Using Core Genome Alignments To Assign Bacterial Species

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 novel Ehrlichia species in blood and Ixodes ornithorhynchi ticks from platypuses ( Ornithorhynchus anatinus ) in Queensland and Tasmania, Australia

(2018) Alexander W. Gofton et al.   Ticks and Tick-Borne Diseases

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Genetic diversity and molecular epidemiology of Anaplasma

(2017) Mara Battilani et al.   INFECTION GENETICS AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Orientia tsutsugamushi: A neglected but fascinating obligate intracellular bacterial pathogen

(2017) Jeanne Salje   PLoS Pathogens

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Molecular survey and characterization of a novel Anaplasma species closely related to Anaplasma capra in ticks, northwestern China

(2016) Jifei Yang et al.   Parasites & Vectors

Wolbachia pipientis should not be split into multiple species: A response to Ramírez-Puebla et al., “Species in Wolbachia ? Proposal for the designation of ‘ Candidatus Wolbachia bourtzisii’, ‘ Candidatus Wolbachia onchocercicola’, ‘ Candidatus Wolbachia blaxteri’, ‘ Candidatus Wolbachia brugii’, ‘ Candidatus Wolbachia taylori’, ‘ Candidatus Wolbachia collembolicola’ and ‘ Candidatus Wolbachia multihospitum’ for the different species within Wolbachia supergroups”

(2016) Amelia R.I. Lindsey et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

International Code of Nomenclature of Prokaryotes

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

Human infection with a novel tick-borne Anaplasma species in China: a surveillance study

(2015) Hao Li et al.   LANCET INFECTIOUS DISEASES

Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus

(2015) Roger Karlsson et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Species in Wolbachia? Proposal for the designation of ‘Candidatus Wolbachia bourtzisii’, ‘Candidatus Wolbachia onchocercicola’, ‘Candidatus Wolbachia blaxteri’, ‘Candidatus Wolbachia brugii’, ‘Candidatus Wolbachia taylori’, ‘Candidatus Wolbachia collembolicola’ and ‘Candidatus Wolbachia multihospitum’ for the different species within Wolbachia supergroups

(2015) Shamayim T. Ramírez-Puebla et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Molecular-genetic and ultrastructural characteristics of ‘Candidatus Ehrlichia khabarensis’, a new member of the Ehrlichia genus

(2015) V.A. Rar et al.   Ticks and Tick-Borne Diseases

A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species

(2014) D. Ramasamy et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Gene gain and loss events in Rickettsia and Orientia species

(2011) Kalliopi Georgiades et al.   Biology Direct

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

(2011) Daniel McDonald et al.   ISME Journal

Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning

(2011) Katrien De Bruyne et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Molecular analyses of a potentially novel Anaplasma species closely related to Anaplasma phagocytophilum detected in sika deer (Cervus nippon yesoensis) in Japan

(2011) Adrian P. Ybañez et al.   VETERINARY MICROBIOLOGY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Classification of Bacteria and Archaea: Past, present and future

(2009) Karl Heinz Schleifer   SYSTEMATIC AND APPLIED MICROBIOLOGY

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree

(2008) Jeffrey P. Townsend et al.   JOURNAL OF MOLECULAR EVOLUTION

Parasitism and Mutualism in Wolbachia: What the Phylogenomic Trees Can and Cannot Say

(2008) S. R. Bordenstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emerging and re-emerging rickettsioses: endothelial cell infection and early disease events

(2008) David H. Walker et al.   NATURE REVIEWS MICROBIOLOGY