Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

Description of Bacillus kexueae sp. nov. and Bacillus manusensis sp. nov., isolated from hydrothermal sediments

(2018) Qing-lei Sun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Nannocystis konarekensis sp. nov., a novel myxobacterium from an Iranian desert

(2018) Kathrin I. Mohr et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Legionella Becoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata

(2017) Jana Říhová et al.   Genome Biology and Evolution

Biological Species Are Universal across Life’s Domains

(2017) Louis-Marie Bobay et al.   Genome Biology and Evolution

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes

(2017) Haiwei Luo et al.   Nature Microbiology

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved

(2016) Dmitrij Turaev et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Comparative genomics ofSynechococcusand proposal of the new genusParasynechococcus

(2016) Felipe Coutinho et al.   PeerJ

Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species

(2015) Morgane Rossi-Tamisier et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Early emergence of Yersinia pestis as a severe respiratory pathogen

(2015) Daniel L. Zimbler et al.   Nature Communications

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

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

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

Strong Genome-Wide Selection Early in the Evolution of Prochlorococcus Resulted in a Reduced Genome through the Loss of a Large Number of Small Effect Genes

(2014) Zhiyi Sun et al.   PLoS One

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

(2014) Steven J. Biller et al.   Scientific Data

Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica

(2013) E. N. Gordienko et al.   JOURNAL OF BACTERIOLOGY

Genomic Taxonomy of the Genus Prochlorococcus

(2013) Cristiane C. Thompson et al.   MICROBIAL ECOLOGY

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation

(2012) Tim Kahlke et al.   BMC GENOMICS

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Towards a genome based taxonomy of Mycoplasmas

(2011) Cristiane C. Thompson et al.   INFECTION GENETICS AND EVOLUTION

Brucellataxonomy and evolution

(2010) Thomas Ficht   Future Microbiology

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS