2014
A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
Preston M, Campino S, Assefa S, Echeverry D, Ocholla H, Amambua-Ngwa A, Stewart L, Conway D, Borrmann S, Michon P, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Pain A, Bousema T, Drakeley C, Fairhurst R, Sutherland C, Roper C, Clark T. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature Communications 2014, 5: 4052. PMID: 24923250, PMCID: PMC4082634, DOI: 10.1038/ncomms5052.Peer-Reviewed Original ResearchMeSH KeywordsGenome, ProtozoanGeographyHumansMalaria, FalciparumPhylogenyPlasmodium falciparumPolymorphism, Single NucleotideConceptsMajor public health problemValuable public health toolSingle nucleotide polymorphismsPublic health problemDrug-resistant parasitesPublic health toolPlasmodium falciparum strainsGlobal eradication campaignHealth problemsFalciparum strainsCase managementHealth toolsPlasmodium falciparumParasite migrationElimination areaEradication campaignApicoplast genomeParasitesPolymorphismInfectionMalariaInternational air travelFalciparum
2013
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
Preston M, Assefa S, Ocholla H, Sutherland C, Borrmann S, Nzila A, Michon P, Hien T, Bousema T, Drakeley C, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Fairhurst R, Conway D, Roper C, Clark T. PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation. The Journal Of Infectious Diseases 2013, 209: 1808-1815. PMID: 24338354, PMCID: PMC4017360, DOI: 10.1093/infdis/jit812.Peer-Reviewed Original ResearchConceptsGenomic variationSingle nucleotide polymorphismsHigh-quality single nucleotide polymorphismsHigh-throughput sequencingInter-population differencesGenetic barcodesPlasmodium biologyGenetic variabilityGenomic dataInformative variantsDrug resistanceParasite populationsDifferential phenotypesLaboratory strainsMalaria parasitesNovel mutationsGlobal public health challengeNew insightsPf isolatesMalaria-endemic regionsPublic health challengePlasmodium falciparum speciesMedicine applicationsWeb-based resourcesClinical studies
2012
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
Preston M, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo J, Nosten F, Anderson T, Clark T. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics 2012, 28: 2983-2985. PMID: 22976080, PMCID: PMC3496337, DOI: 10.1093/bioinformatics/bts557.Peer-Reviewed Original ResearchConceptsNext-generation sequencing dataUser-defined groupsGenomic regionsVariant call format filesSingle nucleotide polymorphismsDrug resistance genesSequence dataSequencing dataStructural variantsImportant antigenicSequence file formatsInformative markersPlasmodium falciparumDifferent continentsFile formatFormat fileUser manualReal timeAnalysis toolsGenesVariantsDeletionPolymorphismVarBFalciparumAnalysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O’Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo J, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara S, Marsh K, Jiang H, Su X, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White N, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail M, Turner D, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan J, Ferdig M, Amambua-Ngwa A, Conway D, Takala-Harrison S, Plowe C, Rayner J, Rockett K, Clark T, Newbold C, Berriman M, MacInnis B, Kwiatkowski D. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012, 487: 375-379. PMID: 22722859, PMCID: PMC3738909, DOI: 10.1038/nature11174.Peer-Reviewed Original Research