2021
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley E, Auburn S, Awandare G, Ba H, Baraka V, Barry A, Bejon P, Bertin G, Boni M, Borrmann S, Bousema T, Branch O, Bull P, Busby G, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp A, Drakeley C, Drury E, Duffy P, Echeverry D, Egwang T, Erko B, Fairhurst R, Faiz A, Fanello C, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton W, Harrison G, Hart L, Henrichs C, Hien T, Hill C, Hodgson A, Hubbart C, Imwong M, Ishengoma D, Jackson S, Jacob C, Jeffery B, Jeffreys A, Johnson K, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski D, Kyaw M, Lim P, Lon C, Loua K, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu O, Montgomery J, Mueller I, Newton P, Nguyen T, Nguyen T, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier L, Ocholla H, Oduro A, Omedo I, Onyamboko M, Ouedraogo J, Oyebola K, Pearson R, Peshu N, Phyo A, Plowe C, Price R, Pukrittayakamee S, Randrianarivelojosia M, Rayner J, Ringwald P, Rockett K, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson V, Stalker J, Su X, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems T, Wendler J, White N, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research 2021, 6: 42. DOI: 10.12688/wellcomeopenres.16168.1.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsStrong geographic differentiationGenome variation dataHigh-quality genotypesGeographic differentiationGenome variationGenetic evidenceShort indelsEvolutionary processesStructural variantsMosquito stagesNumber variantsData-sharing networksNucleotide polymorphismsVariation dataWorldwide sampleAnalysis pipelineGenomic epidemiologyMarker of resistanceDrug resistanceSurveillance toolkitIndelsGenesLociVariants
2017
Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Gómez-Díaz E, Yerbanga R, Lefèvre T, Cohuet A, Rowley M, Ouedraogo J, Corces V. Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae. Scientific Reports 2017, 7: 40655. PMID: 28091569, PMCID: PMC5238449, DOI: 10.1038/srep40655.Peer-Reviewed Original ResearchConceptsAP2 transcription factorsVar genesTranscription factorsAntisense long non-coding RNAProtein-coding transcriptsSingle var geneLong non-coding RNAsVariant gene expressionNon-coding RNAsVar gene transcriptionChromatin statePhenotypic plasticityHistone modificationsMultigene familyEpigenetic regulationAntisense lncRNAsGene transcriptionAnopheles gambiaeGene expressionIntraerythrocytic cycleMosquito hostSporogonic developmentTranscriptionParasite developmentGenes
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 toolsGenesVariantsDeletionPolymorphismVarBFalciparum