Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

(2013) Nicholas J. Croucher et al.   PLoS Genetics

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

A Longitudinal Study of Streptococcus pneumoniae Carriage in a Cohort of Infants and Their Mothers on the Thailand-Myanmar Border

(2012) Paul Turner et al.   PLoS One

A High-Resolution View of Genome-Wide Pneumococcal Transformation

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

Clonal Evolution Leading to Maintenance of Antibiotic Resistance Rates among Colonizing Pneumococci in the PCV7 Era in Portugal

(2011) A. S. Simoes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Shifting Genetic Structure of Invasive Serotype 19A Pneumococci in the United States

(2011) Bernard W. Beall et al.   JOURNAL OF INFECTIOUS DISEASES

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Clonal replacement among 19A Streptococcus pneumoniae in Massachusetts, prior to 13 valent conjugate vaccination

(2011) W.P. Hanage et al.   VACCINE

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumoniae

(2009) Dylan R Pillai et al.   BMC GENOMICS

Changes of serotype and genotype in Streptococcus pneumoniae isolates from a Korean hospital in 2007

(2009) Jae-Hoon Song et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates

(2009) Katherine L O'Brien et al.   LANCET

Continued Impact of Pneumococcal Conjugate Vaccine on Carriage in Young Children

(2009) S. S. Huang et al.   PEDIATRICS

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

(2009) Jing Tang et al.   PLoS Computational Biology

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

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

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

Population Snapshot of Streptococcus pneumoniae Serotype 19A Isolates before and after Introduction of Seven-Valent Pneumococcal Vaccination for French Children

(2008) F. Mahjoub-Messai et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Population Snapshot of EmergentStreptococcus pneumoniaeSerotype 19A in the United States, 2005

(2008) Matthew R. Moore et al.   JOURNAL OF INFECTIOUS DISEASES