Related references
Note: Only part of the references are listed.Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes
Alle A. Y. Lie et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition
Silvia S. Kang et al.
MOLECULAR NEURODEGENERATION (2014)
Pregnancy's Stronghold on the Vaginal Microbiome
Marina R. S. Walther-Antonio et al.
PLOS ONE (2014)
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
James J. Kozich et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data
Charles E. Robertson et al.
BIOINFORMATICS (2013)
Infernal 1.1: 100-fold faster RNA homology searches
Eric P. Nawrocki et al.
BIOINFORMATICS (2013)
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke et al.
NATURE (2013)
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
Nicholas A. Bokulich et al.
NATURE METHODS (2013)
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Robert C. Edgar
NATURE METHODS (2013)
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
Christopher S. Miller et al.
PLOS ONE (2013)
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Paul J. McMurdie et al.
PLOS ONE (2013)
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Sara C. Di Rienzi et al.
ELIFE (2013)
PANDAseq: PAired-eND Assembler for Illumina sequences
Andre P. Masella et al.
BMC BIOINFORMATICS (2012)
Illumina-based analysis of microbial community diversity
Patrick H. Degnan et al.
ISME JOURNAL (2012)
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys
Jeffrey J. Werner et al.
ISME JOURNAL (2012)
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
David A. W. Soergel et al.
ISME JOURNAL (2012)
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
J. Gregory Caporaso et al.
ISME JOURNAL (2012)
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
Doyle V. Ward et al.
PLOS ONE (2012)
The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
Dirk Gevers et al.
PLOS BIOLOGY (2012)
Bioinformatics for the Human Microbiome Project
Dirk Gevers et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
Daniel McDonald et al.
GIGASCIENCE (2012)
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
Andrea K. Bartram et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
William A. Walters et al.
BIOINFORMATICS (2011)
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
PyNAST: a flexible tool for aligning sequences to a template alignment
J. Gregory Caporaso et al.
BIOINFORMATICS (2010)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
Robust Computational Analysis of rRNA Hypervariable Tag Datasets
Maksim Sipos et al.
PLOS ONE (2010)
Forensic identification using skin bacterial communities
Noah Fierer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Infernal 1.0: inference of RNA alignments
Eric P. Nawrocki et al.
BIOINFORMATICS (2009)
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Micah Hamady et al.
GENOME RESEARCH (2009)
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
J. R. Cole et al.
NUCLEIC ACIDS RESEARCH (2009)
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
Zongzhi Liu et al.
NUCLEIC ACIDS RESEARCH (2008)
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
Qiong Wang et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
Catherine A. Lozupone et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
T. Z. DeSantis et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
T. Z. DeSantis et al.
NUCLEIC ACIDS RESEARCH (2006)
APE: Analyses of Phylogenetics and Evolution in R language
E Paradis et al.
BIOINFORMATICS (2004)
Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis
ZT Yu et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)