The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
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February 2018 |
Comparison of Bacterial Diversity in Air and Water of a Major Urban Center
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November 2018 |
Cutadapt removes adapter sequences from high-throughput sequencing reads
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May 2011 |
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
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February 2013 |
First detection and molecular identification of the zoonotic Anaplasma capra in deer in France
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July 2019 |
An evaluation of the accuracy and speed of metagenome analysis tools
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January 2016 |
Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)
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January 2019 |
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
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April 2016 |
Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis
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July 2018 |
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
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January 2016 |
Fast and accurate short read alignment with Burrows-Wheeler transform
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May 2009 |
Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps
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December 2015 |
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
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October 2020 |
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
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September 2019 |
Capturing protein-coding genes across highly divergent species
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June 2013 |
Trimmomatic: a flexible trimmer for Illumina sequence data
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April 2014 |
A method to identify respiratory virus infections in clinical samples using next-generation sequencing
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February 2019 |
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
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January 2011 |
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
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July 2012 |
Reconstructing 16S rRNA genes in metagenomic data
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June 2015 |
Capturing Darwin's dream
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August 2016 |
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
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June 2007 |
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics
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April 2014 |
Best practices for analysing microbiomes
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May 2018 |
Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima
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July 2019 |
Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies
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August 2019 |
Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site
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May 2020 |
SOAP2: an improved ultrafast tool for short read alignment
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June 2009 |
Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats
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June 2018 |
ART: a next-generation sequencing read simulator
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December 2011 |
Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment
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November 2020 |
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak
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January 2010 |
Search and clustering orders of magnitude faster than BLAST
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August 2010 |
UPARSE: highly accurate OTU sequences from microbial amplicon reads
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August 2013 |
Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota
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November 2019 |
Prokka: rapid prokaryotic genome annotation
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March 2014 |
Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
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October 2020 |
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
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August 2012 |
Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community
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December 2018 |
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
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March 2011 |
Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons
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April 2015 |
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
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March 2011 |
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
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September 2015 |
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
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November 1977 |
Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next‐generation sequencing strategy
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July 2019 |
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities: Using
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September 2013 |
Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
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December 2015 |
Species classifier choice is a key consideration when analysing low-complexity food microbiome data
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March 2018 |
Basic local alignment search tool
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October 1990 |
DADA2: High-resolution sample inference from Illumina amplicon data
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May 2016 |
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
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August 2018 |
DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions
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April 2019 |
SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?
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March 2017 |
Towards standards for human fecal sample processing in metagenomic studies
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October 2017 |
Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus
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November 2015 |
Reconciliation between operational taxonomic units and species boundaries
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March 2017 |
High Throughput Sequencing for Detection of Foodborne Pathogens
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October 2017 |
Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used
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September 2016 |
Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)
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January 2019 |
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
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March 2012 |
Metagenomic microbial community profiling using unique clade-specific marker genes
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June 2012 |
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
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February 2021 |
Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles
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July 2014 |
Hybridization capture reveals microbial diversity missed using current profiling methods
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March 2018 |
Coral bacterial community structure responds to environmental change in a host-specific manner
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July 2019 |
Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions
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February 2017 |
Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes
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October 2019 |
Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca
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November 2019 |
Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps
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January 2015 |
The Use of Metagenomic Approaches to Analyze Changes in Microbial Communities
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journal
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January 2013 |
An evaluation of the accuracy and speed of metagenome analysis tools
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dataset
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January 2016 |