Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

An Experimental Group A Streptococcus Vaccine That Reduces Pharyngitis and Tonsillitis in a Nonhuman Primate Model

(2019) Tania Rivera-Hernandez et al.   mBio

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

(2019) Kelly L. Wyres et al.   PLoS Genetics

pyseer: a comprehensive tool for microbial pangenome-wide association studies

(2018) John A Lees et al.   BIOINFORMATICS

Scarlet Fever Epidemic in China Caused by Streptococcus pyogenes Serotype M12: Epidemiologic and Molecular Analysis

(2018) Yuanhai You et al.   EBioMedicine

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

(2017) Laura S. Weyrich et al.   NATURE

Global, Regional, and National Burden of Rheumatic Heart Disease, 1990–2015

(2017) David A. Watkins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

(2017) Sopio Chochua et al.   mBio

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

(2017) Sophia David et al.   PLoS Genetics

Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing

(2017) Georgia Kapatai et al.   PeerJ

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

(2017) Jukka Corander et al.   Nature Ecology & Evolution

Combinatorial Synthetic Peptide Vaccine Strategy Protects against Hypervirulent CovR/S Mutant Streptococci

(2016) Manisha Pandey et al.   JOURNAL OF IMMUNOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

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

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

(2016) Chrispin Chaguza et al.   mBio

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

(2016) John A. Lees et al.   Nature Communications

Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps

(2016) Yun-Juan Bao et al.   Scientific Reports

Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections

(2016) Joe Ibrahim et al.   PLoS One

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus

(2015) Elizabeth M. Driebe et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

The Classical Lancefield Antigen of Group A Streptococcus Is a Virulence Determinant with Implications for Vaccine Design

(2014) Nina M. van Sorge et al.   Cell Host & Microbe

Disease Manifestations and Pathogenic Mechanisms of Group A Streptococcus

(2014) M. J. Walker et al.   CLINICAL MICROBIOLOGY REVIEWS

Deriving Group A Streptococcus Typing Information from Short-Read Whole-Genome Sequencing Data

(2014) T. B. T. Athey et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development

(2014) Martina Sanderson-Smith et al.   JOURNAL OF INFECTIOUS DISEASES

SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

(2014) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance

(2014) Mark R Davies et al.   NATURE GENETICS

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

(2014) W. Nasser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination

(2014) M. J. Bart et al.   mBio

Distribution of small native plasmids in Streptococcus pyogenes in India

(2013) René Bergmann et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration

(2013) Susanne C. Feil et al.   JOURNAL OF MOLECULAR BIOLOGY

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Conserved anchorless surface proteins as group A streptococcal vaccine candidates

(2012) Anna Henningham et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Multi High-Throughput Approach for Highly Selective Identification of Vaccine Candidates: the Group A Streptococcus Case

(2012) Giuliano Bensi et al.   MOLECULAR & CELLULAR PROTEOMICS

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

(2012) Miao He et al.   NATURE GENETICS

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

New 30-valent M protein-based vaccine evokes cross-opsonic antibodies against non-vaccine serotypes of group A streptococci

(2011) James B. Dale et al.   VACCINE

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Streptococcal bacteriocins and the case forStreptococcus salivariusas model oral probiotics

(2009) Philip A Wescombe et al.   Future Microbiology

Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 Å Crystal Structure of the Active Form of ScpA

(2009) Todd F. Kagawa et al.   JOURNAL OF MOLECULAR BIOLOGY

Global emm type distribution of group A streptococci: systematic review and implications for vaccine development

(2009) Andrew C Steer et al.   LANCET INFECTIOUS DISEASES

Plasmid-Borne erm(T) from Invasive, Macrolide-Resistant Streptococcus pyogenes Strains

(2008) R. L. Woodbury et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal