Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

(2019) Vincent Caruso et al.   mSystems

Towards precision quantification of contamination in metagenomic sequencing experiments

(2019) M. S. Zinter et al.   Microbiome

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

(2018) Jeremiah J. Minich et al.   mSystems

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

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

(2017) Benjamin J Callahan et al.   ISME Journal

The Microbiome and the Respiratory Tract

(2016) Robert P. Dickson et al.   Annual Review of Physiology

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

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

Quality filtering of Illumina index reads mitigates sample cross-talk

(2016) Erik Scott Wright et al.   BMC GENOMICS

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

(2016) Vladimir Lazarevic et al.   BMC MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity?

(2016) Lisa Karstens et al.   Frontiers in Cellular and Infection Microbiology

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

(2016) Nicholas A. Bokulich et al.   mSystems

The new world of the urinary microbiota in women

(2015) Linda Brubaker et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

The female urinary microbiome in urgency urinary incontinence

(2015) Meghan M. Pearce et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Microbiota of the indoor environment: a meta-analysis

(2015) Rachel I. Adams et al.   Microbiome

Collection media and delayed freezing effects on microbial composition of human stool

(2015) Roberto Flores et al.   Microbiome

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

The microbiome of the human lower airways: a next generation sequencing perspective

(2015) Velma T. E. Aho et al.   World Allergy Organization Journal

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

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

(2014) Mikhail Tikhonov et al.   ISME Journal

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

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

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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples

(2012) Dana Willner et al.   PLoS One

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One