Dense genomic sampling identifies highways of pneumococcal recombination

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

High Rates of Pneumonia in Children under Two Years of Age in a South East Asian Refugee Population

(2013) Claudia Turner et al.   PLoS One

Fratricide Is Essential for Efficient Gene Transfer between Pneumococci in Biofilms

(2012) Hua Wei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Pre-Vaccination Nasopharyngeal Pneumococcal Carriage in a Nigerian Population: Epidemiology and Population Biology

(2012) Ifedayo M. O. Adetifa et al.   PLoS One

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

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

(2012) R. J. L. Willems et al.   mBio

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Population structure in the Neisseria, and the biological significance of fuzzy species

(2011) J. Corander et al.   Journal of the Royal Society Interface

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

High Levels of Recombination among Streptococcus pneumoniae Isolates from the Gambia

(2011) E. S. Donkor et al.   mBio

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete

(2010) William P. Hanage et al.   Epidemics

Generation of Genic Diversity among Streptococcus pneumoniae Strains via Horizontal Gene Transfer during a Chronic Polyclonal Pediatric Infection

(2010) N. Luisa Hiller et al.   PLoS Pathogens

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC

(2009) V. Eldholm et al.   MICROBIOLOGY-SGM

Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus

(2009) W. P. Hanage et al.   SCIENCE

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

(2009) Jing Tang et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

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