Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

(2017) Karel Sedlar et al.   Computational and Structural Biotechnology Journal

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

(2016) George M. Garrity   JOURNAL OF CLINICAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Swabs to genomes: a comprehensive workflow

(2015) Madison I. Dunitz et al.   PeerJ

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

Whole-genome sequence comparison as a method for improving bacterial species definition

(2014) Wen Zhang et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Advantages and limitations of genomics in prokaryotic taxonomy

(2013) E. Sentausa et al.   CLINICAL MICROBIOLOGY AND INFECTION

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

A Cross-Sectional Survey of Bacterial Species in Plaque from Client Owned Dogs with Healthy Gingiva, Gingivitis or Mild Periodontitis

(2013) Ian J. Davis et al.   PLoS One

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

The Canine Oral Microbiome

(2012) Floyd E. Dewhirst et al.   PLoS One

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

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

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS