Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes

Ecophysiology of Zetaproteobacteria Associated with Shallow Hydrothermal Iron-Oxyhydroxide Deposits in Nagahama Bay of Satsuma Iwo-Jima, Japan

(2016) Tatsuhiko Hoshino et al.   Frontiers in Microbiology

Exploring deep microbial life in coal-bearing sediment down to  2.5 km below the ocean floor

(2015) F. Inagaki et al.   SCIENCE

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

Improving PCR efficiency for accurate quantification of 16S rRNA genes

(2013) Cameron M. Callbeck et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

(2013) Kelvin Li et al.   PLoS One

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples

(2012) Robert Brankatschk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

Molecular quantification of environmental DNA using microfluidics and digital PCR

(2012) Tatsuhiko Hoshino et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

‘Next-base’ effect on PCR amplification

(2011) Eitan Ben-Dov et al.   Environmental Microbiology Reports

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

Differences in amplification efficiency of standard curves in quantitative real-time PCR assays and consequences for gene quantification in environmental samples

(2010) Stefanie Töwe et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number

(2009) Somanath Bhat et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

LNA-Modified Primers Drastically Improve Hybridization to Target RNA and Reverse Transcription†

(2009) Agata Fratczak et al.   BIOCHEMISTRY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data

(2009) J. M. Ruijter et al.   NUCLEIC ACIDS RESEARCH

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

(2008) Cindy J. Smith et al.   FEMS MICROBIOLOGY ECOLOGY

Locked nucleic acids in PCR primers increase sensitivity and performance

(2008) K.N. Ballantyne et al.   GENOMICS

Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device

(2008) Simant Dube et al.   PLoS One