Short CV/Education and training

  • Since 2018
    University of Tartu Natural History Museum and Botanical Garden, Senior Research Fellow in Biodiversity Informatics

  • 2012 – 2018
    University of Tartu Natural History Museum and Botanical Garden, Research Fellow in Biodiversity Informatics

  • 2005 – 2012
    University of Tartu, Faculty of Science and Technology, Institute of Ecology and Earth Sciences, Specialist in Information Technology

  • 2011
    University of Tartu, Ph.D. in botany and mycology

  • 2006
    University of Tartu, M.Sc. in botany and mycology

  • 2004
    University of Tartu, B.Sc in bioinformatics

Selected publications

  • Zanne, A; Abarenkov, K; Afkhami, M.E.; Aguilar-Trigueros, C.A.; Bates, S; Bhatnagar, J.M.; Busby, P.E.; Christian, N.; Cornwell, W.; Crowther, T.; Moreno, H.F.; Floudas D.; Gazis, R.; Hibbett, D.; Kennedy, P.; Lindner, D.; Maynard, D.S.; Milo, A.M.; Nilsson, R.H.;Powell, J.; Schildhauer, M.; Schilling, J.; Treseder, K.K. (2019) Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi. Biological Reviews, 95(2), 409 – 433.

  • Nilsson, R.H.; Larsson, K-H.; Taylor, A.F.S.; Bengtsson-Palme, J.; Jeppesen, T.S.; Schigel, D.; Kennedy, P.; Picard, K.; Glöckner, F.O.; Tedersoo, L.; Saar, I.; Kõljalg, U.; Abarenkov, K. (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications, Nucleic Acids Research, gky1022, https://doi.org/10.1093/nar/gky1022

  • Abarenkov, K.; Somervuo, P.; Nilsson, R.H.; Kirk, P.M.; 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(2), 517 – 525.

  • Tedersoo, L.; Sánchez-Ramírez, S.; Kõljalg, U.; Bahram, M.; Döring, M.; Schigel, D.; May, T.; Ryberg, M.; Abarenkov, K. (2018) High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity, 90(1), 135 – 159.

  • Abarenkov, K.; Adams, R.I.; Laszlo, I.; Agan, A.; Ambrosio, E.; Antonelli, A.; Bahram, M.; Bengtsson-Palme, J.; Bok, G.; Cangren, P.; Coimbra, V.; Coleine, C.; Gustafsson, C.; 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, M.; Unterseher, M.; Visagie, C.; Wurzbacher, C.; Taylor, A.F.S.; Kõljalg, U.; Schriml, L.; Nilsson, R.H. (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 – 15.

  • Kõljalg, U.; Tedersoo, L.; Nilsson, R.H.; Abarenkov, K. (2016). Digital identifiers for fungal species. Science, 352(6290), 1182 – 1183.

  • Nilsson, R.H.; Wurzbacher, C.; Bahram, M.; Coimbra, V.R.M.; Larsson, E.; Tedersoo, L.; Eriksson, J.; Duarte, C.; Svantesson, S.; Sánchez-García, M.; Ryberg, M.K.; Kristiansson, E.; Abarenkov, K. (2016). Top 50 most wanted fungi. MycoKeys, 12, 29 – 40.

  • Hibbett, D.; Abarenkov, K.; Kõljalg, U.; Öpik, M.; Chai, B.; Cole, J.; Wang, Q.;

    Crous, P.; Robert, V.; Helgason, T.; Herr, J.R.; Kirk, P.; Lueschow, S.; O'Donnell, K.; Nilsson, R.H.; Oono, R.; Schoch, C.; Smyth, C.; Walker, D.M.; Porras-Alfaro, A.; Taylor J.W.; Geiser, D.M. (2016). Sequence-based classification and identification of Fungi. Mycologia, 108(6), 1049 – 1068.

  • Tedersoo, L.; Ramirez, K.S.; Nilsson, R.H.; Kaljuvee, A.; Kõljalg, U.; Abarenkov, K. (2015). Standardizing metadata and taxonomic identification in metabarcoding studies. GigaScience, 4:34.

  • Nilsson, R.H.; Tedersoo, L.; Ryberg, M.; Kristiansson, E.; Hartmann, M.; Unterseher, M.; Porter, T.M.; Bengtsson-Palme, J.; Walker, D.M.; De Sousa, F.; Gamper, H.A.; Larsson, E.; Larsson, K.-H.; Kõljalg, U.; Edgar, R.C.; Abarenkov, K. (2015). A comprehensive, automatically updated fungal ITS sequence dataset for referencebased chimera control in environmental sequencing efforts. Microbes and Environments, 30(2), 145 – 150.



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