R. Henrik Nilsson, Ph. D.

Name: R. Henrik Nilsson

Position: Associate professor (docent)
Address: University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden
Phone: +46-31-7862623
Fast lane: henrik dot nilsson at bioenv dot gu dot se

Fungal research interests: systematics, agaricomycetes, cantharelloid clade, Sistotrema, mycorrhiza, environmental sequencing
Computational research interests: bioinformatics, phylogenetic inference, sequence databases, sequence analysis,
                                  Linux/BSD, barcoding, molecular identification, next-generation sequencing, metagenomics


Journal associations: Fungal Diversity (editorial board; 2014-) 
                      Frontiers in Evolutionary and Population Genetics (editorial board; 2011-)
                      MycoKeys (editorial board; 2011-)
                      Frontiers in Microbiology (Fungi and their Interactions) (editorial board; 2017-)
                      Studies in Fungi (editorial board; 2016-)

Review assignments: Systematic Biology  ;  Molecular Biology and Evolution  ;  Genome Biology  ;  Molecular Ecology  ;  New Phytologist  ;  GigaScience
                    Nature Climate Change  ;  The ISME Journal  ;  Molecular Phylogenetics and Evolution  ;  FEMS Microbiology Ecology  ;  Bioinformatics  ;  Microbiome
		    FEMS Microbiology Letters  ;   Molecular Biotechnology  ; BMC Genomics  ;  BMC Evolutionary Biology  ; Nucleic Acids Research  ;  Mycologia
                    Studies in Mycology  ;  Environmental Pollution and Climate Change  ;  Computational and Structural Biotechnology Journal
                    Fungal Genetics and Biology  ;  Fungal Diversity  ;  BMC Microbiology  ;  Microbial Ecology  ;  Applied and Environmental Microbiology  ;  Database
		    Applied Soil Ecology  ;  Soil Biology and Biochemistry  ;  BMC Bioinformatics  ;  Fungal Biology  ;  BMC Ecology  ;  Molecular Ecology Resources
		    Methods in Ecology and Evolution  ;  Ecology and Evolution  ;  Evolutionary Bioinformatics  ;  Bioinformatics and Biology Insights  ;  PeerJ
		    Journal of Biogeography  ;  Frontiers in Evolutionary and Population Genetics  ;  Antonie van Leeuwenhoek  ;  Mycological Progress  ;  Data
                    Frontiers in Plant Science  ;  Biodiversity Data Journal  ;  Bionomina  ;  Fungal Ecology  ;  TAXON  ;  Gene  ;  Cladistics  ;  PLoS ONE  ; JoVe
                    Mycorrhiza  ;  Mycology  ;  Scientific Reports  ;  Canadian Journal of Microbiology  ;  Central European Journal of Biology  ;  Systainability
                    Science of the Total Environment  ;  Anales del Real Jardín Botánico de Madrid  ;  Folia Microbiologica  ;  African Journal of Agricultural Research
                    Environmental Microbiology  ;  Zoologica Scripta  ;  African Journal of Microbiology Research  ;  Environmental Microbiology Reports  ;  Applied Sciences
                    Journal of Biodiversity, Bioprospecting and Development  ;  Mycological Research  ;  Frontiers in Cellular and Infection Microbiology
                    Ecological Genetics and Genomics  ;  Frontiers in Ecology and Evolution  ;  Frontiers in Microbiology  ;  Frontiers in Marine Sciences
                    International Journal of Plant and Soil Science  ;  Canadian Journal of Forest Research  ;  Silva Fennica  ;  SpringerPlus  ;  AIMS Genetics
                    Journal of the Arkansas Academy of Science  ;  BMC Research Notes  ;  Advances in Dairy Research  ;  Applied Microbiology (Open Access)  ;  Molecules
                    Diagnostic Cytopathology  ;  International Journal of Molecular Sciences  ;  Pathogens  ;  HortScience  ;  African Journal of Biotechnology
                    Sustainability  ;  Mediterranean Marine Science  ;  Mycology and Virology  ;  Journal of the Botanical Research Institute of Texas  ;  Biodiversitas
                    Frontiers in Genetics  ;  Journal of Ayurveda and Integrative Medicine  ;  African Journal of Plant Science  ;  Journal of Bioresearch Communications 
                    Indian Journal of Traditional Knowledge  ;  Journal of Bacteriology and Parasitology

Thesis: Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota).
        (ISBN 978-91-85529-10-0; defended June 8, 2007; opponent: Pedro W. Crous).

h citation index: 46 (Google Scholar page) (ResearchGate page) (Publons reviewer profile) (ORCiD profile)


-> Awards and Recognitions <-
The Albert Wallin Science Prize 2011 (The Royal Society of Arts and Sciences in Gothenburg)
Top 10 Reviewer for Sweden 2016/2017 (Publons)
Peer Review Awards 2018 (Publons)
Highly Cited Resercher 2017 (Clarivate Analytics/Web of Science)

-> Selected publications <-
Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson MK, Bilodeau GJ,
Johnson RM, Hartmann M, Nilsson RH. 2018. Metaxa2 Database Builder: Enabling taxonomic identification from metagenomic
or metabarcoding data using any genetic marker. Bioinformatics bty482. open access
Tedersoo L, Bahram M, Puusepp R, Nilsson RH, James TY. 2017. Novel soil-inhabiting clades fill gaps in the fungal tree
of life.
Microbiome 5: 42. open access
Kõljalg U, Tedersoo L, Nilsson RH, Abarenkov K. 2016. Digital identifiers for fungal species. Science 352: 1182-1183.
Nilsson RH, Wurzbacher C, Bahram M, Coimbra VRM, Larsson E, Tedersoo L, Eriksson J, Duarte Ritter C, Svantesson S,
Sanchez-García M, Ryberg M, Kristiansson E, Abarenkov K. 2016. Top 50 most wanted fungi. MycoKeys 12: 29-40.
open access  As covered in IMA Fungus  As covered by BBC Mundo
 
Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A,
Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R,
Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S,
Kulik T, Liimatainen K, Lindahl B, Lindner D, Liu J-K, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA,
Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sanchez-García M, de Sousa F,
Stefaczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E,
Larsson K-H, Kõljalg U, Abarenkov K. 2014. Improving ITS sequence data for identification of plant pathogenic
fungi. Fungal Diversity 67: 11-19.
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, 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, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M,
Larsson KH. 2013. Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology 22: 5271-5277.
Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger M,
de Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson MK,
Vik U, Veldre V, Nilsson RH. 2013. 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 4:914-919. software site
Hyde KD, Udayanga D, Manamgoda DS, Tedersoo L, Larsson E, Abarenkov K, Bertrand YJK, Oxelman B, Hartmann M,
Kauserud H, Ryberg M, Kristiansson E, Nilsson RH. 2013. Incorporating molecular data in fungal systematics:
a guide for aspiring researchers. Current Research in Environmental and Applied Mycology 3: 1-32. open access
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 KM, Larsson K-H,
Larsson E. 2012. Five simple guidelines for establishing basic authenticity and reliability of newly generated
fungal ITS sequences. MycoKeys 4: 37-63. open access  As covered in IMA Fungus
Nilsson RH, Tedersoo L, Lindahl BD, 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 Phytologist 191: 314-318.
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. software homepage
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.
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. open access

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. open access
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. As covered in Science
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
 


-> Other publications <-

Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M. 2018. Great differences in performance and outcome of
high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39: 29-40. open access
Abarenkov K, Somervuo P, Nilsson RH, Kirk PM, Huotari T, Abrego N, Ovaskainen O. 2018. Protax-fungi: a web-based tool for probabilistic
taxonomic placement of fungal internal transcribed spacer sequences. New Phytologist 220: 517-525.
Ritter CD, Zizka A, Barnes C, Nilsson RH, Roger F, Antonelli A. 2018. Locality or habitat? Exploring predictors of biodiversity in Amazonia.
Ecography (in press).
Ryberg M, Nilsson RH. 2018. New light on names and naming of dark taxa. MycoKeys (30): 31-39. open access
Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L,
Irsenaite R, Martin-Sanchez PM, Meyer M, Oh S-Y, Sampaio JP, Seifert KA, Sklenar F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M,
Visagie CM, Weiss M, Woudenberg J, Wurzbacher C, Van den Wyngaert S, Yilmaz N, Yurkov A, Koljalg U, Abarenkov K. 2018. Taxonomic annotation
of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82.
open access
Unterseher M, Karunarathna SC, Cruz GR, Dagamac NH, Dahl MB, Dool SE, Galla M, Herbst L, Nilsson RH, Puechmaille SJ, Schöner C, Schöner M,
Siddique AB, Teltewskoi A, Wicke K, Würth DG, Wurzbacher C, Hyde KD. 2018. 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
(in press).
Sandova M, Nilsson RH, Kolarik M. 2017. Relationships within Capitotricha bicolor (Lachnaceae, Ascomycota) as inferred from ITS rDNA sequences,
including some notes on the Brunnipila and Erioscyphella clades. Mycological Progress (in press)
Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E. 2017. Read quality-based trimming of the distal ends of
public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. open access
Wurzbacher C, Nilsson RH, Rautio M, Peura S. 2017. Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.
ISME Journal 11: 1938-1941. open access
Radek R, Wurzbacher C, Gisder S, Nilsson RH, Owerfeldt A, Genersch E, Kirk PM, Voigt K. 2017. Morphologic and molecular data help adopting
the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota.
MycoKeys 25: 31-50. open access
Jeppson M, Altés A, Moreno G, Nilsson RH, Loarce Y, de Bustos A, Larsson E. 2017. Unexpected high species diversity among European stalked
puffballs - a contribution to the phylogeny and taxonomy of the genus Tulostoma (Agaricales). MycoKeys 21: 33-88. open access
Halwachs B, Madhusudhan N, Krause R, Nilsson RH, Moissl-Eichinger C, Hoegenauer C, Thallinger GG, Gorkiewicz G. 2017. Critical issues in
mycobiota analysis. Frontiers in Microbiology 8: 180. open access 
Duarte CD, McCrate G, Nilsson RH, Fearnside PM, Palme U, Antonelli A. 2017. Environmental impact assessment in Brazilian Amazonia: Challenges
and prospects to assess biodiversity. Biological Conservation 206: 161-168. open access 
Hembrom ME, Das K, Nilsson RH, Parihar A, Baghela A, Mehta N, Singh SK, Hallenberg N. 2017. Morphology and phylogeny reveal a novel hydnoid
taxon from India: Mycorrhaphoides stalpersii gen. and sp. nov. Nordic Journal of Botany 35: 85-94.
Hibbett D, Abarenkov K, Kõljalg U, Öpik M, Chai B, Cole JR, Wang Q, Crous PW, Robert VARG, Helgason T, Herr J, Kirk P, Lueschow S,
O'Donnell K, Nilsson RH, Oono R, Schoch CL, Smyth C, Walker D, Porras-Alfaro A, Taylor JW, Geiser DM. 2016. Sequence-based classification
and identification of Fungi. Mycologia 108: 1049-1068.
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. (2016) Towards a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa (SUPERSMART).
Systematic Biology (in press)
Eusemann P, Schnittler M, Nilsson RH, Jumpponen A, Dahl MB, Würth DG, Buras A, Wilkming M, Unterseher M. 2016. Habitat conditions
and phenological tree traits overrule the influence of tree genotype in the needle mycobiome Picea glauca system at an arctic
treeline ecotone. New Phytologist 211: 1221-1231.
Abarenkov K, Adams RI, Laszlo I, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra Victor RM, Coleine C,
Gustafsson CGR, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M,
Svantesson S, Scharn R, Svensson O, Töpel MH, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH. 2016.
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: 1-16. open access 
Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH. 2016. Metaxa2 Diversity Tools: Easing microbial community analysis
with Metaxa2. Ecological Informatics 33: 45-50.
Alm Rosenblad M, Martin MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH. 2016. Detection of signal
recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal
fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. open access 
Nilsson RH, Abarenkov K, Kõljalg U. 2016 Molecular techniques in mycological studies and sequence data curating: quality control and
challenges. In: Biology of Microfungi (p. 47-64, ed. De-Wei L.), Springer International Publishing. (book chapter)
Wang Z, Nilsson RH, James TY, Dai Y, Townsend JP. 2016. Future perspectives and challenges of fungal systematics in the age of big data.
In: Biology of Microfungi (p. 25-46, ed. De-Wei L.), Springer International Publishing. (book chapter)
Tedersoo L, Bahram M, Põlme S, Anslan S, Riit T, Kõljalg U, Nilsson RH, Hildebrand F, Abarenkov K. 2015. Response to comment on
"Global diversity and geography of soil fungi". Science 349: 936.
Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson RH, Pierson DL, Perry J, Venkateswaran K.
2015. Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.
Microbiome 3: 50. open access 
Jayasiri SC, Hyde KD, Ariyawansa HA, Bhat J, Buyck B, Cai L, Dai Y-C, Abd-Elsalam KA, Ertz D, Hidayat I, Jeewon R, Jones EBG,
Bahkali AH, Karunarathna SC, Liu J-K, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SSN, McKenzie EHC, Moncalvo J-M, Ghobad-Nejhad M,
Nilsson RH, Pang K-L, Pereira OL, Phillips AJL, Raspé O, Rollins AW, Romero AI, Etayo J, Selçuk F, Stephenson SL, Suetrong S, Taylor JE,
Tsui CKM, Vizzini A, Abdel-Wahab MA, Wen T-C, Boonmee S, Dai DQ, Daranagama DA, Dissanayake AJ, Ekanayaka AH, Fryar SC, Hongsanan S,
Jayawardena RS, Li W-J, Perera RH, Phookamsak R, de Silva NI, Thambugala KM, Tian Q, Wijayawardene NN, Zhao R-L, Zhao Q, Kang J-C,
Promputtha I. 2015. The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. Fungal Diversity 74: 3-18.
Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM. 2015. Metagenomic sequencing of
marine periphyton: taxonomic and functional insights into biofilm communities. Frontiers in Microbiology 6: 1192. open access
Tedersoo L, Ramirez KS, Nilsson RH, Kaljuvee A, Kõljalg U, Abarenkov K. 2015. Standardizing metadata and taxonomic identification
in metabarcoding studies. GigaScience 4: 34. open access
Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K. 2015.
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi.
MycoKeys 10: 1-43. open access
Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH. 2015. Metaxa2: improved identification
and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources 15: 1403-1414.
Elliott DR, Caporn S, Nwaishi F, Nilsson RH, Sen R. 2015. Bacterial and fungal communities in a degraded ombrotrophic peatland
undergoing natural and managed re-vegetation. PLoS ONE 10: e0124726. open access 
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 K-H, Kõljalg U, Edgar R, Abarenkov K. 2015. A comprehensive, automatically updated fungal ITS sequence dataset for 
reference-based chimera control in environmental sequencing efforts. Microbes and Environments 30: 145-150. open access
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 K-H, Kohout P, Hosaka K, Hiiesalu I,
Henkel TW, Harend H, Guo L-D,  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. 2014. Global diversity and geography of soil fungi. Science 346: 6213.
Hyde KD, Nilsson RH, Alias SA, Ariyawansa HA, Blair JE, Cai L, de Cock AWAM, Dissanayake AJ, Glockling SL, Goonasekara ID, Gorczak M,
Hahn M, Jayawardena RS, van Kan KAL, Laurence MH, Lévesque CA, Li X, Liu J-K, Maharachchikumbura SSN, Manamgoda DS, Martin FN, McKenzie EHC,
McTaggart AR, Mortimer PE, Nair PVR, Pawlowska J, Rintoul TL, Shivas RG, Spies CFJ, Summerell BA, Taylor PWJ, Terhem RB, Udayanga D, Vaghefi N,
Walther G, Wilk M, Wrzosek M, Xu JC, Yan J, Zhou N. 2014 One stop shop: backbones trees for important phytopathogenic genera: I (2014).
Fungal Diversity 67: 21-125.
Hibbett DS, Bauer R, Binder M, Giachini AJ, Hosaka K, Justo A, Larsson E, Larsson K-H, Lawrey JD, Miettinen O, Nagy L, Nilsson RH,
Weiß M, Thorn RG. 2014. Agaricomycetes. [book chapter] Pages 373-429 in The Mycota, eds. McLaughlin DJ and Spatafora JW, Springer, Berlin.
Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH et al. 2014 Finding needles in haystacks:
linking scientific names, reference specimens and molecular data for Fungi. Database (Oxford): 10.1093/database/bau061.
open access
Jeppson M, Nilsson RH, Larsson E. 2013. European earthstars in Geastraceae (Geastrales, Phallomycetidae) - a systematic approach
using morphology and molecular sequence data. Systematics and Biodiversity 11: 437-465.
Lindner DL, Carlsen T, Nilsson RH, Davey M, Schumacher T, Kauserud H. 2013. Employing 454 amplicon pyrosequencing to
reveal intragenomic divergence in the internal transcribed spacer (ITS) rDNA region in fungi. Ecology and Evolution 3: 1751-1764.
open access
Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjöller R, Koljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H.
2013. Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytologist 199: 288-299.
open access
Kerekes J, Kaspari M, Stevenson B, Nilsson RH, Hartmann M, Amend A, Bruns TD. 2013. Nutrient enrichment increased
species richness of leaf litter fungal assemblages in a tropical forest. Molecular Ecology 22: 2827-2838.
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, Wegener Parfrey L, Stajich JE.
2013. Meeting Report: Fungal ITS Workshop (October 2012). Standards in Genomics Sciences 8: 118-123. open access
Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH. 2013. Metaxa, overview. In: Nelson K. (Ed.) Encyclopedia of Metagenomics.
Springer-Verlag Berlin Heidelberg. [book chapter/dictionary entry]
Hallenberg N, Nilsson RH, Robledo G. 2013. Species complexes in Hericium (Russulales, Agaricomycota) and a new species
- Hericium rajchenbergii - from southern South America. Mycological Progress 12: 413-420.
Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H. 2013. ITS1 versus ITS2 as DNA metabarcodes for fungi.
Molecular Ecology Resources 13: 218-224.
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.
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. open access
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.
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. 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. open access
 
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 the fungus Sistotrema sp. (Basidiomycota). Mycological Progress 11: 817-826.
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.
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.
Ryberg M, Nilsson RH, Matheny PB. 2011. DivBayes and SubT: exploring species diversification using Bayesian statistics.
Bioinformatics 27: 2439-2440.
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 Leeuwenhoek 100: 471-475 software homepage
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. 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. software homepage
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 SATe alignments for environmental ITS data. PLoS ONE 6: e19039.
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.
[review article] open access
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. Mycoscience 52: 278-282.
Nilsson RH, Ryberg M, Sjökvist E, Abarenkov K. 2011. Rethinking taxon sampling in the light of environmental
sequencing. Cladistics 27: 197-203.
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. [review article] open access
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 Bioinformatics 6: 189-196.
 
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 the Corticiales. TAXON 59: 1519-1534.
Nilsson RH, Abarenkov K, Veldre V, Nylinder S, De Wit P, Brosche S, Alfredsson JF, Ryberg M, Kristiansson E. 2010.
An open source chimera checker for the fungal ITS region. Molecular Ecology Resources 10: 1076-1081.
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 Ecology 3: 284-287.
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 Phytologist 188: 291-301. * = equal contribution
Begerow D, Nilsson RH, Unterseher M, Maier W. 2010. Current state and perspectives of fungal DNA barcoding
and rapid identification procedures. Applied Microbiology and Biotechnology 87: 99-108. [review article]
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.
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 Diversity 42: 107-118.
Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009. 454 pyrosequencing analyses of
forest soils reveal an unexpectedly high fungal diversity. New Phytologist 184: 449-456.
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.
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. open access
Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH. 2009. 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.
New Phytologist 181: 471-477.
 
Bidartondo M, ..., Nilsson RH et al. 2008. Preserving accuracy in GenBank. Science 319: 1616 (Letter to Science).
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.
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.
open access
Ryberg M, Nilsson RH, Kristiansson E, Topel 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.
open access
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.
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.
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.
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.
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.
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.
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. open access emerencia online
 
Parmasto E, Nilsson RH, Larsson K-H. 2004. Cortbase version 2 - extensive updates of a nomenclatural
database for corticioid fungi (Hymenomycetes). Phyloinformatics 1: 5. open acccess  As covered in Science
Nilsson RH, Rajashekar B, Larsson K-H, Ursing BM. 2004. galaxieEST: addressing EST identity through
automated phylogenetic analysis. BMC Bioinformatics 5: 87. open access
Nilsson RH, Larsson K-H, Ursing B. 2004. galaxie - CGI scripts for sequence identification through
automated phylogenetic analysis. Bioinformatics 20: 1447-1452.
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.
Nilsson RH, Hallenberg N. 2003. Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS
sequence data. Mycologia 95: 54-60.


  -> Popular science and non-reviewed papers<-

Ryberg M, Kristiansson E, Wurzbacher C, Nilsson RH. 2016. New Ph.D. students in the empirical sciences should be
recruited into ongoing scientific studies right from the start. Journal of Brief Ideas DOI 10.5281/zenodo.48158
Nilsson RH. 2015. Unifying fungi. Science & Technology 14: 204-206.
Nilsson RH. 2007. Mellan myensk och myling - några trender inom svampforskningen. Magasin Brun 6: 10-14.
Nilsson RH. 2007. Något är konstigt i kantarellgruppen. Puggehatten 20: 2-4.
Nilsson RH. 2007-2015. Various contributions to the Swedish Wikipedia pages, mainly on mycology, systematics,
and taxonomy.


-> Less related <-

Nilsson RH and the Amicable Numbers project. 2017. 20988037843979290210 & 24557150368838629790 - and other new amicable number pairs.
Nilsson RH and the PrimeGrid project. 2017. 663*2^3390469+1 - a Proth megaprime of 1,020,636 digits (the world's 205th largest
prime as of April 23, 2017).  press release (PDF)
Nilsson RH and the PrimeGrid project. 2016. 35538016^32768+1 - a Generalized Fermat Prime (GFN15 search) of 247,422 digits.
Nilsson RH and the PrimeGrid project. 2016-2017. New arithmetic progressions of primes (lengths 20-24).
Nilsson RH and the PrimeGrid project. 2016. 4329134^131072+1 - a Generalized Fermat Prime (GFN17-low search) of 869,847 digits.
(the world's 254th largest prime as of June 4, 2016).
Nilsson RH and the PrimeGrid project. 2016. 12764608^65536+1 - a Generalized Fermat Prime (GFN16 search) of 465,700 digits.
(the world's 1782th largest prime as of May 26, 2016).
Nilsson RH and the PrimeGrid project. 2016. 23142958^32768+1 - a Generalized Fermat Prime (GFN15 search) of 241,318 digits.
Nilsson RH and the PrimeGrid project. 2016. 2707653311055*2^1290000-1 - a new prime (SGS search) of 388,342 digits (the world's
3872th largest prime as of April 21, 2016).
Nilsson RH and the PrimeGrid project. 2016. 7651*2^1384544+1 - a Proth prime of 416,794 digits (the world's 2264th largest prime
as of February 12, 2016).
Nilsson RH. 2015. 978847155 * 2^1226476-1 - a new prime of 369 216 digits (the world's 4888th largest prime as of January 29, 2015).
Nilsson RH. 2013. 978847155 * 2^1123391-1 - a new prime of 338 184 digits (the world's 3151th largest prime as of September 13, 2013).
Nilsson RH. 2012. 978847155 * 2^1024053-1 - a new prime of 308 280 digits (the world's 1693th largest prime as of August 8, 2012).
Nilsson RH. 2011. 978847155 * 2^942278-1 - a new prime of 283 663 digits (the world's 1155th largest prime as of September 15, 2011).
Nilsson RH. 2011. 978847155 * 2^900770-1 - a new prime of 271 168 digits (the world's 952th largest prime as of March 23, 2011).
Nilsson RH. 2010. 978847155 * 2^855371-1 - a new prime of 257 502 digits (the world's 837th largest prime as of November 3, 2010).
Nilsson RH. 2009. 978847155 * 2^638344-1 - a new prime of 192 170 digits (the world's 1345th largest prime as of June 30, 2009).
Nilsson RH, Yamada S. 2009. 112919520*2^350008-1 - a new prime of 105 371 digits. Through the SIGPS project.
Nilsson RH, Yamada S. 2009. 98504246^16384+1 and 98503336^16384+1 - two new generalized Fermat primes of 130965 digits each
(the 4022th and 4023th largest primes as of May 13, 2009). Through the SIGPS project.
Nilsson RH. 2009. 978847155 * 2^603383-1 - a new prime of 181 646 digits (the world's 1360th largest prime as of April 15, 2009).
Nilsson RH, Yamada S. 2009. 98475208^16384+1 and 98473506^16384+1 - two new generalized Fermat primes of 130963 digits each
(the 3458th and 3459th largest primes as of April 10, 2009). Through the SIGPS project.
Nilsson RH. 2009. 7113920990529996490449608242781773 - a new 34-digit factor of a number of the form  x^y + y^x (x=146, y=39, P34 * C160).
Through the XYYX project.
Nilsson RH. 2009. 107360611828005050854420395187722811 - a new 36-digit factor of a number of the form x^y + y^x (x=135, y=121, P36 * P193).
Through the XYYX project.
Nilsson RH, Yamada S. 2009. Numerous new large generalized Fermat divisor PRPs (list). Through the SIGPS project.
Nilsson RH, Yamada S. 2009. 102623730 * 2^350008-1 - a new prime of 105 371 digits. Through the SIGPS project.
Nilsson RH. 2008. 978847155 * 2^561111-1 - a new prime of 168 921 digits (the world's 1077th largest prime as of June 10, 2008).
(my largest prime numbers are indexed at the top 5000 primes list.
Nilsson RH. 2008. 978847155 * 2^533895-1 - a new prime of 160 728 digits (the world's 1105th largest prime as of March 26, 2008).
Nilsson RH. 2008. 978847155 * 2^529577-1 - a new prime of 159 428 digits (the world's 1108th largest prime as of March 13, 2008).
Nilsson RH. 2007. 978847155 * 2^446715-1 - a new prime of 134 484 digits (the world's 1226th largest prime as of June 29, 2007).
Nilsson RH. 2007. 978847155 * 2^429357-1 - a new prime of 129 259 digits (the world's 1335th largest prime as of May 31, 2007).
Nilsson RH. 2007. 978847155 * 2^400352-1 - a new prime of 120 527 digits (the world's 1448th largest prime as of March 2, 2007).
Nilsson RH. 2007. 978847155 * 2^382902-1 and 978847155 * 2^381039-1: new primes of more than 110 000 digits (the world's
1614th and 1642th largest primes as of February 8 and 5, 2007).
Nilsson RH. 2006. More  primes of the form 15k * 2^n-1. Through the 15k.org project.
Nilsson RH. 2005. New primes of the form 15k * 2^n-1 - some too small to be indexed. Through the 15k.org project.
Nilsson RH. 2004. Some new primes of the form 15k * 2^n-1. Through the 15k.org project.
Nilsson RH. 2004. Some new factors of numbers of the form k * 2^n+-1. Through the k * 2^n+-1 project.
Nilsson RH, Pulkkinen MAS. 2003. 33616218135121889904001 - a new divisor of M3326400, M37800, and 2^18900+1.
Through the ElevenSmooth project.
Nilsson RH and Pulkkinen MAS. 2003. 22988509871279248951201 - a new divisor of M3326400 and M8400. Through the ElevenSmooth project.
Nilsson RH. 2003. 1489091294332340899201 - a new divisor of M3326400 and 415800. Through the ElevenSmooth project.
Nilsson RH. 2003. 10400423476871101020265601 - a new 26 digit factor of M3326400, M17600, and 2^8800+1. Through
the ElevenSmooth project.
Nilsson RH. 2003. 3218581070622527887201 - a new factor of 2^46200+1, M92400, and M3326400. Through the ElevenSmooth project.
Nilsson RH and Nilsson MI. 2002. Two new primes of the form k * 2^n+1: (k=497, n=86135, 25932 dgs; k=493, n=81776, 24620 dgs).
Through the Prothsearch.net initiative.


This webpage does not comply with the suggested graphical profile of University of Gothenburg employees.

Any and all opinions expressed on this webpage are those of its author (R. Henrik Nilsson) and not necessarily those of
University of Gothenburg.


Last update: October 1, 2018.