Featured Publications
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation
Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nature Communications 2020, 11: 3442. PMID: 32651390, PMCID: PMC7351774, DOI: 10.1038/s41467-020-17327-w.Peer-Reviewed Original ResearchConceptsNatural colonisationHost microevolutionNucleotide substitution ratesWhole-genome sequencingGenomic evolutionNeutral evolutionGenetic diversityHomologous recombinationParallel evolutionGenomic changesAdhesion genesSubstitution ratesHuman-adapted pathogenMicroevolutionStrain variantsColonisationImmune evasionStreptococcus pneumoniaeAntibiotic resistanceGenesEvolutionSequencingDiversityNasopharyngeal carriageBacteria
2021
RCandy: an R package for visualizing homologous recombinations in bacterial genomes
Chaguza C, Tonkin-Hill G, Lo S, Hadfield J, Croucher N, Harris S, Bentley S. RCandy: an R package for visualizing homologous recombinations in bacterial genomes. Bioinformatics 2021, 38: 1450-1451. PMID: 34864895, PMCID: PMC8826011, DOI: 10.1093/bioinformatics/btab814.Peer-Reviewed Original ResearchConceptsBacterial genomesHomologous recombinationRecombination eventsImportant evolutionary processPlatform-independent R packageGenomic sequence diversityValuable biological insightsSuch recombination eventsR packageGenomic regionsSequence diversityBiological insightsEvolutionary processesGenomeSupplementary dataRecombinationMIT licenseProkaryotesBioinformaticsDiversityBacteriaMacOSXAdaptation