Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

Estimation of sequencing error rates in short reads

(2012) Xin Victoria et al.   BMC BIOINFORMATICS

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

(2012) Viggó Thór Marteinsson et al.   ISME Journal

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

Global biogeography of SAR11 marine bacteria

(2012) Mark V Brown et al.   Molecular Systems Biology

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Exploring the Diversity of Gardnerella vaginalis in the Genitourinary Tract Microbiota of Monogamous Couples Through Subtle Nucleotide Variation

(2011) A. Murat Eren et al.   PLoS One

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

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

SHREC: a short-read error correction method

(2009) J. Schroder et al.   BIOINFORMATICS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing

(2009) W. Qu et al.   GENOME RESEARCH

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics