List of works - Kessy Abarenkov

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

scientific article published on 15 July 2010

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

scientific article published on 19 March 2015

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

scientific article published in 2011

A price tag on species

scientific article published on 17 June 2022

An open source chimera checker for the fungal ITS region

scientific article published on November 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

scholarly article by Henrik Nilsson et al published November 2010 in Fungal Ecology

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)

scientific article (publication date: 26 September 2016)

Connecting the multiple dimensions of global soil fungal diversity

scientific article published in December 2023

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

scientific article published in 2021

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

scientific article (publication date: 29 November 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)

scientific article

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

scientific article

Digital identifiers for fungal species

scientific article

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

scientific article published on 26 March 2020

Enabling Community Curation of Biological Source Annotations of Molecular Data Through PlutoF and the ELIXIR Contextual Data Clearinghouse

scientific article published in 2022

Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences

scientific article published in 2013

FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".

scientific article published on 27 August 2015

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

scientific article

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

scientific article

Fungal biogeography. Global diversity and geography of soil fungi

scientific article

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

scientific article

FungalRoot v.2.0 – an empirical database of plant mycorrhizal traits

scientific article published in 2022

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

scientific article published in November 2020

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses

scientific article

Global patterns in endemicity and vulnerability of soil fungi

scientific article published in 2022

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

scientific article published on 16 May 2018

ITS1 versus ITS2 as DNA metabarcodes for fungi

scientific article published on 25 January 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

article

Improving ITS sequence data for identification of plant pathogenic fungi

article

Linking Between Molecular and Biodiversity Data: A BiCIKL Perspective

scientific article published in 2024

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

scientific article

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

scientific article published on 15 June 2011

Molecular Identification of Fungi: Rationale, Philosophical Concerns, and the UNITE Database

Molecular Techniques in Mycological Studies and Sequence Data Curating: Quality Control and Challenges

Mycorrhizal symbionts of Pisonia grandis and P. sechellarum in Seychelles: identification of mycorrhizal fungi and description of new Tomentella species

scientific article

PlutoF: Biodiversity data management platform for the complete data lifecycle

scientific article published in 2019

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

scientific article

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

scientific article published in 2024

Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

scientific article published on 14 August 2017

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

scientific article published on 04 September 2020

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

scientific article

Rethinking taxon sampling in the light of environmental sequencing

article by Henrik Nilsson et al published 25 August 2010 in Cladistics

Sequence-based classification and identification of Fungi ⬇️

scientific article

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

scientific article

Standardizing metadata and taxonomic identification in metabarcoding studies

scientific article published on 31 July 2015

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

scientific article published on 22 September 2015

Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers

scientific article

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

scientific article

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective

scientific article published in 2006

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research ⬇️

scholarly article published in 2021

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

scientific article

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

scientific article published on 30 November 2020

The UNITE Database for Molecular Identification and for Communicating Fungal Species

scientific article published in 2019

The UNITE database for molecular identification of fungi--recent updates and future perspectives

scientific article published in April 2010

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

scholarly article by Henrik Nilsson et al published 29 October 2018 in Nucleic Acids Research

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

scientific article published in 2021

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi

scientific article

Top 50 most wanted fungi

scientific article

Towards a unified paradigm for sequence-based identification of fungi

scientific article

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

scientific article published in 2011

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

scientific article published on 14 July 2015

UNITE Species Hypotheses Matching Analysis

scientific article published in 2022

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

scientific article

V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets

scientific article published on 27 April 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

scientific article published on 27 August 2010

Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

scientific article published in 2018

The curse of the uncultured fungus ⬇️

scholarly article published in 2022

List of works by Kessy Abarenkov

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

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

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

A price tag on species

An open source chimera checker for the fungal ITS region

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

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)

Connecting the multiple dimensions of global soil fungal diversity

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

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

Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Digital identifiers for fungal species

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

Enabling Community Curation of Biological Source Annotations of Molecular Data Through PlutoF and the ELIXIR Contextual Data Clearinghouse

Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences

FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".

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

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

Fungal biogeography. Global diversity and geography of soil fungi

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

FungalRoot v.2.0 – an empirical database of plant mycorrhizal traits

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

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses

Global patterns in endemicity and vulnerability of soil fungi

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

ITS1 versus ITS2 as DNA metabarcodes for fungi

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

Improving ITS sequence data for identification of plant pathogenic fungi

Linking Between Molecular and Biodiversity Data: A BiCIKL Perspective

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

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

Molecular Identification of Fungi: Rationale, Philosophical Concerns, and the UNITE Database

Molecular Techniques in Mycological Studies and Sequence Data Curating: Quality Control and Challenges

Mycorrhizal symbionts of Pisonia grandis and P. sechellarum in Seychelles: identification of mycorrhizal fungi and description of new Tomentella species

PlutoF: Biodiversity data management platform for the complete data lifecycle

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

Prototype Biodiversity Digital Twin: Phylogenetic Diversity

Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

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

Rethinking taxon sampling in the light of environmental sequencing

Sequence-based classification and identification of Fungi ⬇️

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

Standardizing metadata and taxonomic identification in metabarcoding studies

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research ⬇️

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

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

The UNITE Database for Molecular Identification and for Communicating Fungal Species

The UNITE database for molecular identification of fungi--recent updates and future perspectives

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

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi

Top 50 most wanted fungi

Towards a unified paradigm for sequence-based identification of fungi

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

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

UNITE Species Hypotheses Matching Analysis

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

V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets

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

Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

﻿The curse of the uncultured fungus ⬇️

The curse of the uncultured fungus ⬇️