2024
Computational reassessment of RNA-seq data reveals key genes in active tuberculosis
Arya R, Shakya H, Chaurasia R, Kumar S, Vinetz J, Kim J. Computational reassessment of RNA-seq data reveals key genes in active tuberculosis. PLOS ONE 2024, 19: e0305582. PMID: 38935691, PMCID: PMC11210783, DOI: 10.1371/journal.pone.0305582.Peer-Reviewed Original ResearchConceptsMolecular Complex DetectionProtein-protein interactionsDeregulated genesGene OntologyRNA-seq dataGene Expression Omnibus (GEO) databaseIncreasing prevalence of multidrug-resistantGEO2R online toolPrevalence of multidrug resistancePathway enrichment analysisExpression levelsPatterns of variationGene expression levelsArea under curveInnate immune responseGene networksCore genesMicroarray datasetsSTRING databaseTranscript levelsEnrichment analysisGenesInterferon signalingInterferon-gamma signalingResponse to Mtb infection
2022
Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior
Alvarez M, Alonso D, Kadri S, Rufalco-Moutinho P, Bernardes I, de Mello A, Souto A, Carrasco-Escobar G, Moreno M, Gamboa D, Vinetz J, Conn J, Ribolla P. Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior. Parasites & Vectors 2022, 15: 106. PMID: 35346342, PMCID: PMC8961893, DOI: 10.1186/s13071-022-05219-5.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphism (SNP) markersGenome-wide studiesLow-coverage whole-genome sequencingGenomic sequencing dataMajor malaria vectorCircadian rhythm genesFemale timingPopulation stratification analysisWhole-genome sequencingMicrogeographic scaleSNP markersPolymorphism markersPopulation structureSequencing dataAssociation studiesInsecticide resistanceDusk/dawnRhythm genesGenotype imputationGenesFemale mosquitoesMalaria vectorsBlood mealGenetic association
2021
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare G, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, 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. PMID: 33824913, PMCID: PMC8008441, DOI: 10.12688/wellcomeopenres.16168.2.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 toolkitIndelsGenesLociVariantsAn 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
2001
Disruption of Plasmodium falciparumChitinase Markedly Impairs Parasite Invasion of Mosquito Midgut
Tsai Y, Hayward R, Langer R, Fidock D, Vinetz J. Disruption of Plasmodium falciparumChitinase Markedly Impairs Parasite Invasion of Mosquito Midgut. Infection And Immunity 2001, 69: 4048-4054. PMID: 11349075, PMCID: PMC98468, DOI: 10.1128/iai.69.6.4048-4054.2001.Peer-Reviewed Original ResearchConceptsMosquito midgutChitinase geneAvian malaria parasite Plasmodium gallinaceumMalaria parasite Plasmodium gallinaceumMutant ookinetesGenome databasePeritrophic matrixGene productsIntracellular traffickingBp upstreamOokinete invasionStop codonParasite invasionChitinolytic activityPfCHT1MidgutOokinetesOokinete formationGenesConfocal microscopyBlood mealApical endPlasmodium gallinaceumP. falciparumInvasion
1999
Chitinases of human parasites and their implications as antiparasitic targets.
Shahabuddin M, Vinetz J. Chitinases of human parasites and their implications as antiparasitic targets. EXS 1999, 87: 223-34. PMID: 10906963, DOI: 10.1007/978-3-0348-8757-1_16.Peer-Reviewed Original ResearchConceptsDevelopmental stage-specific mannerStage-specific mannerAmino acid sequenceChitin-containing structuresPathogenic parasitesAnimal diseasesAntiparasitic targetsChitinase geneInsect vectorsAcid sequenceSuccessful infectionChitinasesHuman parasitesParasitesNumber of humanGenesLife cycleChitinAnimal bodyPathogensRecent studiesHarsh conditionsVertebratesChitinaseOrganisms