Kessy Abarenkov

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PlutoF – cloud database and computing services supporting biological research

Kessy Abarenkov, 2011 .

Integration and validation of resources for high-throughput classification of fungal communities

R. Henrik Nilsson, Gerhard G. Thallinger, Kessy Abarenkov, 2014, ECCB 2014.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

R. Henrik Nilsson, Frank Oliver Glöckner, Kessy Abarenkov, 2018, Nucleic Acids Res..

The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa

Kessy Abarenkov, Karl-Henrik Larsson, Dmitry Schigel, 2020, Microorganisms.

PlutoF: Biodiversity data management platform for the complete data lifecycle

Veljo Runnel, Kessy Abarenkov, Urmas Kõljalg, 2019 .

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

R. Henrik Nilsson, Kessy Abarenkov, Karl-Henrik Larsson, 2010, Evolutionary Bioinformatics Online.

Protax-fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences.

Panu Somervuo, Kessy Abarenkov, Otso Ovaskainen, 2018, The New phytologist.

DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe

Javier R. Viguri, Patricia Mergen, Lyubomir Penev, 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)

R. Henrik Nilsson, Gunilla Bok, Erik Kristiansson, 2016 .

Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences

R. Henrik Nilsson, Panu Somervuo, Kessy Abarenkov, 2019 .

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

R. Henrik Nilsson, Kazuaki Tanaka, Qing Cai, 2014, Database J. Biol. Databases Curation.

Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi.

Jana Albrechtová, Petr Kohout, Petr Baldrian, 2020, The New phytologist.

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.

Erik Kristiansson, Kessy Abarenkov, Martin Ryberg, 2009, FEMS microbiology letters.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

R. Henrik Nilsson, Erik Kristiansson, Kessy Abarenkov, 2015, Microbes and environments.

Resistance and resilience of the forest soil microbiome to logging-associated compaction

Kessy Abarenkov, Stefan Schmutz, Martin Hartmann, 2013, The ISME Journal.

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

R. Henrik Nilsson, Kessy Abarenkov, Zheng Wang, 2011, Mycoscience.

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.

R. Henrik Nilsson, Erik Kristiansson, Nils Hallenberg, 2012 .

Rethinking taxon sampling in the light of environmental sequencing

Kessy Abarenkov, Martin Ryberg, M. Ryberg, 2011 .

V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.

Kessy Abarenkov, Martin Hartmann, Charles G Howes, 2010, Journal of microbiological methods.

High-level classification of the Fungi and a tool for evolutionary ecological analyses

Kessy Abarenkov, Dmitry Schigel, Martin Ryberg, 2018, Fungal Diversity.

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

R. Henrik Nilsson, Erik Kristiansson, Kessy Abarenkov, 2006, PloS one.

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

Erik Kristiansson, Kevin D. Hyde, Kessy Abarenkov, 2013, 1302.3244.

Top 50 most wanted fungi

R. Henrik Nilsson, Erik Kristiansson, Kessy Abarenkov, 2016 .

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

Robin Sen, Kessy Abarenkov, Karl-Henrik Larsson, 2005, The New phytologist.

Tidying up international nucleotide sequence databases

R. Henrik Nilsson, Petr Kohout, Kessy Abarenkov, 2011 .

Standardizing metadata and taxonomic identification in metabarcoding studies

Kessy Abarenkov, Urmas Kõljalg, Aivi Kaljuvee, 2015, GigaScience.

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

R. Henrik Nilsson, Erik Kristiansson, Zheng Wang, 2013 .

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

R. Henrik Nilsson, Petr Kohout, Kessy Abarenkov, 2011, PloS one.

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

R. Henrik Nilsson, Erik Kristiansson, Kessy Abarenkov, 2010 .

FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Martti Vasar, Hans-Peter Grossart, M. Catherine Aime, 2020, Fungal Diversity.

Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide

Kessy Abarenkov, Urmas Kõljalg, Søren Rosendahl, 2013, The New phytologist.

Improving ITS sequence data for identification of plant pathogenic fungi

R. Henrik Nilsson, Daniel Lindner, Kevin D. Hyde, 2014, Fungal Diversity.

Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.

Kessy Abarenkov, Karl-Henrik Larsson, Christopher Quince, 2011, The New phytologist.

Towards a unified paradigm for sequence‐based identification of fungi

Michael Weiss, Petr Kohout, Kessy Abarenkov, 2013, Molecular ecology.

Global diversity and geography of soil fungi

R. Henrik Nilsson, Erki Saluveer, Petr Kohout, 2014, Science.