Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

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

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Temporal variability in the diversity and composition of stream bacterioplankton communities

(2012) Maria C. Portillo et al.   ENVIRONMENTAL MICROBIOLOGY

Lake microbial communities are resilient after a whole-ecosystem disturbance

(2012) Ashley Shade et al.   ISME Journal

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

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study

(2012) Blaire Steven et al.   Environmental Microbiology Reports

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

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

(2011) Jeffrey J Werner et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacterial community assembly based on functional genes rather than species

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

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Global patterns in the biogeography of bacterial taxa

(2010) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake

(2010) Ryan J. Newton et al.   ENVIRONMENTAL MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

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

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Photosynthetic picoplankton in Lake Tanganyika: biomass distribution patterns with depth, season and basin

(2009) S. Stenuite et al.   JOURNAL OF PLANKTON RESEARCH

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA