RESCRIPt: Reproducible sequence taxonomy reference database management

Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups

(2021) Kaleb Abram et al.   Communications Biology

The use of taxon-specific reference databases compromises metagenomic classification

(2020) Vanessa R. Marcelino et al.   BMC GENOMICS

Standardised Suffixes in the Nomenclature of the Higher Taxa of Prokaryotes an Aid to Data Mining, Database Administration and Automatic Assignment of Names to Taxonomic Ranks

(2020) B. J. Tindall   CURRENT MICROBIOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

(2020) R. A. Barco et al.   mBio

PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

(2020) Elisa Banchi et al.   Database-The Journal of Biological Databases and Curation

No raw data, no science: another possible source of the reproducibility crisis

(2020) Tsuyoshi Miyakawa   Molecular Brain

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

(2020) Isabel F. Escapa et al.   Microbiome

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

(2020) Maria A. Sierra et al.   Genes

18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability

(2019) Justin M. Waraniak et al.   Ecology and Evolution

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

(2019) Peter J. Walker et al.   ARCHIVES OF VIROLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

(2019) Marco Meola et al.   BMC GENOMICS

HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples

(2019) Matteo Soverini et al.   BMC GENOMICS

GenBank is a reliable resource for 21st century biodiversity research

(2019) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species abundance information improves sequence taxonomy classification accuracy

(2019) Benjamin D. Kaehler et al.   Nature Communications

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database

(2018) Matthieu Leray et al.   BIOINFORMATICS

Why are so many effectively published names of prokaryotic taxa never validated?

(2018) Aharon Oren et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding

(2018) Yukuto Sato et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

(2018) Patrick D. Schloss   mBio

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Taxonomy annotation and guide tree errors in 16S rRNA databases

(2018) Robert Edgar   PeerJ

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments

(2018) Keri Ann Lydon et al.   PeerJ

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

(2018) Alexandre Almeida et al.   GigaScience

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator

(2018) Philip Heller et al.   Scientific Data

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

(2018) Robin R. Rohwer et al.   mSphere

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals

(2018) Michelle A. Jusino et al.   Molecular Ecology Resources

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

(2018) Nicholas A. Bokulich et al.   mSystems

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

GenBank

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

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa )

(2017) Michael S. Robeson et al.   Ecology and Evolution

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

(2016) Alexey M. Kozlov et al.   NUCLEIC ACIDS RESEARCH

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

(2016) Christopher P. Stefan et al.   Scientific Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

International Code of Nomenclature of Prokaryotes

(2015) Charles T Parker et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mycobiome: Approaches to analysis of intestinal fungi

(2015) Jie Tang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

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

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

(2015) Tyler R. Kartzinel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Proposals to clarify and enhance the naming of fungi under the International Code of Nomenclature for algae, fungi, and plants

(2015) David L. Hawksworth   IMA Fungus

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison)

(2015) Gaddy T. Bergmann et al.   PLoS One

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Then and now: a systematic review of the systematics of prokaryotes in the last 80 years

(2013) Aharon Oren et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

(2013) Nicholas A. Bokulich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

(2013) Alexander F. Koeppel et al.   NUCLEIC ACIDS RESEARCH

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

(2013) Daniel Garijo et al.   PLoS One

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems

(2011) Simon Roux et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2011) Daniel McDonald et al.   ISME Journal

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

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

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

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

En route to a genome-based classification of Archaea and Bacteria?

(2010) H.-P. Klenk et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

GENETICS: GenBank--Natural History in the 21st Century?

(2008) B. J. Strasser   SCIENCE