Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

The microbiota of high-moisture mozzarella cheese produced with different acidification methods

(2016) Angela Guidone et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

UMI-4C for quantitative and targeted chromosomal contact profiling

(2016) Omer Schwartzman et al.   NATURE METHODS

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems

(2015) Jun Gong et al.   ENVIRONMENTAL MICROBIOLOGY

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems

(2015) Christopher E. Lawson et al.   ENVIRONMENTAL MICROBIOLOGY

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

(2015) Yuting Liang et al.   ISME Journal

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

(2015) Lucas Sinclair et al.   PLoS One

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Microbial responses to southward and northward Cambisol soil transplant

(2015) Mengmeng Wang et al.   MicrobiologyOpen

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

(2014) Aibin Zhan et al.   CONSERVATION GENETICS

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

(2014) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry

(2014) Shanshan Liu et al.   ENVIRONMENTAL MICROBIOLOGY

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale

(2014) Eva L. M. Figuerola et al.   ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues

(2014) Zhao-Ming Gao et al.   MICROBIAL ECOLOGY

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

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

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

(2014) Johan Decelle et al.   PLoS One

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community

(2014) Masayuki Ushio et al.   SOIL BIOLOGY & BIOCHEMISTRY

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities

(2014) Aibin Zhan et al.   Methods in Ecology and Evolution

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags

(2013) Xin Peng et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Dynamics of Seawater Bacterial Communities in a Shellfish Hatchery

(2013) S. M. Powell et al.   MICROBIAL ECOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea

(2013) Gregor Gorkiewicz et al.   PLoS One

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

High-Throughput Sequencing: A Roadmap Toward Community Ecology

(2013) Timothée Poisot et al.   Ecology and Evolution

Actinobacterial Nitrate Reducers and Proteobacterial Denitrifiers Are Abundant in N2O-Metabolizing Palsa Peat

(2012) Katharina Palmer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Low sequencing efforts bias analyses of shared taxa in microbial communities

(2012) Leandro N. Lemos et al.   FOLIA MICROBIOLOGICA

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

(2012) J Gregory Caporaso et al.   ISME Journal

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

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

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Bugs, Stool, and the Irritable Bowel Syndrome: Too Much Is as Bad as Too Little?

(2011) Nicholas J. Talley et al.   GASTROENTEROLOGY

Barcoding bias in high-throughput multiplex sequencing of miRNA

(2011) S. Alon et al.   GENOME RESEARCH

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

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

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Soil genomics

(2009) Brajesh K. Singh et al.   NATURE REVIEWS MICROBIOLOGY

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

(2008) Micah Hamady et al.   NATURE METHODS