Gene content dissimilarity for subclassification of highly similar microbial strains

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

(2015) Ankit Gupta et al.   BMC GENOMICS

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Microbial species delineation using whole genome sequences

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

Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

(2015) Michiel Vos et al.   TRENDS IN MICROBIOLOGY

Genomic insights into the taxonomic status of the Bacillus cereus group

(2015) Yang Liu et al.   Scientific Reports

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

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Parallel independent evolution of pathogenicity within the genus Yersinia

(2014) S. Reuter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mojo Hand, a TALEN design tool for genome editing applications

(2013) Kevin L Neff et al.   BMC BIOINFORMATICS

Microbial genomic taxonomy

(2013) Cristiane C Thompson et al.   BMC GENOMICS

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

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

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra

(2012) L.N. Ikryannikova et al.   CLINICAL MICROBIOLOGY AND INFECTION

Lateral gene transfer as a support for the tree of life

(2012) S. S. Abby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Time for order in microbial systematics

(2012) Simonetta Gribaldo et al.   TRENDS IN MICROBIOLOGY

Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia

(2012) Guanghong Zuo et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Prokaryotic systematics in the genomics era

(2011) Xiao-Yang Zhi et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Genomic fluidity: an integrative view of gene diversity within microbial populations

(2011) Andrey O Kislyuk et al.   BMC GENOMICS

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Differentiation between Shigella, enteroinvasive Escherichia coli (EIEC) and noninvasive Escherichia coli

(2011) M. J. C. Beld et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Microbiology and the species problem

(2010) Marc Ereshefsky   BIOLOGY & PHILOSOPHY

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus

(2009) O. O. Glazunova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY 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

Is 16S rDNA a Reliable Phylogenetic Marker to Characterize Relationships Below the Family Level in the Enterobacteriaceae?

(2008) Marianna Naum et al.   JOURNAL OF MOLECULAR EVOLUTION

Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention

(2008) Niyaz Ahmed et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives

(2008) Mogens Kilian et al.   PLoS One