Related references
Note: Only part of the references are listed.Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
Alessandra Lochen et al.
PLOS COMPUTATIONAL BIOLOGY (2022)
Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Anna Both et al.
PLOS PATHOGENS (2021)
Pneumococcal Meningitis Outbreaks in Africa, 2000-2018: Systematic Literature Review and Meningitis Surveillance Database Analyses
Kat Franklin et al.
JOURNAL OF INFECTIOUS DISEASES (2021)
A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus
Feroze Ganaie et al.
MBIO (2020)
Increased pathogenicity of pneumococcal serotype 1 is driven by rapid autolysis and release of pneumolysin
Laura C. Jacques et al.
NATURE COMMUNICATIONS (2020)
High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi
Todd D. Swarthout et al.
NATURE COMMUNICATIONS (2020)
Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae
Kevin C. Ma et al.
NATURE COMMUNICATIONS (2020)
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism
Chrispin Chaguza et al.
COMMUNICATIONS BIOLOGY (2020)
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Guillaume Holley et al.
GENOME BIOLOGY (2020)
Producing polished prokaryotic pangenomes with the Panaroo pipeline
Gerry Tonkin-Hill et al.
GENOME BIOLOGY (2020)
Persistence of Nasopharyngeal Pneumococcal Vaccine Serotypes and Increase of Nonvaccine Serotypes Among Vaccinated Infants and Their Mothers 5 Years After Introduction of Pneumococcal Conjugate Vaccine 13 in The Gambia
Effua Usuf et al.
CLINICAL INFECTIOUS DISEASES (2019)
Fast and flexible bacterial genomic epidemiology with PopPUNK
John A. Lees et al.
GENOME RESEARCH (2019)
y Fast hierarchical Bayesian analysis of population structure
Gerry Tonkin-Hill et al.
NUCLEIC ACIDS RESEARCH (2019)
Panton-Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS
Bernadette C. Young et al.
ELIFE (2019)
International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact
Rebecca A. Gladstone et al.
EBIOMEDICINE (2019)
The relative invasive disease potential of Streptococcus pneumoniae among children after PCV introduction: A systematic review and meta-analysis
Evelyn Balsells et al.
JOURNAL OF INFECTION (2018)
Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths
D. M. Leigh et al.
MOLECULAR ECOLOGY RESOURCES (2018)
Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis
Francesc Coll et al.
NATURE GENETICS (2018)
Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15
Brian Wahl et al.
LANCET GLOBAL HEALTH (2018)
Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis
Guillaume Meric et al.
NATURE COMMUNICATIONS (2018)
Microbial genome-wide association studies: lessons from human GWAS
Robert A. Power et al.
NATURE REVIEWS GENETICS (2017)
Comparative Genomic Analysis and In Vivo Modeling of Streptococcus pneumoniae ST3081 and ST618 Isolates Reveal Key Genetic and Phenotypic Differences Contributing to Clonal Replacement of Serotype 1 in The Gambia
Laura Bricio-Moreno et al.
JOURNAL OF INFECTIOUS DISEASES (2017)
Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
John A. Lees et al.
ELIFE (2017)
An outbreak of pneumococcal meningitis among older children (≥ 5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana
Brenda Anna Kwambana-Adams et al.
BMC INFECTIOUS DISEASES (2016)
Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013
Mignon du Plessis et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2016)
Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule
Chrispin Chaguza et al.
MBIO (2016)
phylosignal: an R package to measure, test, and explore the phylogenetic signal
Francois Keck et al.
ECOLOGY AND EVOLUTION (2016)
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Wei Shen et al.
PLOS ONE (2016)
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Ola Brynildsrud et al.
GENOME BIOLOGY (2016)
limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie et al.
NUCLEIC ACIDS RESEARCH (2015)
Pneumococcal carriage in rural Gambia prior to the introduction of pneumococcal conjugate vaccine: a population-based survey
Effua Usuf et al.
TROPICAL MEDICINE & INTERNATIONAL HEALTH (2015)
Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia
Anna Roca et al.
VACCINE (2015)
Temporal changes in nasopharyngeal carriage of Streptococcus pneumoniae serotype 1 genotypes in healthy Gambians before and after the 7-valent pneumococcal conjugate vaccine
Chinelo Ebruke et al.
PEERJ (2015)
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Nicholas J. Croucher et al.
NUCLEIC ACIDS RESEARCH (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
Matthew W. Pennell et al.
BIOINFORMATICS (2014)
Predicting the virulence of MRSA from its genome sequence
Maisem Laabei et al.
GENOME RESEARCH (2014)
Dense genomic sampling identifies highways of pneumococcal recombination
Claire Chewapreecha et al.
NATURE GENETICS (2014)
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
Timothy D. Read et al.
GENOME MEDICINE (2014)
Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes
Claire Chewapreecha et al.
PLOS GENETICS (2014)
Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick E. Wood et al.
GENOME BIOLOGY (2014)
Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
Samuel K. Sheppard et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
The Pneumococcus: Epidemiology, Microbiology, and Pathogenesis
Birgitta Henriques-Normark et al.
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2013)
The fundamental link between pneumococcal carriage and disease
Birgit Simell et al.
EXPERT REVIEW OF VACCINES (2012)
What is different about serotype 1 pneumococci?
Neil D. Ritchie et al.
FUTURE MICROBIOLOGY (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
Rates of Acquisition and Clearance of Pneumococcal Serotypes in the Nasopharynges of Children in Kilifi District, Kenya
Osman Abdullahi et al.
JOURNAL OF INFECTIOUS DISEASES (2012)
Genome-wide efficient mixed-model analysis for association studies
Xiang Zhou et al.
NATURE GENETICS (2012)
Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach
Dean B. Everett et al.
PLOS ONE (2012)
phytools: an R package for phylogenetic comparative biology (and other things)
Liam J. Revell
METHODS IN ECOLOGY AND EVOLUTION (2012)
The variant call format and VCFtools
Petr Danecek et al.
BIOINFORMATICS (2011)
FaST linear mixed models for genome-wide association studies
Christoph Lippert et al.
NATURE METHODS (2011)
Effects of Community-Wide Vaccination with PCV-7 on Pneumococcal Nasopharyngeal Carriage in The Gambia: A Cluster-Randomized Trial
Anna Roca et al.
PLOS MEDICINE (2011)
Molecular epidemiology of a Streptococcus pneumoniae serotype 1 outbreak in a Tunisian jail
Emna Mehiri-Zghal et al.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2010)
Systematic Evaluation of Serotypes Causing Invasive Pneumococcal Disease among Children Under Five: The Pneumococcal Global Serotype Project
Hope L. Johnson et al.
PLOS MEDICINE (2010)
Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: Expansion of ST217 hypervirulent clonal complex in West Africa
Martin Antonio et al.
BMC MICROBIOLOGY (2008)
A generic mechanism in Neisseria meningitidis for enhanced resistance against bactericidal antibodies
Maria Jose Uria et al.
JOURNAL OF EXPERIMENTAL MEDICINE (2008)
The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease
Aras Kadioglu et al.
NATURE REVIEWS MICROBIOLOGY (2008)
PLINK: A tool set for whole-genome association and population-based linkage analyses
Shaun Purcell et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2007)
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Alexandros Stamatakis
BIOINFORMATICS (2006)
Nasopharyngeal carriage of Streptococcus pneumoniae in Gambian villagers
Philip C. Hill et al.
CLINICAL INFECTIOUS DISEASES (2006)
ACT: the Artemis comparison tool
TJ Carver et al.
BIOINFORMATICS (2005)
An outbreak of serotype 1 Streptococcus pneumoniae meningitis in northern Ghana with features that are characteristic of Neisseria meningitidis meningitis epidemics
J Leimkugel et al.
JOURNAL OF INFECTIOUS DISEASES (2005)
Streptococcus pneumoniae colonisation:: the key to pneumococcal disease
D Bogaert et al.
LANCET INFECTIOUS DISEASES (2004)
APE: Analyses of Phylogenetics and Evolution in R language
E Paradis et al.
BIOINFORMATICS (2004)
IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks
CY Soto et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2004)
Geographic distribution and clonal diversity of Streptococcus pneumoniae serotype 1 isolates
AB Brueggemann et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2003)
Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential
AB Brueggemann et al.
JOURNAL OF INFECTIOUS DISEASES (2003)
Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
H Tettelin et al.
SCIENCE (2001)