Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

(2016) Claus Pelikan et al.   ENVIRONMENTAL MICROBIOLOGY

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing

(2016) Wenke Smets et al.   SOIL BIOLOGY & BIOCHEMISTRY

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

An assessment of US microbiome research

(2016) Elizabeth Stulberg et al.   Nature Microbiology

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

(2015) Fernando Puente-Sánchez et al.   NUCLEIC ACIDS RESEARCH

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

(2015) Ann McCarthy et al.   PLoS One

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

(2014) Thomas S. B. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

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

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

(2014) Sarah A. Munro et al.   Nature Communications

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

A mechanistic basis for amplification differences between samples and between genome regions

(2012) Colin D Veal et al.   BMC GENOMICS

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

(2012) J Gregory Caporaso et al.   ISME Journal

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY