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Kessy Abarenkov

https://www.etis.ee/CV/Kessy_Abarenkov/eng
18.12.1980
kessy.abarenkov@ut.ee
H-9611-2015

Career

Institutions and positions
01.09.2015–...   
University of Tartu, University of Tartu Natural History Museum and Botanical Garden, Research Fellow (1,00)
01.10.2018–31.08.2019   
University of Tartu, University of Tartu Natural History Museum and Botanical Garden, Senior Research Fellow in Biodiversity Informatics (0,25)
01.12.2017–30.09.2018   
University of Tartu, University of Tartu Natural History Museum and Botanical Garden, Senior Research Fellow in Biodiversity Informatics (1,00)
01.01.2014–31.08.2015   
University of Tartu, University of Tartu Natural History Museum and Botanical Garden, Research Fellow (1,00)
01.09.2012–31.12.2013   
University of Tartu, University of Tartu Museum, Research Fellow (1,00)
01.01.2005–31.07.2007   
University of Tartu, Faculty of Biology and Geography, Institute of Botany and Ecology, Specialist (0,50)
2004–2004   
University of Tartu, Faculty of Biology and Geography, Institute of Botany and Ecology, arvutispetsialist (0,50)

Qualifications

Academic degrees
Kessy Abarenkov, Doctor's Degree, 2011, (sup) Urmas Kõljalg, PlutoF - cloud database and computing services supporting biological research, University of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University, Department of Botany.
Kessy Abarenkov, Master's Degree, 2006, (sup) Urmas Kõljalg, Biogeography of the genera Tomentella and Thelephora (Thelephorales, Basidiomycota) (Biogeography of the genera Tomentella and Thelephora (Thelephorales, Basidiomycota)), University of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University, Chair of Mycology.
 
 
Fields of research
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.12. Biotechnology, Molecular Biology, Cell Biology, Biophysics and Economic and Technological Research relating to Bio- and Environmental Sciences; CERCS CLASSIFICATION: B110 Bioinformatics, medical informatics, biomathematics, biometrics
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.4. Ecology, Biosystematics and -physiology
 
 
Additional information
Main fields of research:
Biological and bioinformatics, database and system development, fungal barcoding and identification.
International activities:
Technical Committee of the DINA consortium (http://www.dina-project.net/), representative
UNITE (https://unite.ut.ee), Board member
COST Action CA15219 (DNAqua-Net), workgroup leader


Dissertations under supervision

Supervised dissertations

Publications

Category
Year
Publication
 
1.1.
2020
Zanne, Amy E.; Abarenkov, Kessy; Afkhami, Michelle E.; Aguilar-Trigueros, Carlos A.; Bates, Scott; Bhatnagar, Jennifer M.; Busby, Posy E.; Christian, Natalie; Cornwell, William K.; Crowther, Thomas W.; Flores-Moreno, Habacuc; Floudas, Dimitrios; Gazis, Romina; Hibbett, David; Kennedy, Peter; Lindner, Daniel L.; Maynard, Daniel S.; Milo, Amy M.; Nilsson, R. Henrik; Powell, Jeff ... Treseder, Kathleen K. (2020). Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biological Reviews, 95 (2), 409−433. DOI: 10.1111/brv.12570.
1.1.
2020
Kõljalg, Urmas; Nilsson, Henrik R.; Schigel, Dmitry; Tedersoo, Leho; Larsson, Karl-Henrik; May, Tom W.; Taylor, Andy F. S.; Jeppesen, Thomas Stjernegaard; Frøslev, Tobias Guldberg; Lindahl, Björn D.; Põldmaa, Kadri; Saar, Irja; Suija, Ave; Savchenko, Anton; Yatsiuk, Iryna; Adojaan, Kristjan; Ivanov, Filipp; Piirmann, Timo; Pöhönen, Raivo; Zirk, Allan ... Abarenkov, Kessy (2020). The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa. Microorganisms, 8 (12), 1910. DOI: 10.3390/microorganisms8121910.
1.1.
2020
Tedersoo, Leho; Anslan, Sten; Bahram, Mohammad; Drenkhan, Rein; Pritsch, Karin; Buegger, Franz; Padari, Allar; Hagh-Doust, Niloufar; Mikryukov, Vladimir; Gohar, Daniyal; Amiri, Rasekh; Hiiesalu, Indrek; Lutter, Reimo; Rosenvald, Raul; Rähn, Elisabeth; Adamson, Kalev; Drenkhan, Tiia; Tullus, Hardi; Jürimaa, Katrin; Sibul, Ivar ... Abarenkov, Kessy (2020). Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe. Frontiers in Microbiology, 11, ARTN 1953. DOI: 10.3389/fmicb.2020.01953.
1.1.
2019
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 Acid Research, 47 (Database issue), D259−D264.10.1093/nar/gky1022.
1.1.
2018
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, 517−525.10.1111/nph.15301.
1.1.
2018
Tedersoo, L.; Kõljalg, U.; Bahram, M.; Döring, M.; Schigel, D.; May, T.; Sanchez-Ramirez, S.; Ryberg, M.; Abarenkov, K. (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity, 90, 135−159. DOI: 10.1007/s13225-018-0401-0.
1.1.
2017
Kulik, Tomasz; Abarenkov, Kessy; Buśko, Maciej; Bilska, Katarzyna; van Diepeningen, Anne D.; Ostrowska-Kołodziejczak, Anna; Krawczyk, Katarzyna; Brankovics, Balázs; Stenglein, Sebastian; Sawicki, Jakub; Perkowski, Juliusz; (2017). ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium. PeerJ, 5, e2992.10.7717/peerj.2992.
1.1.
2016
Bahram, Mohammad; Kohout, Petr; Anslan, Sten; Harend, Helery; Abarenkov, Kessy; Tedersoo, Leho (2016). Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. The ISME Journal, 10 (4), 885−896. DOI: 10.1038/ismej.2015.164.
1.1.
2016
Garnica, Sigisfredo; Schön, Max Emil; Abarenkov, Kessy; Riess, Kai; Liimatainen, Kare; Niskanen, Tuula; Dima, Bálint; Soop, Karl; Frøslev, Tobias Guldberg; Jeppesen, Thomas Stjernegaard; Peintner, Ursula; Kuhnert-Finkernagel, Regina; Brandrud, Tor Erik; Saar, Günter; Oertel, Bernhard; Ammirati, Joseph F. (2016). Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiology Ecology, 1−42. DOI: 10.1093/femsec/fiw045.
1.1.
2016
Nilsson, R.H., Wurzbacher, C., Bahram, M., Coimbra, V.R., Larsson, E., Tedersoo, L., Eriksson, J., Duarte, C., Svantesson, S., Sánchez-García, M., Ryberg, M.K. (2016). Top 50 most wanted fungi. MycoKeys, 12, 29−40. DOI: 10.3897/mycokeys.12.7553.
1.1.
2016
Tedersoo, L.; Bahram, M.; Cajthaml, T.; Põlme, S.; Hiiesalu, I.; Anslan, S.; Harend, H.; Buegger, F.; Pritsch, K.; Koricheva, J.; Abarenkov, K. (2016). Tree diversity and species identity effects on soil fungi, protists and animals are context-dependent. The ISME Journal, 10 (2), 346−362. DOI: 10.1038/ismej.2015.116.
1.1.
2016
Abarenkov, K.; Adams, R.I.; Irinyi, L.; 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. ... 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. DOI: 10.3897/mycokeys.16.10000.
1.1.
2016
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 H, 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 (6), 1049−1068. DOI: 10.3852/16-130.
6.8.
2016
Kõljalg, U.; Tedersoo, L.; Nilsson, R.H.; Abarenkov, K. (2016). Digital identifiers for fungal species. Science, 352, 1182−1183. DOI: 10.1126/science.aaf7115.
1.1.
2015
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 reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30 (2), 145−150. DOI: 10.1264%2Fjsme2.ME14121.
1.1.
2015
Tedersoo, Leho; Anslan, Sten; Bahram, Mohammad; Põlme, Sergei; Riit, Taavi; Liiv, Ingrid; Kõljalg, Urmas; Kisand, Veljo; Nilsson, R. Henrik; Hildebrand, Falk; Bork, Peer; Abarenkov, Kessy (2015). Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys, 10, 1−43. DOI: 10.3897/mycokeys.10.4852.
6.8.
2015
Tedersoo, Leho; Ramirez, Kelly S.; Nilsson, R Henrik; Kaljuvee, Aivi; Kõljalg, Urmas; Abarenkov, Kessy (2015). Standardizing metadata and taxonomic identification in metabarcoding studies. GigaScience, 4 (34), 1−4. DOI: 10.1186/s13742-015-0074-5.
1.1.
2014
Tedersoo, L.; Bahram, M.; Põlme, S.; Kõljalg, U.; Yorou, N.S.; Wijesundera, R.; Villarreal-Ruiz, L.; Vasco-Palacios, A.; Quang Thu, P.; Suija, A.; Smith, M.E.; Sharp, C.; Saluveer, E.; Saitta, A.; Ratkowsky, D.; Pritsch, K.; Riit, T.; Põldmaa, K.; Piepenbring, M.; Phosri, C. ... Abarenkov, K. (2014). Global diversity and geography of soil fungi. Science, 346 (6213), 1078. DOI: 10.1126/science.1256688.
1.1.
2014
Nilsson, R. Henrik; Hyde, Kevin D.; Pawłowska, Julia; Ryberg, Martin; Tedersoo, Leho; Aas, Anders Bjørnsgard; Alias, Siti A.; Alves, Artur; Anderson, Cajsa Lisa; Antonelli, Alexandre; Arnold, A. Elizabeth; Bahnmann, Barbara; Bahram, Mohammad; Bengtsson-Palme, Johan; Berlin, Anna; Branco, Sara; Chomnunti, Putarak; Dissanayake, Asha; Drenkhan, Rein; Friberg, Hanna ... Abarenkov, Kessy (2014). Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67 (1), 11−19. DOI: 10.1007/s13225-014-0291-8.
1.1.
2014
Tedersoo, L.; Bahram, M.; Ryberg, M.; Otsing, E.; Kõljalg, U.; Abarenkov, K. (2014). Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetics analyses. Molecular Ecology, 23 (16), 4168−4183. DOI: 10.1111/mec.12849.
1.1.
2014
Hartmann, Martin; Niklaus, Pascal A; Zimmermann, Stephan; Schmutz, Stefan; Kremer, Johann; Abarenkov, Kessy; Lüscher, Peter; Widmer, Franco; Frey, Beat (2014). Resistance and resilience of the forest soil microbiome to logging-associated compaction. The ISME Journal, 8 (1), 226−244.10.1038/ismej.2013.141.
1.1.
2013
Bengtsson-Palme, Johan; Ryberg, Martin; Hartmann, Martin; Branco, Sara; Wang, Zheng; Godhe, Anna; De Wit, Pierre; Sánchez-García, Marisol; Ebersberger, Ingo; de Sousa, Filipe; Amend, Anthony; Jumpponen, Ari; Unterseher, Martin; Kristiansson, Erik; Abarenkov, Kessy; Bertrand, Yann J. K.; Sanli, Kemal; Eriksson, K. Martin; Vik, Unni; Veldre, Vilmar ... Nilsson, R. Henrik (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 (10), 914−919.10.1111/2041-210X.12073.
1.1.
2013
Kõljalg, Urmas; Nilsson, Henrik; Abarenkov, Kessy; Tedersoo, Leho; Taylor, Andy; Bahram, Mohammad; Bates, Scott; Bruns, Thomas; Bengtsson-Palme, Johan; O'Callaghan, Tony; Douglas, Brian; Drenkhan, Tiia; Eberhardt, Ursula; Dueñas, Margarita; Grebenc, Tine; Griffith, Gareth; Hartmann, Martin; Kirk, Paul; Kohout, Petr; Larsson, Ellen ... Larsson, Karl-Henrik (2013). Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22 (21), 5271−5277. DOI: 10.1111/mec.12481.
1.1.
2013
Veldre, V.; Abarenkov, K.; Bahram, M.; Martos, F.; Selosse, M.-A.; Tamm, H.; Kõljalg, U.; Tedersoo, L. (2013). Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences. Fungal Ecology, 6 (4), 256−268. DOI: 10.1016/j.funeco.2013.03.004.
1.1.
2013
Lindahl, Björn D.; Nilsson, R. Henrik; Tedersoo, Leho; Abarenkov, Kessy; Carlsen, Tor; Kjøller, Rasmus; Kõljalg, Urmas; Pennanen, Taina; Rosendahl, Søren; Stenlid, Jan; Kauserud, Håvard (2013). Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide. New Phytologist, 199 (1), 288−299.10.1111/nph.12243.
1.1.
2013
Blaalid, R.; Kumar, S.; Nilsson, R.H.; Abarenkov, K.; Kirk, P.M.; Kauserud, H. (2013). ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources, 13 (2), 218−224.10.1111/1755-0998.12065.
1.2.
2013
Hyde, K.D.; Udayanga, D.; Manamgoda, D.S.; Tedersoo, L.; Larsson, E.; Abarenkov, K., Bertrand, Y.; Oxelman, B.; Hartmann, M.; Kauserud, H.; Ryberg, M.; Kristiansson, E.; Nilsson, R.H. (2013). Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Current Research in Environmental & Applied Mycology, 3 (1), 1−32. DOI: 10.5943/cream/3/1/1.
1.1.
2012
Bengtsson, J.; Hartmann, M.; Unterseher, M.; Vaishampayan, P.; Abarenkov, K.; Durso, L.; Bik, E.M.; Garey, J.R.; Eriksson, K.M.; Nilsson, R.H. (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, 407−412.10.1016/j.resmic.2012.07.001.
1.2.
2012
Nilsson, R.H.; Tedersoo, L.; Abarenkov, K.; Ryberg, M.; Kristiansson, E.; Hartmann, M.; Schoch, C.L.; Nylander, J.A.A.; Bergsten, J.; Porter, T.M.; Jumpponen, A.; Vaishampayan, P.; Ovaskainen, O.; Hallenberg, N.; Bengtsson-Palme, J.; Eriksson, K.M.; Larsson, K.-H.; Larsson, E.; Kõljalg, U. (2012). Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys, 4, 37−62. DOI: 10.3897/mycokeys.4.3606.
1.1.
2011
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 (4), 278−282.10.1007/s10267-010-0086-z.
1.1.
2011
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 rRNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiology Letters, 319 (2), 140−145.10.1111/j.1574-6968.2011.02274.x.
1.1.
2011
Tedersoo, L; Abarenkov, K; Nilsson, RH; Schüβler, 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 (9), e24940. DOI: 10.1371/journal.pone.0024940.
1.1.
2011
Nilsson, R.H.; Tedersoo, L.; Lindahl, B.; Kjoller, 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 (2), 314−318.
1.1.
2010
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 taxonomic research, with an online implementation for fungal ITS sequences. Evolutionary Bioinformatics, 189−196. DOI: 10.4137/EBO.S6271.
1.1.
2010
Hartmann, M.; Howes, C.G.; Abarenkov, K.; Mohn, W.W.; Nilsson, R.H. (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 (2), 250−253.
1.1.
2010
Nilsson, R.H.; Abarenkov, K.; Veldre, V.; Nylinder, S.; De Wit, P.; Brosche, S.; Alfredsson, J.F.; Ryberg, M.; Kristiansson, E. (2010). An open source chimera checker for the fungal ITS region. Molecular Ecology Resources, 10 (6), 1076−1081.10.1111/j.1755-0998.2010.02850.x.
1.1.
2010
Nilsson, R.H.; 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 (4), 284−287.10.1016/j.funeco.2010.05.002.
1.1.
2010
Nilsson, R.H.; Ryberg, M.; Sjökvist, E.; Abarenkov, K. (2010). Rethinking taxon sampling in the light of environmental sequencing. Cladistics, 26, 1−7.
1.1.
2010
Tedersoo, L.; Nilsson, R.H.; 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 (1), 291−301. DOI: 10.1111/j.1469-8137.2010.03373.x.
1.1.
2010
Abarenkov, Kessy; Nilsson, R. Henrik; Larsson, Karl-Henrik; Alexander, Ian J.; Eberhardt, Ursula; Erland, Susanne; Høiland, Klaus; Kjøller, Rasmus; Larsson, Ellen; Pennanen, Taina; Sen, Robin; Taylor, Andy F. S.; Tedersoo, Leho; Ursing, Björn M.; Vrålstad, Trude; Liimatainen, Kare; Peintner, Ursula; Kõljalg, Urmas (2010). The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist, 186 (2), 281−285.10.1111/j.1469-8137.2009.03160.x.
1.1.
2010
Suvi, T.; Tedersoo, L.; Abarenkov, K.; Beaver, K.; Gerlach, J.; Kõljalg, U. (2010). Mycorrhizal symbionts of Pisonia grandis and P. sechellarum in Seychelles: identification of mycorrhizal fungi and description of new Tomentella species. Mycologia, 102 (3), 522−533. DOI: 10.3852/09-147.
1.1.
2009
Nilsson, R.H.; 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 (1), 97−101.
1.1.
2008
Tedersoo, L.; Jairus, T.; Horton, B.M.; Abarenkov, A.; Suvi, T.; Saar, I.; Kõljalg, U. (2008). Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytologist, 180 (2), 479−490. DOI: 10.1111/j.1469-8137.2008.02561.x.
1.2.
2006
Nilsson, R.H.; 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 (1), e59 . DOI: 10.1371/journal.pone.0000059.
1.1.
2005
Koljalg, U.; Larsson, KH.; Abarenkov, K.; Nilsson, RH.; Alexander, IJ.; Eberhardt, U.; Erland, S.; Hoiland, K.; Kjoller, R.; Larsson, E.; Pennanen, T.; Sen, R.; Taylor, AFS.; Tedersoo, L.; Vralstad, T.; Ursing, BM. (2005). UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist, 166 (3), 1063−1068.
4.03.2021

Kessy Abarenkov

https://www.etis.ee/CV/Kessy_Abarenkov/est
18.12.1980
kessy.abarenkov@ut.ee
H-9611-2015

Teenistuskäik

Töökohad ja ametid
01.09.2015–...   
Tartu Ülikool, Tartu Ülikooli loodusmuuseum ja botaanikaaed, bioloogilise informaatika teadur (1,00)
01.10.2018–31.08.2019   
Tartu Ülikool, Tartu Ülikooli loodusmuuseum ja botaanikaaed, elurikkuse informaatika vanemteadur (0,25)
01.12.2017–30.09.2018   
Tartu Ülikool, Tartu Ülikooli loodusmuuseum ja botaanikaaed, elurikkuse informaatika vanemteadur (1,00)
01.01.2014–31.08.2015   
Tartu Ülikool, Tartu Ülikooli loodusmuuseum ja botaanikaaed, teadur (1,00)
01.09.2012–31.12.2013   
Tartu Ülikool, Tartu Ülikooli muuseum, teadur (1,00)
01.01.2005–31.07.2007   
Tartu Ülikool, Bioloogia-geograafiateaduskond, Botaanika ja ökoloogia instituut, arvutispetsialist (0,50)
2004–2004   
Tartu Ülikool, Bioloogia-geograafiateaduskond, Botaanika ja ökoloogia instituut, arvutispetsialist (0,50)

Kvalifikatsioon

Teaduskraadid
Kessy Abarenkov, Doctor's Degree, 2011, (sup) Urmas Kõljalg, PlutoF - cloud database and computing services supporting biological research, University of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University, Department of Botany.
Kessy Abarenkov, Master's Degree, 2006, (sup) Urmas Kõljalg, Biogeography of the genera Tomentella and Thelephora (Thelephorales, Basidiomycota) (Biogeography of the genera Tomentella and Thelephora (Thelephorales, Basidiomycota)), University of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University, Chair of Mycology.
 
 
Teadustöö põhisuunad
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.12. Bio- ja keskkonnateadustega seotud uuringud, näiteks biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika, majandus- ja tehnoloogiauuringud; CERCS KLASSIFIKAATOR: B110 Bioinformaatika, meditsiiniinformaatika, biomatemaatika, biomeetrika
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.4. Ökoloogia, biosüstemaatika ja -füsioloogia
 
 
Lisainfo
Teadustöö põhisuunad: elurikkuse informaatika, seente triipkoodistamine, seotud andmebaaside ja süsteemide arendus.

Juhendamisel väitekirjad

Juhendatud väitekirjad

Publikatsioonid

Klass
Aasta
Publikatsioon
 
1.1.
2020
Zanne, Amy E.; Abarenkov, Kessy; Afkhami, Michelle E.; Aguilar-Trigueros, Carlos A.; Bates, Scott; Bhatnagar, Jennifer M.; Busby, Posy E.; Christian, Natalie; Cornwell, William K.; Crowther, Thomas W.; Flores-Moreno, Habacuc; Floudas, Dimitrios; Gazis, Romina; Hibbett, David; Kennedy, Peter; Lindner, Daniel L.; Maynard, Daniel S.; Milo, Amy M.; Nilsson, R. Henrik; Powell, Jeff ... Treseder, Kathleen K. (2020). Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biological Reviews, 95 (2), 409−433. DOI: 10.1111/brv.12570.
1.1.
2020
Kõljalg, Urmas; Nilsson, Henrik R.; Schigel, Dmitry; Tedersoo, Leho; Larsson, Karl-Henrik; May, Tom W.; Taylor, Andy F. S.; Jeppesen, Thomas Stjernegaard; Frøslev, Tobias Guldberg; Lindahl, Björn D.; Põldmaa, Kadri; Saar, Irja; Suija, Ave; Savchenko, Anton; Yatsiuk, Iryna; Adojaan, Kristjan; Ivanov, Filipp; Piirmann, Timo; Pöhönen, Raivo; Zirk, Allan ... Abarenkov, Kessy (2020). The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa. Microorganisms, 8 (12), 1910. DOI: 10.3390/microorganisms8121910.
1.1.
2020
Tedersoo, Leho; Anslan, Sten; Bahram, Mohammad; Drenkhan, Rein; Pritsch, Karin; Buegger, Franz; Padari, Allar; Hagh-Doust, Niloufar; Mikryukov, Vladimir; Gohar, Daniyal; Amiri, Rasekh; Hiiesalu, Indrek; Lutter, Reimo; Rosenvald, Raul; Rähn, Elisabeth; Adamson, Kalev; Drenkhan, Tiia; Tullus, Hardi; Jürimaa, Katrin; Sibul, Ivar ... Abarenkov, Kessy (2020). Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe. Frontiers in Microbiology, 11, ARTN 1953. DOI: 10.3389/fmicb.2020.01953.
1.1.
2019
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 Acid Research, 47 (Database issue), D259−D264.10.1093/nar/gky1022.
1.1.
2018
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, 517−525.10.1111/nph.15301.
1.1.
2018
Tedersoo, L.; Kõljalg, U.; Bahram, M.; Döring, M.; Schigel, D.; May, T.; Sanchez-Ramirez, S.; Ryberg, M.; Abarenkov, K. (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity, 90, 135−159. DOI: 10.1007/s13225-018-0401-0.
1.1.
2017
Kulik, Tomasz; Abarenkov, Kessy; Buśko, Maciej; Bilska, Katarzyna; van Diepeningen, Anne D.; Ostrowska-Kołodziejczak, Anna; Krawczyk, Katarzyna; Brankovics, Balázs; Stenglein, Sebastian; Sawicki, Jakub; Perkowski, Juliusz; (2017). ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium. PeerJ, 5, e2992.10.7717/peerj.2992.
1.1.
2016
Bahram, Mohammad; Kohout, Petr; Anslan, Sten; Harend, Helery; Abarenkov, Kessy; Tedersoo, Leho (2016). Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. The ISME Journal, 10 (4), 885−896. DOI: 10.1038/ismej.2015.164.
1.1.
2016
Garnica, Sigisfredo; Schön, Max Emil; Abarenkov, Kessy; Riess, Kai; Liimatainen, Kare; Niskanen, Tuula; Dima, Bálint; Soop, Karl; Frøslev, Tobias Guldberg; Jeppesen, Thomas Stjernegaard; Peintner, Ursula; Kuhnert-Finkernagel, Regina; Brandrud, Tor Erik; Saar, Günter; Oertel, Bernhard; Ammirati, Joseph F. (2016). Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiology Ecology, 1−42. DOI: 10.1093/femsec/fiw045.
1.1.
2016
Nilsson, R.H., Wurzbacher, C., Bahram, M., Coimbra, V.R., Larsson, E., Tedersoo, L., Eriksson, J., Duarte, C., Svantesson, S., Sánchez-García, M., Ryberg, M.K. (2016). Top 50 most wanted fungi. MycoKeys, 12, 29−40. DOI: 10.3897/mycokeys.12.7553.
1.1.
2016
Tedersoo, L.; Bahram, M.; Cajthaml, T.; Põlme, S.; Hiiesalu, I.; Anslan, S.; Harend, H.; Buegger, F.; Pritsch, K.; Koricheva, J.; Abarenkov, K. (2016). Tree diversity and species identity effects on soil fungi, protists and animals are context-dependent. The ISME Journal, 10 (2), 346−362. DOI: 10.1038/ismej.2015.116.
1.1.
2016
Abarenkov, K.; Adams, R.I.; Irinyi, L.; 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. ... 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. DOI: 10.3897/mycokeys.16.10000.
1.1.
2016
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 H, 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 (6), 1049−1068. DOI: 10.3852/16-130.
6.8.
2016
Kõljalg, U.; Tedersoo, L.; Nilsson, R.H.; Abarenkov, K. (2016). Digital identifiers for fungal species. Science, 352, 1182−1183. DOI: 10.1126/science.aaf7115.
1.1.
2015
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 reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30 (2), 145−150. DOI: 10.1264%2Fjsme2.ME14121.
1.1.
2015
Tedersoo, Leho; Anslan, Sten; Bahram, Mohammad; Põlme, Sergei; Riit, Taavi; Liiv, Ingrid; Kõljalg, Urmas; Kisand, Veljo; Nilsson, R. Henrik; Hildebrand, Falk; Bork, Peer; Abarenkov, Kessy (2015). Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys, 10, 1−43. DOI: 10.3897/mycokeys.10.4852.
6.8.
2015
Tedersoo, Leho; Ramirez, Kelly S.; Nilsson, R Henrik; Kaljuvee, Aivi; Kõljalg, Urmas; Abarenkov, Kessy (2015). Standardizing metadata and taxonomic identification in metabarcoding studies. GigaScience, 4 (34), 1−4. DOI: 10.1186/s13742-015-0074-5.
1.1.
2014
Tedersoo, L.; Bahram, M.; Põlme, S.; Kõljalg, U.; Yorou, N.S.; Wijesundera, R.; Villarreal-Ruiz, L.; Vasco-Palacios, A.; Quang Thu, P.; Suija, A.; Smith, M.E.; Sharp, C.; Saluveer, E.; Saitta, A.; Ratkowsky, D.; Pritsch, K.; Riit, T.; Põldmaa, K.; Piepenbring, M.; Phosri, C. ... Abarenkov, K. (2014). Global diversity and geography of soil fungi. Science, 346 (6213), 1078. DOI: 10.1126/science.1256688.
1.1.
2014
Nilsson, R. Henrik; Hyde, Kevin D.; Pawłowska, Julia; Ryberg, Martin; Tedersoo, Leho; Aas, Anders Bjørnsgard; Alias, Siti A.; Alves, Artur; Anderson, Cajsa Lisa; Antonelli, Alexandre; Arnold, A. Elizabeth; Bahnmann, Barbara; Bahram, Mohammad; Bengtsson-Palme, Johan; Berlin, Anna; Branco, Sara; Chomnunti, Putarak; Dissanayake, Asha; Drenkhan, Rein; Friberg, Hanna ... Abarenkov, Kessy (2014). Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67 (1), 11−19. DOI: 10.1007/s13225-014-0291-8.
1.1.
2014
Tedersoo, L.; Bahram, M.; Ryberg, M.; Otsing, E.; Kõljalg, U.; Abarenkov, K. (2014). Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetics analyses. Molecular Ecology, 23 (16), 4168−4183. DOI: 10.1111/mec.12849.
1.1.
2014
Hartmann, Martin; Niklaus, Pascal A; Zimmermann, Stephan; Schmutz, Stefan; Kremer, Johann; Abarenkov, Kessy; Lüscher, Peter; Widmer, Franco; Frey, Beat (2014). Resistance and resilience of the forest soil microbiome to logging-associated compaction. The ISME Journal, 8 (1), 226−244.10.1038/ismej.2013.141.
1.1.
2013
Bengtsson-Palme, Johan; Ryberg, Martin; Hartmann, Martin; Branco, Sara; Wang, Zheng; Godhe, Anna; De Wit, Pierre; Sánchez-García, Marisol; Ebersberger, Ingo; de Sousa, Filipe; Amend, Anthony; Jumpponen, Ari; Unterseher, Martin; Kristiansson, Erik; Abarenkov, Kessy; Bertrand, Yann J. K.; Sanli, Kemal; Eriksson, K. Martin; Vik, Unni; Veldre, Vilmar ... Nilsson, R. Henrik (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 (10), 914−919.10.1111/2041-210X.12073.
1.1.
2013
Kõljalg, Urmas; Nilsson, Henrik; Abarenkov, Kessy; Tedersoo, Leho; Taylor, Andy; Bahram, Mohammad; Bates, Scott; Bruns, Thomas; Bengtsson-Palme, Johan; O'Callaghan, Tony; Douglas, Brian; Drenkhan, Tiia; Eberhardt, Ursula; Dueñas, Margarita; Grebenc, Tine; Griffith, Gareth; Hartmann, Martin; Kirk, Paul; Kohout, Petr; Larsson, Ellen ... Larsson, Karl-Henrik (2013). Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22 (21), 5271−5277. DOI: 10.1111/mec.12481.
1.1.
2013
Veldre, V.; Abarenkov, K.; Bahram, M.; Martos, F.; Selosse, M.-A.; Tamm, H.; Kõljalg, U.; Tedersoo, L. (2013). Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences. Fungal Ecology, 6 (4), 256−268. DOI: 10.1016/j.funeco.2013.03.004.
1.1.
2013
Lindahl, Björn D.; Nilsson, R. Henrik; Tedersoo, Leho; Abarenkov, Kessy; Carlsen, Tor; Kjøller, Rasmus; Kõljalg, Urmas; Pennanen, Taina; Rosendahl, Søren; Stenlid, Jan; Kauserud, Håvard (2013). Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide. New Phytologist, 199 (1), 288−299.10.1111/nph.12243.
1.1.
2013
Blaalid, R.; Kumar, S.; Nilsson, R.H.; Abarenkov, K.; Kirk, P.M.; Kauserud, H. (2013). ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources, 13 (2), 218−224.10.1111/1755-0998.12065.
1.2.
2013
Hyde, K.D.; Udayanga, D.; Manamgoda, D.S.; Tedersoo, L.; Larsson, E.; Abarenkov, K., Bertrand, Y.; Oxelman, B.; Hartmann, M.; Kauserud, H.; Ryberg, M.; Kristiansson, E.; Nilsson, R.H. (2013). Incorporating molecular data in fungal systematics: a guide for aspiring researchers. Current Research in Environmental & Applied Mycology, 3 (1), 1−32. DOI: 10.5943/cream/3/1/1.
1.1.
2012
Bengtsson, J.; Hartmann, M.; Unterseher, M.; Vaishampayan, P.; Abarenkov, K.; Durso, L.; Bik, E.M.; Garey, J.R.; Eriksson, K.M.; Nilsson, R.H. (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, 407−412.10.1016/j.resmic.2012.07.001.
1.2.
2012
Nilsson, R.H.; Tedersoo, L.; Abarenkov, K.; Ryberg, M.; Kristiansson, E.; Hartmann, M.; Schoch, C.L.; Nylander, J.A.A.; Bergsten, J.; Porter, T.M.; Jumpponen, A.; Vaishampayan, P.; Ovaskainen, O.; Hallenberg, N.; Bengtsson-Palme, J.; Eriksson, K.M.; Larsson, K.-H.; Larsson, E.; Kõljalg, U. (2012). Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys, 4, 37−62. DOI: 10.3897/mycokeys.4.3606.
1.1.
2011
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 (4), 278−282.10.1007/s10267-010-0086-z.
1.1.
2011
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 rRNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiology Letters, 319 (2), 140−145.10.1111/j.1574-6968.2011.02274.x.
1.1.
2011
Tedersoo, L; Abarenkov, K; Nilsson, RH; Schüβler, 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 (9), e24940. DOI: 10.1371/journal.pone.0024940.
1.1.
2011
Nilsson, R.H.; Tedersoo, L.; Lindahl, B.; Kjoller, 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 (2), 314−318.
6.3.
2011
Kõljalg, Urmas; Abarenkov, Kessy (2011). Elurikkuse informaatika. Parmasto, Erast; Laisk, Agu; Kaljo, Dimitri. (Toim.). Teadusmõte Eestis. Elu ja Maateadused (17−26). . Tallinn: Eesti Teaduste Akadeemia: Eesti Teaduste Akadeemia Toimetised.
1.1.
2010
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 taxonomic research, with an online implementation for fungal ITS sequences. Evolutionary Bioinformatics, 189−196. DOI: 10.4137/EBO.S6271.
1.1.
2010
Hartmann, M.; Howes, C.G.; Abarenkov, K.; Mohn, W.W.; Nilsson, R.H. (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 (2), 250−253.
1.1.
2010
Nilsson, R.H.; Abarenkov, K.; Veldre, V.; Nylinder, S.; De Wit, P.; Brosche, S.; Alfredsson, J.F.; Ryberg, M.; Kristiansson, E. (2010). An open source chimera checker for the fungal ITS region. Molecular Ecology Resources, 10 (6), 1076−1081.10.1111/j.1755-0998.2010.02850.x.
1.1.
2010
Nilsson, R.H.; 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 (4), 284−287.10.1016/j.funeco.2010.05.002.
1.1.
2010
Nilsson, R.H.; Ryberg, M.; Sjökvist, E.; Abarenkov, K. (2010). Rethinking taxon sampling in the light of environmental sequencing. Cladistics, 26, 1−7.
1.1.
2010
Tedersoo, L.; Nilsson, R.H.; 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 (1), 291−301. DOI: 10.1111/j.1469-8137.2010.03373.x.
1.1.
2010
Abarenkov, Kessy; Nilsson, R. Henrik; Larsson, Karl-Henrik; Alexander, Ian J.; Eberhardt, Ursula; Erland, Susanne; Høiland, Klaus; Kjøller, Rasmus; Larsson, Ellen; Pennanen, Taina; Sen, Robin; Taylor, Andy F. S.; Tedersoo, Leho; Ursing, Björn M.; Vrålstad, Trude; Liimatainen, Kare; Peintner, Ursula; Kõljalg, Urmas (2010). The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist, 186 (2), 281−285.10.1111/j.1469-8137.2009.03160.x.
1.1.
2010
Suvi, T.; Tedersoo, L.; Abarenkov, K.; Beaver, K.; Gerlach, J.; Kõljalg, U. (2010). Mycorrhizal symbionts of Pisonia grandis and P. sechellarum in Seychelles: identification of mycorrhizal fungi and description of new Tomentella species. Mycologia, 102 (3), 522−533. DOI: 10.3852/09-147.
1.1.
2009
Nilsson, R.H.; 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 (1), 97−101.
1.1.
2008
Tedersoo, L.; Jairus, T.; Horton, B.M.; Abarenkov, A.; Suvi, T.; Saar, I.; Kõljalg, U. (2008). Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytologist, 180 (2), 479−490. DOI: 10.1111/j.1469-8137.2008.02561.x.
3.3.
2008
Abarenkov, Kessy; Kõljalg, Urmas; Parmasto, Erast; Kuslapuu, Aavo (2008). PlutoF 1.0. Veebi-töölaud andmete sisestamiseks, toimetamiseks ja vaatamiseks (vaatlused, kollektsioonid, liigid jt. taksonid, DNA-andmed jm). Kasutusjuhend looduseuurijale. Tartu: Tartu Ülikooli Kirjastus.
1.2.
2006
Nilsson, R.H.; 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 (1), e59 . DOI: 10.1371/journal.pone.0000059.
1.1.
2005
Koljalg, U.; Larsson, KH.; Abarenkov, K.; Nilsson, RH.; Alexander, IJ.; Eberhardt, U.; Erland, S.; Hoiland, K.; Kjoller, R.; Larsson, E.; Pennanen, T.; Sen, R.; Taylor, AFS.; Tedersoo, L.; Vralstad, T.; Ursing, BM. (2005). UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist, 166 (3), 1063−1068.
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ProgramTypeNumberNameProject startProject endPrincipal investigatorInstitutionFinancing
ETFETF7434Ecology and biogeography of African ectomycorrhizal fungi01.01.200831.12.2011Leho TedersooUniversity of Tartu, Faculty of Biology and Geography; University of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University; University of Tartu, Faculty of Science and Technology (old)71 043,20 EUR
EMPEMP265Biodiversity in the dark: High-throughput sequence analyses of arctic fungal communities (BioFun)03.09.201331.08.2016Leho TedersooUniversity of Tartu, Faculty of Science and Technology (old)270 000,00 EUR
MUUSP2RT14010DataCite Estonia01.01.201401.03.2015Liisi LembinenUniversity of Tartu; University of Tartu, Tartu University Library247 117,00 EUR
ETFETF8235Coevolution of selected taxa of ectomycorrhizal fungi and their plant hosts01.01.201031.12.2013Urmas KõljalgUniversity of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University67 492,28 EUR
MUUMP1LM12220REU-BON - Building the European Biodiversity Observation Network01.12.201231.05.2017Urmas KõljalgUniversity of Tartu, University of Tartu Natural History Museum and Botanical Garden, Museums of Tartu University, Museum of Nature221 080,00 EUR
TKSLTOM16131T (TK131)Ecology of global change: natural and managed ecosystems (TK131)01.01.201601.03.2023Martin ZobelUniversity of Tartu, Faculty of Science and Technology, Institute of Ecology and Earth Sciences3 198 027,47 EUR
1.2.3.4.MP6LM20156R (871043)Distributed System of Scientific Collections - Preparatory Phase Project01.02.202031.01.2023Urmas KõljalgUniversity of Tartu, University of Tartu Natural History Museum and Botanical Garden, Museums of Tartu University, Museum of Nature70 749,00 EUR
SFSF0182536As03Taxonomy, molecular phylogenetic and ecological studies of basidio- and ascomycetes (including lichenized fungi)01.01.200331.12.2007Urmas KõljalgUniversity of Tartu, Faculty of Biology and Geography283 256,43 EUR
ETFETF6606Biogeography and autecology of Thelephorales (Basidiomycota, Fungi).01.01.200631.12.2009Urmas KõljalgUniversity of Tartu; University of Tartu, Faculty of Science and Technology (old)62 294,25 EUR
PRGPRG1170Discovering and communicating species01.01.202131.12.2025Urmas KõljalgUniversity of Tartu, Faculty of Science and Technology, Institute of Ecology and Earth Sciences257 125,00 EUR
HLKHLK06-4Loodusteaduslike kogude veebipõhine andmebaas01.01.200631.12.2008Urmas KõljalgUniversity of Tartu, University of Tartu Natural History Museum and Botanical Garden, Museums of Tartu University47 509,23 EUR
MOBERCMOBERC1Global biogeography and climate change effects on microbes and their functions in soil: FunGlobe01.01.201628.02.2017Leho TedersooUniversity of Tartu87 600,00 EUR
MOBERCMOBERC10Global biogeography of soil microorganisms01.03.201728.02.2018Leho TedersooUniversity of Tartu81 250,00 EUR
SFSF0180153s08Specific and integrated questions in ecology, taxonomy and biogeography of mycorhizal and lichenized fungi.01.01.200831.12.2013Urmas KõljalgUniversity of Tartu, Faculty of Science and Technology (old), Institute of Ecology and Earth Sciences, Tartu University681 835,04 EUR
IUTIUT20-30Big data – integrated study of fungal species and their interactions01.01.201431.12.2019Urmas KõljalgUniversity of Tartu, Faculty of Science and Technology, Institute of Ecology and Earth Sciences1 013 400,00 EUR