High-resolution phylogenetic microbial community profiling

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

(2014) Esther A. Gies et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing

(2014) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

(2014) Shunsuke Takahashi et al.   PLoS One

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

(2014) Jerome T. Babauta et al.   Frontiers in Microbiology

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

FunGene: the functional gene pipeline and repository

(2013) Jordan A. Fish et al.   Frontiers in Microbiology

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel 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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

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

(2011) William A. Walters et al.   BIOINFORMATICS

Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera

(2011) M. G. Kalyuzhnaya et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

(2011) Henk Bolhuis et al.   ISME Journal

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Methane formation and oxidation in the meromictic oligotrophic Lake Gek-Gel (Azerbaijan)

(2010) N. V. Pimenov et al.   MICROBIOLOGY

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

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

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

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing

(2009) Vladimir Lazarevic et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2008) Micah Hamady et al.   NATURE METHODS