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

Genomic analysis of extra-intestinal pathogenic Escherichia coli urosepsis

(2013) A. McNally et al.   CLINICAL MICROBIOLOGY AND INFECTION

Functional Analysis of Pneumococcal Drug Efflux Pumps Associates the MATE DinF Transporter with Quinolone Susceptibility

(2012) Nadia Tocci et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution View of Genome-Wide Pneumococcal Transformation

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

Identification, variation and transcription of pneumococcal repeat sequences

(2011) Nicholas J Croucher et al.   BMC GENOMICS

Death or survival from invasive pneumococcal disease in Scotland: associations with serogroups and multilocus sequence types

(2011) D. Inverarity et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

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

Molecular epidemiology and genetic diversity of pneumococcal carriage among children in Beni State, Bolivia

(2011) D. Inverarity et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE

Overexpression ofpatAandpatB, Which Encode ABC Transporters, Is Associated with Fluoroquinolone Resistance in Clinical Isolates ofStreptococcus pneumoniae

(2010) Mark I. Garvey et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Fluoroquinolones induce the expression of patA and patB, which encode ABC efflux pumps in Streptococcus pneumoniae

(2010) Farid El Garch et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Immunogenicity and Safety of 13-Valent Pneumococcal Conjugate Vaccine in Infants and Toddlers

(2010) S. H. Yeh et al.   PEDIATRICS

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections

(2010) Maxime Levert et al.   PLoS Pathogens

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders 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

Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance

(2009) J. Feng et al.   GENOME RESEARCH

Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

(2009) P. Romero et al.   JOURNAL OF BACTERIOLOGY

A simple method for directional transcriptome sequencing using Illumina technology

(2009) N. J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Pneumococcal Serotypes and Mortality following Invasive Pneumococcal Disease: A Population-Based Cohort Study

(2009) Zitta B. Harboe et al.   PLOS MEDICINE

The Efflux Pump Inhibitor Reserpine Selects Multidrug-Resistant Streptococcus pneumoniae Strains That Overexpress the ABC Transporters PatA and PatB

(2008) M. I. Garvey et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae

(2008) M. Brochet et al.   JOURNAL OF BACTERIOLOGY

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

Transmission of Streptococcus pneumoniae in an urban slum community

(2008) Joice Neves Reis et al.   JOURNAL OF INFECTION

Molecular characteristics of serotype 3 Streptococcus pneumoniae isolates among community-acquired pneumonia patients in Japan

(2008) Rie Isozumi et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS