Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

Mixture models for analysis of the taxonomic composition of metagenomes

(2011) Peter Meinicke et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments

(2011) Takahiko Nagahama et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads

(2011) Gail L. Rosen et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

Discovery of novel intermediate forms redefines the fungal tree of life

(2011) Meredith D. M. Jones et al.   NATURE

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

(2011) Teresita M. Porter et al.   NEW PHYTOLOGIST

Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences

(2011) László G. Nagy et al.   NEW PHYTOLOGIST

Where are all the undocumented fungal species? A study of Mortierella demonstrates the need for sequence-based classification

(2011) David Hibbett et al.   NEW PHYTOLOGIST

Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

(2011) A. Rosling et al.   SCIENCE

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

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

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

(2011) David S. Hibbett et al.   Fungal Biology Reviews

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

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

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Identifying wood-inhabiting fungi with 454 sequencing – what is the probability that BLAST gives the correct species?

(2010) Otso Ovaskainen et al.   Fungal Ecology

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS

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

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

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

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

DNA barcoding of arbuscular mycorrhizal fungi

(2010) Herbert Stockinger et al.   NEW PHYTOLOGIST

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

(2010) A. S. Amend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Diverse and Seasonally Dynamic Protist Community in a Pristine Peat Bog

(2010) Enrique Lara et al.   PROTIST

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

(2009) Daniel Faith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Progress towards DNA barcoding of fungi

(2009) KEITH A. SEIFERT   Molecular Ecology Resources

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

DNA-based species level detection ofGlomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi

(2009) Manuela Krüger et al.   NEW PHYTOLOGIST

The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

(2009) Enrique Lara et al.   PROTIST

Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario

(2008) TERESITA M. PORTER et al.   MOLECULAR ECOLOGY

How to know unknown fungi: the role of a herbarium

(2008) Patrick M. Brock et al.   NEW PHYTOLOGIST

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

Fast phylogenetic DNA barcoding

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

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life

(2007) T.M. Porter et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION