Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

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

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

(2016) Chrispin Chaguza et al.   mBio

Pneumococcal Capsules and Their Types: Past, Present, and Future

(2015) K. Aaron Geno et al.   CLINICAL MICROBIOLOGY REVIEWS

Effect of Serotype on Pneumococcal Competition in a Mouse Colonization Model

(2015) Krzysztof Trzciński et al.   mBio

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Selective and Genetic Constraints on Pneumococcal Serotype Switching

(2015) Nicholas J. Croucher et al.   PLoS Genetics

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

(2015) Nicholas J. Croucher et al.   Scientific Data

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

(2014) Nicholas J Croucher et al.   BMC BIOLOGY

A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence

(2014) Thierry O Schaffner et al.   BMC MICROBIOLOGY

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

(2014) Nicholas J. Croucher et al.   Genome Biology and Evolution

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

Population-Based Analysis of Invasive Nontypeable Pneumococci Reveals That Most Have Defective Capsule Synthesis Genes

(2014) In Ho Park et al.   PLoS One

Parallel Evolution of Streptococcus pneumoniae and Streptococcus mitis to Pathogenic and Mutualistic Lifestyles

(2014) M. Kilian et al.   mBio

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

(2014) Rafal Mostowy et al.   PLoS Genetics

Inference of the Properties of the Recombination Process from Whole Bacterial Genomes

(2013) M. Azim Ansari et al.   GENETICS

Discovery ofStreptococcus pneumoniaeSerotype 6 Variants with Glycosyltransferases Synthesizing Two Differing Repeating Units

(2013) Melissa B. Oliver et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates

(2012) S. J. Salter et al.   MICROBIOLOGY-SGM

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

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

(2012) E. Bapteste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) S. Cobey et al.   SCIENCE

Sequence Diversity within the Capsular Genes of Streptococcus pneumoniae Serogroup 6 and 19

(2011) Karin Elberse et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

Capsules ofStreptococcus pneumoniaeand Other Bacteria: Paradigms for Polysaccharide Biosynthesis and Regulation

(2010) Janet Yother   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A report of Streptococcus pneumoniae serotype 6D in Europe

(2010) M. H. Nahm et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Evolution of the capsular gene locus of Streptococcus pneumoniae serogroup 6

(2010) P. E. Bratcher et al.   MICROBIOLOGY-SGM

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Streptococcus pneumoniae Capsule Inhibits Complement Activity and Neutrophil Phagocytosis by Multiple Mechanisms

(2009) C. Hyams et al.   INFECTION AND IMMUNITY

Evolution of the Capsular Regulatory Genes inStreptococcus pneumoniae

(2009) Sirkka‐Liisa Varvio et al.   JOURNAL OF INFECTIOUS DISEASES

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

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

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

The rise and fall of bacterial clones: Streptococcus pneumoniae

(2008) Birgitta Henriques-Normark et al.   NATURE REVIEWS MICROBIOLOGY

The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease

(2008) Aras Kadioglu et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives

(2008) Mogens Kilian et al.   PLoS One