The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

(2017) Nicholas J. Croucher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Pneumococcal protein antigen serology varies with age and may predict antigenic profile of colonizing isolates

(2016) T Azarian et al.   JOURNAL OF INFECTIOUS DISEASES

Whole genome sequencing ofStreptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline

(2016) Georgia Kapatai et al.   PeerJ

Effect of the 13-valent pneumococcal conjugate vaccine on invasive pneumococcal disease in England and Wales 4 years after its introduction: an observational cohort study

(2015) Pauline A Waight et al.   LANCET INFECTIOUS DISEASES

Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae

(2015) Eleanor R. Watkins et al.   PLoS Pathogens

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution

(2013) Guy Baele et al.   BMC BIOINFORMATICS

Current status and perspectives on protein-based pneumococcal vaccines

(2013) Michelle Darrieux et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

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

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

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Niche and Neutral Effects of Acquired Immunity Permit Coexistence of Pneumococcal Serotypes

(2012) S. Cobey et al.   SCIENCE

A High-Resolution View of Genome-Wide Pneumococcal Transformation

(2012) Nicholas J. Croucher et al.   PLoS Pathogens

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Impact of More Than a Decade of Pneumococcal Conjugate Vaccine Use on Carriage and Invasive Potential in Native American Communities

(2011) Jennifer R. Scott et al.   JOURNAL OF INFECTIOUS DISEASES

Serotype replacement in disease after pneumococcal vaccination

(2011) Daniel M Weinberger et al.   LANCET

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Invasive Pneumococcal Disease a Decade after Pneumococcal Conjugate Vaccine Use in an American Indian Population at High Risk for Disease

(2010) Robert Weatherholtz et al.   CLINICAL INFECTIOUS DISEASES

Testing Spatiotemporal Hypothesis of Bacterial Evolution Using Methicillin-Resistant Staphylococcus aureus ST239 Genome-wide Data within a Bayesian Framework

(2010) R. R. Gray et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nasopharyngeal Carriage of Streptococcus pneumoniae in Navajo and White Mountain Apache Children Before the Introduction of Pneumococcal Conjugate Vaccine

(2010) Eugene V. Millar et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Carried Pneumococci in Massachusetts Children

(2010) William P. Hanage et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

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

(2010) Claudio Donati et al.   GENOME BIOLOGY

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sustained Reductions in Invasive Pneumococcal Disease in the Era of Conjugate Vaccine

(2009) Tamara Pilishvili et al.   JOURNAL OF INFECTIOUS DISEASES

Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence

(2009) Daniel M. Weinberger et al.   PLoS Pathogens

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone Streptococcus pneumoniaeSpain23F ST81

(2008) N. J. Croucher et al.   JOURNAL OF BACTERIOLOGY