Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

Oral Metallo-Beta-Lactamase Protects the Gut Microbiome From Carbapenem-Mediated Damage and Reduces Propagation of Antibiotic Resistance in Pigs

(2019) Sheila Connelly et al.   Frontiers in Microbiology

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

(2019) Alexander T. Dilthey et al.   Nature Communications

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments

(2018) Suchitra K. Hourigan et al.   Frontiers in Microbiology

Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling

(2018) Fei Teng et al.   Scientific Reports

A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

(2018) Monika Roy et al.   International Journal of Environmental Research and Public Health

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(2017) Michael Tessler et al.   Scientific Reports

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing

(2016) Kirsten J.M. van Nimwegen et al.   CLINICAL CHEMISTRY

Cross-talk among flesh-eatingAeromonas hydrophilastrains in mixed infection leading to necrotizing fasciitis

(2016) Duraisamy Ponnusamy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges

(2016) Martin J. Blaser et al.   mBio

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

(2015) Mads Albertsen et al.   PLoS One

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments

(2014) Christine E Sharp et al.   ISME Journal

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

PCR-based amplification and heterologous expression of Pseudomonas alcohol dehydrogenase genes from the soil metagenome for biocatalysis

(2013) Nobuya Itoh et al.   ENZYME AND MICROBIAL TECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size

(2012) Anne Chao et al.   ECOLOGY

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

(2012) John Wieczorek et al.   PLoS One

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Standardization and Omics Science: Technical and Social Dimensions Are Inseparable and Demand Symmetrical Study

(2010) Christina Holmes et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial biodiversity of thermophilic communities in hot mineral soils of Tramway Ridge, Mount Erebus, Antarctica

(2009) Rochelle M. Soo et al.   ENVIRONMENTAL MICROBIOLOGY

Novel genes retrieved from environmental DNA by polymerase chain reaction: Current genome-walking techniques for future metagenome applications

(2009) Michael Kotik   JOURNAL OF BIOTECHNOLOGY

'Omics Data Sharing

(2009) D. Field et al.   SCIENCE

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Metagenomics

(2008) R.D. Sleator et al.   LETTERS IN APPLIED MICROBIOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

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

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

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

(2008) J. F. Biddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA