Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

(2021) Brendan Furneaux et al.   Molecular Ecology Resources

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest

(2020) Stephanie N. Kivlin et al.   ECOLOGY

Optimized metabarcoding with Pacific biosciences enables semi‐quantitative analysis of fungal communities

(2020) Carles Castaño et al.   NEW PHYTOLOGIST

Climatic controls of decomposition drive the global biogeography of forest-tree symbioses

(2019) B. S. Steidinger et al.   NATURE

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

Combining the 5.8S and ITS 2 to improve classification of fungi

(2019) Felix Heeger et al.   Methods in Ecology and Evolution

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens

(2019) Kaire Loit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative analysis of Illumina and Ion Torrent high-throughput sequencing platforms for identification of plant components in herbal teas

(2018) Anna S. Speranskaya et al.   FOOD CONTROL

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

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Sequence clustering threshold has little effect on the recovery of microbial community structure

(2018) Synnøve Smebye Botnen et al.   Molecular Ecology Resources

Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows

(2018) Timothy J. Divoll et al.   Molecular Ecology Resources

Probing promise versus performance in longer read fungal metabarcoding

(2018) Peter G. Kennedy et al.   NEW PHYTOLOGIST

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

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

(2018) Kessy Abarenkov et al.   NEW PHYTOLOGIST

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

(2018) Adithya Murali et al.   Microbiome

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

(2018) Sydney I. Glassman et al.   mSphere

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

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

(2016) Geoffrey L. House et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Unbiased probabilistic taxonomic classification for DNA barcoding

(2016) Panu Somervuo et al.   BIOINFORMATICS

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

What you need is what you eat? Prey selection by the bat Myotis daubentonii

(2016) Eero J. Vesterinen et al.   MOLECULAR ECOLOGY

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

(2016) Hector Urbina et al.   MYCOSCIENCE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

(2016) Jennifer Fouquier et al.   Microbiome

Top 50 most wanted fungi

(2016) R. Henrik Nilsson et al.   MycoKeys

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

(2015) Erik S. Wright   BMC BIOINFORMATICS

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

(2015) Martin Ryberg   MOLECULAR ECOLOGY

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

(2015) Leho Tedersoo et al.   MycoKeys

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

(2014) Mohammad Bahram et al.   NEW PHYTOLOGIST

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales

(2013) Mohammad Bahram et al.   JOURNAL OF ECOLOGY

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

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

(2012) R. Henrik Nilsson et al.   Evolutionary Bioinformatics

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions

(2012) Brian J. Pickles et al.   MOLECULAR ECOLOGY

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) R. Henrik Nilsson et al.   MycoKeys

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

(2011) Kuan-Liang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar

(2011) LEHO TEDERSOO et al.   MOLECULAR ECOLOGY

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

(2011) Daniel L. Lindner et al.   MYCOLOGIA

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

(2009) Leho Tedersoo et al.   MYCORRHIZA

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

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

(2008) Leho Tedersoo et al.   NEW PHYTOLOGIST

Fast phylogenetic DNA barcoding

(2008) K. Munch et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Preserving Accuracy in GenBank

(2008) M. I. Bidartondo   SCIENCE

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY