region.". (2010): http://europepmc.org/abstract/med/21565119.
    10.1111/j.1755-0998.2010.02850.x
  77. Tedersoo L; Nilsson RH; Abarenkov K; Jairus T; Sadam A; Saar I; Bahram M; et al. "454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.". (2010): http://europepmc.org/abstract/med/20636324.
    10.1111/j.1469-8137.2010.03373.x
  78. Begerow D; Nilsson H; Unterseher M; Maier W. "Current state and perspectives of fungal DNA barcoding and rapid identification procedures.". (2010): http://europepmc.org/abstract/med/20405123.
    10.1007/s00253-010-2585-4
  79. Abarenkov K; Henrik Nilsson R; Larsson KH; Alexander IJ; Eberhardt U; Erland S; Høiland K; et al. "The UNITE database for molecular identification of fungi--recent updates and future perspectives.". (2010): http://europepmc.org/abstract/med/20409185.
    10.1111/j.1469-8137.2009.03160.x
  80. Ghobad-Nejhad, M.; Nilsson, R.H.; Hallenberg, N.. "Phylogeny and taxonomy of the genus Vuilleminia (Basidiomycota) based on molecular and morphological evidence, with new insights into Corticiales". Taxon 59 5 (2010): 1519-1534. http://www.scopus.com/inward/record.url?eid=2-s2.0-78149255996&partnerID=MN8TOARS.
  81. Nilsson, R.H.; Veldre, V.; Hartmann, M.; Unterseher, M.; Amend, A.; Bergsten, J.; Kristiansson, E.; et al. "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 Ecology 3 4 (2010): 284-287. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956292565&partnerID=MN8TOARS.
    10.1016/j.funeco.2010.05.002
  82. Abarenkov, K.; Tedersoo, L.; Nilsson, R.H.; Vellak, K.; Saar, I.; Veldre, V.; Parmasto, E.; et al. "Plutof-a web based workbench for ecological and taxonomic research, with an online implementation for fungal its sequences". Evolutionary Bioinformatics 2010 6 (2010): 189-196. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650578953&partnerID=MN8TOARS.
    10.4137/EBO.S6271
  83. Wu, S.-H.; Nilsson, H.R.; Chen, C.-T.; Yu, S.-Y.; Hallenberg, N.. "The white-rotting genus Phanerochaete is polyphyletic and distributed throughout the phleboid clade of the Polyporales (Basidiomycota)". Fungal Diversity 42 (2010): 107-118. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951576650&partnerID=MN8TOARS.
    10.1007/s13225-010-0031-7
  84. Buée 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.". (2009): http://europepmc.org/abstract/med/19703112.
    10.1111/j.1469-8137.2009.03003.x
  85. Eriksson KM; Antonelli A; Nilsson RH; Clarke AK; Blanck H. "A phylogenetic approach to detect selection on the target site of the antifouling compound irgarol in tolerant periphyton communities.". (2009): http://europepmc.org/abstract/med/19453608.
    10.1111/j.1462-2920.2009.01928.x
  86. Nilsson RH; Ryberg M; Abarenkov K; Sjökvist E; Kristiansson E. "The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.". (2009): http://europepmc.org/abstract/med/19459974.
    10.1111/j.1574-6968.2009.01618.x
  87. Ryberg M; Kristiansson E; Sjökvist E; Nilsson RH. "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.". (2009): http://europepmc.org/abstract/med/19121041.
    10.1111/j.1469-8137.2008.02667.x
  88. Nilsson RH; Bok G; Ryberg M; Kristiansson E; Hallenberg N. "A software pipeline for processing and identification of fungal ITS sequences.". (2009): http://europepmc.org/abstract/med/19146660.
    10.1186/1751-0473-4-1
  89. Hallenberg, N.; Ryberg, M.; Nilsson, R.H.; Wood, A.R.; Wu, S.-H.. "Pseudolagarobasidium (Basidiomycota): On the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi". Botany 86 11 (2008): 1319-1325. http://www.scopus.com/inward/record.url?eid=2-s2.0-56049106605&partnerID=MN8TOARS.
    10.1139/B08-088
  90. Ryberg M; Nilsson RH; Kristiansson E; Töpel M; Jacobsson S; Larsson E. "Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota).". (2008): http://europepmc.org/abstract/med/18282272.
    10.1186/1471-2148-8-50
  91. Bruns, T.D.; Blackwell, M.; Edwards, I.; Taylor, A.F.S.; Horton, T.; Zhang, N.; Kõljalg, U.; et al. "Preserving accuracy in GenBank". Science 319 5870 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-84881085358&partnerID=MN8TOARS.
  92. Nilsson, R.H.; Kristiansson, E.; Ryberg, M.; Hallenberg, N.; Larsson, K.-H.. "Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification". Evolutionary Bioinformatics 2008 4 (2008): 193-201. http://www.scopus.com/inward/record.url?eid=2-s2.0-45749142504&partnerID=MN8TOARS.
  93. Bienert GP; Thorsen M; Schüssler MD; Nilsson HR; Wagner A; Tamás MJ; Jahn TP. "A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)3 and Sb(OH)3 across membranes.". (2008): http://europepmc.org/abstract/med/18544156.
    10.1186/1741-7007-6-26
  94. Hallenberg N; Nilsson RH; Antonelli A; Wu SH; Maekawa N; Nordén B. "The Peniophorella praetermissa species complex (Basidiomycota).". (2007): http://europepmc.org/abstract/med/18023990.
    10.1016/j.mycres.2007.10.001
  95. Matheny PB; Wang Z; Binder M; Curtis JM; Lim YW; Nilsson RH; Hughes KW; et al. "Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi).". (2007): http://europepmc.org/abstract/med/17081773.
    10.1016/j.ympev.2006.08.024
  96. Paulus, B.; Nilsson, H.; Hallenberg, N.. "Phylogenetic studies in Hypochnicium (Basidiomycota), with special emphasis on species from New Zealand". New Zealand Journal of Botany 45 1 (2007): 139-150. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247341748&partnerID=MN8TOARS.
  97. Nilsson RH; Larsson KH; Larsson E; Kõljalg U. "Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota).". (2006): http://europepmc.org/abstract/med/17123810.
    10.1016/j.mycres.2006.09.017
  98. Aime MC; Matheny PB; Henk DA; Frieders EM; Nilsson RH; Piepenbring M; McLaughlin DJ; et al. "An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences.". (2006): http://europepmc.org/abstract/med/17486966.
    10.3852/mycologia.98.6.896
  99. Moncalvo JM; Nilsson RH; Koster B; Dunham SM; Bernauer T; Matheny PB; Porter TM; et al. "The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods.". (2006): http://europepmc.org/abstract/med/17486970.
    10.3852/mycologia.98.6.937
  100. Nilsson RH; Ryberg M; Kristiansson E; Abarenkov K; Larsson KH; Kõljalg U. "Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.". (2006): http://europepmc.org/abstract/med/17183689.
    10.1371/journal.pone.0000059
  101. Hibbett DS; Nilsson RH; Snyder M; Fonseca M; Costanzo J; Shonfeld M. "Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi).". (2005): http://europepmc.org/abstract/med/16126660.
    10.1080/10635150590947104
  102. Kõljalg U; Larsson KH; Abarenkov K; Nilsson RH; Alexander IJ; Eberhardt U; Erland S; et al. "UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.". (2005): http://europepmc.org/abstract/med/15869663.
    10.1111/j.1469-8137.2005.01376.x
  103. Nilsson RH; Kristiansson E; Ryberg M; Larsson KH. "Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi.". (2005): http://europepmc.org/abstract/med/16022740.
    10.1186/1471-2105-6-178
  104. Nilsson RH; Rajashekar B; Larsson KH; Ursing BM. "galaxieEST: addressing EST identity through automated phylogenetic analysis.". (2004): http://europepmc.org/abstract/med/15236648.
    10.1186/1471-2105-5-87
  105. Nilsson RH; Larsson KH; Ursing BM. "galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.". (2004): http://europepmc.org/abstract/med/14976034.
    10.1093/bioinformatics/bth119
  106. Nilsson, Rolf. "Cortbase version 2 – extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes)". Phyloinformatics (2004): https://zenodo.org/record/59794#.WbGzsdMjHMU.
    10.5281/zenodo.59794
  107. Henrik Nilsson, R.; Hallenberg, N.. "Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data". Mycologia 95 1 (2003): 54-60. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037281558&partnerID=MN8TOARS.
  108. Nilsson, R.H.; Hallenberg, N.; Nordén, B.; Maekawa, N.; Wu, S.-H.. "Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere". Mycological Research 107 6 (2003): 645-652. http://www.scopus.com/inward/record.url?eid=2-s2.0-0042706234&partnerID=MN8TOARS.
    10.1017/S0953756203007925

Other

Other output
  1. Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing. 2012. Xu L; Ravnskov S; Larsen J; Nilsson RH; Nicolaisen M. http://europepmc.org/abstract/AGR/IND44711645.
    10.1016/j.soilbio.2011.11.010
Activities

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2017/01/01 - 2020/12/31 Member of various Ph.D. student committees at University of Gothenburg and University of Stockholm
Member
 Göteborgs Universitet, Sweden
Distinctions

Award

2019 Highly Cited Researcher by Web of Science
Clarivate Analytics Deutschland GmbH, Germany
2011 Albert Wallin Science Prize