Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus

Simulating Illumina Metagenomic Data with InSilicoSeq

(2018) Hadrien Gourlé et al.   BIOINFORMATICS

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

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

(2018) Seong-In Na et al.   JOURNAL OF MICROBIOLOGY

Leptospira Genomospecies and Sequence Type Prevalence in Small Mammal Populations in Germany

(2018) Stefan Fischer et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Precision identification of diverse bloodstream pathogens in the gut microbiome

(2018) Fiona B. Tamburini et al.   NATURE MEDICINE

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

(2018) Chirag Jain et al.   Nature Communications

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Streptococcus thermophilus APC151 Strain Is Suitable for the Manufacture of Naturally GABA-Enriched Bioactive Yogurt

(2016) Daniel M. Linares et al.   Frontiers in Microbiology

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity

(2016) Simon J. S. Cameron et al.   PLoS One

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

(2014) Xiao-Yang Gao et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The pathogenicity of the Streptococcus genus

(2013) W. Krzyściak et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

A novel method for rapid detection of Streptococcus pneumoniae antigen in sputum and its application in adult respiratory tract infections

(2008) N. Ehara et al.   JOURNAL OF MEDICAL MICROBIOLOGY