Parsing ecological signal from noise in next generation amplicon sequencing

Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity

(2014) Naomichi Yamamoto et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Obtaining a spore free fungal community composition

(2013) Sietse van der Linde et al.   Fungal Ecology

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

(2013) Alexandra A-T. Weber et al.   PLoS One

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

Fungi at a Small Scale: Spatial Zonation of Fungal Assemblages around Single Trees

(2013) Sara Branco et al.   PLoS One

Different bacterial communities in ectomycorrhizae and surrounding soil

(2013) Unni Vik et al.   Scientific Reports

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC 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

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

The contribution of tef-1 sequences to species delimitation in the Cantharellus cibarius complex in the southeastern USA

(2011) B. Buyck et al.   FUNGAL DIVERSITY

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

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

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Pooled samples bias fungal community descriptions

(2009) P. G. AVIS et al.   Molecular Ecology Resources

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

(2009) Leho Tedersoo et al.   MYCORRHIZA

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE