Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework

(2019) Gemma Henderson et al.   PeerJ

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

(2019) Jessica L. Mark Welch et al.   Annual Review of Microbiology

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

(2018) Junyi Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The Gut Microbiota of Marine Fish

(2018) Sian Egerton et al.   Frontiers in Microbiology

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

(2018) Alexandre Almeida et al.   GigaScience

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2018) Adithya Murali et al.   Microbiome

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

(2018) Robin R. Rohwer et al.   mSphere

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

(2018) Joshua P. Earl et al.   Microbiome

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

(2018) Isabel F. Escapa et al.   mSystems

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

(2017) Benjamin J Callahan et al.   ISME Journal

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

(2017) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

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

(2016) Vinita Deshpande et al.   MYCOLOGIA

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

SPINGO: a rapid species-classifier for microbial amplicon sequences

(2015) Guy Allard et al.   BMC BIOINFORMATICS

Comparing K-mer based methods for improved classification of 16S sequences

(2015) Hilde Vinje et al.   BMC BIOINFORMATICS

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417

(2015) Roeland L. Berendsen et al.   BMC GENOMICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb)

(2015) Aram Mikaelyan et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

MiDAS: the field guide to the microbes of activated sludge

(2015) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples

(2015) Nezar Noor Al-Hebshi et al.   Journal of Oral Microbiology

TIPP: taxonomic identification and phylogenetic profiling

(2014) Nam-phuong Nguyen et al.   BIOINFORMATICS

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

(2014) Henning Seedorf et al.   PeerJ

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

(2013) J. Oh et al.   GENOME RESEARCH

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

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

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

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier

(2012) Irene LG Newton et al.   BMC MICROBIOLOGY

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project

(2012) Sean Conlan et al.   PLoS One

Shifts in human skin and nares microbiota of healthy children and adults

(2012) Julia Oh et al.   Genome Medicine

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Correction: Thymosin Beta 4 Prevents Oxidative Stress by Targeting Antioxidant and Anti-Apoptotic Genes in Cardiac Fibroblasts

(2011) Sandeep Kumar et al.   PLoS One

Endotracheal tube biofilm inoculation of oral flora and subsequent colonization of opportunistic pathogens

(2010) Sarah D. Perkins et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

(2010) Christopher J van der Gast et al.   ISME Journal

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE