Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

(2021) Chang Liu et al.   Microbiome

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Structural basis of transcription-translation coupling

(2020) Chengyuan Wang et al.   SCIENCE

The biogeography of Streptomyces in New Zealand enabled by high‐throughput sequencing of genus‐specific rpoB amplicons

(2020) S. A. Higgins et al.   ENVIRONMENTAL MICROBIOLOGY

Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core and pan genome analyses

(2019) Irina M Velsko et al.   Genome Biology and Evolution

The multiple flavors of GoU pairs in RNA

(2019) Eric Westhof et al.   JOURNAL OF MOLECULAR RECOGNITION

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

(2019) Jean-Claude Ogier et al.   BMC MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function

(2019) Smita P. Pilla et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred

(2018) Apuã C. M. Paquola et al.   JOURNAL OF MOLECULAR EVOLUTION

Translation: The Universal Structural Core of Life

(2018) Chad R Bernier et al.   MOLECULAR BIOLOGY AND EVOLUTION

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort

(2018) Shantelle Claassen-Weitz et al.   Scientific Reports

Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA

(2018) Romilio T. Espejo et al.   Frontiers in Microbiology

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach

(2018) Maxwell J Farrell et al.   GENOME

Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

(2017) Saurav Mallik et al.   Genome Biology and Evolution

Architecture of a transcribing-translating expressome

(2017) R. Kohler et al.   SCIENCE

Structure of RNA polymerase bound to ribosomal 30S subunit

(2017) Gabriel Demo et al.   eLife

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

(2017) Baknoon Ham et al.   Frontiers in Microbiology

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

Legionella clemsonensissp. nov.: a green fluorescingLegionellastrain from a patient with pneumonia

(2016) Allison Palmer et al.   MICROBIOLOGY AND IMMUNOLOGY

Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene

(2015) Ren-Mao Tian et al.   Genome Biology and Evolution

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

(2015) Abiyad Baig et al.   Frontiers in Microbiology

Comparative Genomic Analysis of 45 Type Strains of the Genus Bifidobacterium: A Snapshot of Its Genetic Diversity and Evolution

(2015) Zhihong Sun et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

(2014) Qiyun Zhu et al.   BMC GENOMICS

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

(2014) Reuben W. Nowell et al.   Genome Biology and Evolution

Presence of Potential Toxin-Producing Cyanobacteria in an Oligo-Mesotrophic Lake in Baltic Lake District, Germany: An Ecological, Genetic and Toxicological Survey

(2014) Pawan Dadheech et al.   Toxins

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The dynamics of alternative pathways to compensatory substitution

(2013) Chris A Nasrallah   BMC BIOINFORMATICS

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

(2012) Michiel Vos et al.   PLoS One

Ribosomal History Reveals Origins of Modern Protein Synthesis

(2012) Ajith Harish et al.   PLoS One

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

(2010) A. Y. Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics

(2010) Luis Alcaraz et al.   BMC GENOMICS

Genetic diversity of elite rhizobial strains of subtropical and tropical legumes based on the 16S rRNA and glnII genes

(2010) Ilmara Varotto Roma Neto et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

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

Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis

(2009) William J. Lane et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Evolution of Multisubunit RNA Polymerases: Sequence Analysis

(2009) William J. Lane et al.   JOURNAL OF MOLECULAR BIOLOGY

Analysis of RNA Polymerase Beta Subunit (rpoB) Gene Sequences for the Discriminative Power of Marine Vibrio Species

(2009) Jang-Seu Ki et al.   MICROBIAL ECOLOGY

Estimation of prediction error by using K-fold cross-validation

(2009) Tadayoshi Fushiki   STATISTICS AND COMPUTING

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY