Reference databases for taxonomic assignment in metagenomics

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

(2011) Kuan-Liang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Flexible taxonomic assignment of ambiguous sequencing reads

(2011) José C Clemente et al.   BMC BIOINFORMATICS

Analysis of 16S rRNA environmental sequences using MEGAN

(2011) Suparna Mitra et al.   BMC GENOMICS

Computational challenges of sequence classification in microbiomic data

(2011) P. Ribeca et al.   BRIEFINGS IN BIOINFORMATICS

Metagenomic Analysis of Brain Abscesses Identifies Specific Bacterial Associations

(2011) M. Al Masalma et al.   CLINICAL INFECTIOUS DISEASES

On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys

(2011) Patricio Jeraldo et al.   ENVIRONMENTAL MICROBIOLOGY

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

(2011) O.-S. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2011) Daniel McDonald et al.   ISME Journal

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The International Nucleotide Sequence Database Collaboration

(2011) I. Karsch-Mizrachi et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants

(2011) Mariam Susan LaTuga et al.   PLoS One

Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks

(2011) Giovanna Carpi et al.   PLoS One

Release LTPs104 of the All-Species Living Tree

(2011) Raúl Munoz et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

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

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

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

(2010) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

(2010) Mahmoud A. Ghannoum et al.   PLoS Pathogens

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

Metagenomics: Concept, methodology, ecological inference and recent advances

(2009) Jagtar Singh et al.   Biotechnology Journal

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

The ITS2 Database III—sequences and structures for phylogeny

(2009) Christian Koetschan et al.   NUCLEIC ACIDS RESEARCH

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS

5.8S-28S rRNA interaction and HMM-based ITS2 annotation

(2008) Alexander Keller et al.   GENE

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

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