2024
Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US
Lopes R, Pham K, Klaassen F, Chitwood M, Hahn A, Redmond S, Swartwood N, Salomon J, Menzies N, Cohen T, Grubaugh N. Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US. Cell Reports 2024, 43: 114451. PMID: 38970788, DOI: 10.1016/j.celrep.2024.114451.Peer-Reviewed Original Research
2021
Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements
Crava C, Varghese F, Pischedda E, Halbach R, Palatini U, Marconcini M, Gasmi L, Redmond S, Afrane Y, Ayala D, Paupy C, Carballar‐Lejarazu R, Miesen P, van Rij R, Bonizzoni M. Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements. Molecular Ecology 2021, 30: 1594-1611. PMID: 33432714, PMCID: PMC8048955, DOI: 10.1111/mec.15798.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsArboviral vector Aedes aegyptiEndogenous viral elementsPopulation genomicsGenomic architectureViral elementsVector Aedes aegyptiPiRNA-mediated silencingNonretroviral RNA virusesGenome-wide screenHorizontal gene transferSequence-specific mechanismWild-caught mosquitoesA. aegyptiEndogenization eventsAedes aegyptiAdaptive evolutionPiRNA clustersEukaryotic cellsGermline cellsTransposable elementsGeographical populationsHost genomeHost functionsCognate virus
2020
Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti
Redmond S, Sharma A, Sharakhov I, Tu Z, Sharakhova M, Neafsey D. Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti. BMC Biology 2020, 18: 26. PMID: 32164699, PMCID: PMC7068900, DOI: 10.1186/s12915-020-0757-y.Peer-Reviewed Original ResearchConceptsChromosomal inversionsFuture population genetic studiesRelated sister speciesPolytene chromosome analysisArboviral vector Aedes aegyptiLinked-read sequencingPopulation genetic studiesChromosome banding patternsHost-feeding preferencesAedes aegyptiPhenotypic divergenceSister speciesSecondary contactChromosomal diversityDeep Illumina sequencingDipteran insectsRepetitive genomesIllumina sequencingFeeding preferencesGenomic rearrangementsHost preferenceSequencing dataVector Aedes aegyptiGenetic studiesSubspecies
2019
In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex
Love R, Redmond S, Pombi M, Caputo B, Petrarca V, della Torre A, Consortium T, Besansky N. In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex. G3: Genes, Genomes, Genetics 2019, 9: 3249-3262. PMID: 31391198, PMCID: PMC6778791, DOI: 10.1534/g3.119.400445.Peer-Reviewed Original ResearchConceptsInversion genotypesSingle nucleotide polymorphismsInversion polymorphismTag single nucleotide polymorphismsChromosomal inversion polymorphismTag SNP genotypesAnopheles gambiae complexParacentric inversion polymorphismEnvironmental heterogeneityChromosomal rearrangementsImportant phenotypesMalaria mosquitoesSilico karyotypingNatural variationGambiae complexMosquito speciesTraditional cytogeneticsCytogenetic methodsBiallelic genotypesSignificant vectorSNP genotypesGonotrophic stagesNucleotide polymorphismsGenomeHuman malariaA chromosome-scale assembly of the major African malaria vector Anopheles funestus
Ghurye J, Koren S, Small S, Redmond S, Howell P, Phillippy A, Besansky N. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. GigaScience 2019, 8: giz063. PMID: 31157884, PMCID: PMC6545970, DOI: 10.1093/gigascience/giz063.Peer-Reviewed Original ResearchConceptsReference genomeHigh-quality reference genomeCurrent reference assemblyHaploid genome sizeMajor African malaria vector Anopheles funestusN50 scaffold sizeChromosome-scale assemblyReference genome assemblyN50 contig sizeChromosome-scale scaffoldsMalaria vector Anopheles funestusAfrican malaria vector Anopheles funestusMbp of sequenceSingle-molecule sequencingPrimary assemblyAnopheles funestusHi-C dataImportant disease vectorChromosome scaffoldingGenome sizeGenome assemblyContig sizeReference assemblyGenomic variationAssociation of phenotypic
2018
Improved reference genome of Aedes aegypti informs arbovirus vector control
Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018, 563: 501-507. PMID: 30429615, PMCID: PMC6421076, DOI: 10.1038/s41586-018-0692-z.Peer-Reviewed Original ResearchMeSH KeywordsAedesAnimalsArbovirus InfectionsArbovirusesDengue VirusDNA Copy Number VariationsFemaleGenetic VariationGenetics, PopulationGenome, InsectGenomicsGlutathione TransferaseInsect ControlInsecticide ResistanceMaleMolecular Sequence AnnotationMosquito VectorsMultigene FamilyPyrethrinsReference StandardsSex Determination ProcessesConceptsGenome assemblySex-determining M locusHigh-quality genome assemblyInsecticide resistancePopulation genomic analysesQuantitative trait lociGlutathione S-transferase geneEgg-laying sitesNew biological insightsDangerous viral pathogensCopy number variationsDengue vector competenceCytogenetic mapTrait lociReference genomeGenomic analysisBiological insightsDisease vectorsM locusFemale Aedes aegypti mosquitoesIonotropic receptorsVector competenceHuman hostAedes aegypti mosquitoesLociMutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility
Demas A, Sharma A, Wong W, Early A, Redmond S, Bopp S, Neafsey D, Volkman S, Hartl D, Wirth D. Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: 12799-12804. PMID: 30420498, PMCID: PMC6294886, DOI: 10.1073/pnas.1812317115.Peer-Reviewed Original ResearchConceptsCRISPR/Cas9-mediated gene editingDomain protein familyWhole genome sequence analysisProtein familySecond geneFunctional validationMutant formsDifferent genesMolecular mechanismsParental linesSequence analysisType of resistanceGene editingAfrican parasitesArtemisinin susceptibilityMechanisms of resistanceGenesGenetic determinantsParental parasitesMutationsSurvival assaysIndependent selectionParasite clonesProteinActive formDe Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE. De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria. Molecular Biology And Evolution 2018, 35: 1678-1689. PMID: 29722884, PMCID: PMC5995194, DOI: 10.1093/molbev/msy059.Peer-Reviewed Original ResearchConceptsDe novo mutationsEvolutionary ratesSlow evolutionary rateNovo mutationsComplex life cycleSlow generation timeLow-complexity regionsGenomic regionsLarge genomesGenomic epidemiology approachReintroduction scenariosCombination of sequencingP. falciparumViral speciesMutation rateClonal lineagesGenomeMutation studiesLibrary preparationIdentical parasitesGeneration timeBacterial pathogensMalaria parasitesMutationsGenomic epidemiology
2017
Genetic diversity of the African malaria vector Anopheles gambiae
Miles A, Harding N, Bottà G, Clarkson C, Antão T, Kozak K, Schrider D, Kern A, Redmond S, Sharakhov I, Pearson R, Bergey C, Fontaine M, Donnelly M, Lawniczak M, Kwiatkowski D, Donnelly M, Ayala D, Besansky N, Burt A, Caputo B, della Torre A, Fontaine M, Godfray H, Hahn M, Kern A, Kwiatkowski D, Lawniczak M, Midega J, Neafsey D, O’Loughlin S, Pinto J, Riehle M, Sharakhov I, Vernick K, Weetman D, Wilding C, White B, Troco A, Pinto J, Diabaté A, O’Loughlin S, Burt A, Costantini C, Rohatgi K, Besansky N, Elissa N, Pinto J, Coulibaly B, Riehle M, Vernick K, Pinto J, Dinis J, Midega J, Mbogo C, Bejon P, Wilding C, Weetman D, Mawejje H, Donnelly M, Weetman D, Wilding C, Donnelly M, Stalker J, Rockett K, Drury E, Mead D, Jeffreys A, Hubbart C, Rowlands K, Isaacs A, Jyothi D, Malangone C, Vauterin P, Jeffery B, Wright I, Hart L, Kluczyński K, Cornelius V, MacInnis B, Henrichs C, Giacomantonio R, Kwiatkowski D. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017, 552: 96-100. PMID: 29186111, PMCID: PMC6026373, DOI: 10.1038/nature24995.Peer-Reviewed Original Research
2016
Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
Oyola S, Ariani C, Hamilton W, Kekre M, Amenga-Etego L, Ghansah A, Rutledge G, Redmond S, Manske M, Jyothi D, Jacob C, Otto T, Rockett K, Newbold C, Berriman M, Kwiatkowski D. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria Journal 2016, 15: 597. PMID: 27998271, PMCID: PMC5175302, DOI: 10.1186/s12936-016-1641-7.Peer-Reviewed Original ResearchConceptsVenous bloodSelective whole genome amplificationMalaria patientsDBS samplesBlood spotsPlasmodium falciparumClinical samplesSymptomatic malaria patientsHigh quality clinical samplesDried Blood SpotsP. falciparum DNAMalaria parasite Plasmodium falciparumHead comparisonParasite Plasmodium falciparumDrug resistance lociHealthcare applicationsPatientsWhole-genome sequencingGenome amplificationDBS extractsSNP concordanceWhole genome amplificationFalciparumCurrent dataScalable wayGenomic Dark Matter Illuminated: Anopheles Y Chromosomes
Redmond S, Neafsey D. Genomic Dark Matter Illuminated: Anopheles Y Chromosomes. Trends In Parasitology 2016, 32: 585-587. PMID: 27263828, DOI: 10.1016/j.pt.2016.05.008.Commentaries, Editorials and Letters
2015
Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae
Redmond S, Eiglmeier K, Mitri C, Markianos K, Guelbeogo W, Gneme A, Isaacs A, Coulibaly B, Brito-Fravallo E, Maslen G, Mead D, Niare O, Traore S, Sagnon N, Kwiatkowski D, Riehle M, Vernick K. Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae. BMC Genomics 2015, 16: 779. PMID: 26462916, PMCID: PMC4603968, DOI: 10.1186/s12864-015-2009-z.Peer-Reviewed Original ResearchConceptsGenetic mappingFounder coloniesHigh nucleotide diversityNon-model genomesLow linkage disequilibriumPhenotype-genotype mappingPopulation stratificationParasite infection levelsHuman malaria parasiteGenotyping of SNPsNucleotide diversityPooled sequencesAssociation mappingGenomic lociLinkage mappingPlasmodium falciparumSignificant SNPsMosquito systemMarker densityDNA poolsAnopheles gambiaeNatural variationIndividual mosquitoesLinkage disequilibriumSequencing identifies
2014
Characterization of Plasmodium developmental transcriptomes in Anopheles gambiae midgut reveals novel regulators of malaria transmission
Akinosoglou K, Bushell E, Ukegbu C, Schlegelmilch T, Cho J, Redmond S, Sala K, Christophides G, Vlachou D. Characterization of Plasmodium developmental transcriptomes in Anopheles gambiae midgut reveals novel regulators of malaria transmission. Cellular Microbiology 2014, 17: 254-268. PMID: 25225164, PMCID: PMC4371638, DOI: 10.1111/cmi.12363.Peer-Reviewed Original ResearchConceptsTranscriptional programsOokinete developmentRodent malaria parasite Plasmodium bergheiMalaria parasite Plasmodium bergheiDistinct transcriptional programsMosquito midgut invasionMalaria parasite populationsDevelopmental transcriptomeAnopheles gambiae mosquitoesPenetrant lossFunction phenotypesMidgut invasionHomologous recombinationGamete releasePlasmodium developmentMutant parasitesDevelopmental processesDNA microarraysGranular localizationInfection phenotypesEstablishment of infectionMosquito midgutShort polypeptidesParasite populationsParasite development
2013
The zebrafish reference genome sequence and its relationship to the human genome
Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, Collins J, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett J, Koch R, Rauch G, White S, Chow W, Kilian B, Quintais L, Guerra-Assunção J, Zhou Y, Gu Y, Yen J, Vogel J, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire S, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster S, Carter N, Harrow J, Ning Z, Herrero J, Searle S, Enright A, Geisler R, Plasterk R, Lee C, Westerfield M, de Jong P, Zon L, Postlethwait J, Nüsslein-Volhard C, Hubbard T, Crollius H, Rogers J, Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496: 498-503. PMID: 23594743, PMCID: PMC3703927, DOI: 10.1038/nature12111.Peer-Reviewed Original ResearchConceptsHigh-quality sequence assembliesHuman protein-coding genesProtein-coding genesReference genome sequenceKey genomic featuresHuman reference genomeZebrafish genomeZebrafish orthologueReference genomeGenome sequenceHuman genomeSequence assemblyGenomic featuresLarge genesGenomeGenesOrthologuesVertebratesSequenceAssembly
2012
Transcriptome of the adult female malaria mosquito vector Anopheles albimanus
Martínez-Barnetche J, Gómez-Barreto R, Ovilla-Muñoz M, Téllez-Sosa J, López D, Dinglasan R, Mohien C, MacCallum R, Redmond S, Gibbons J, Rokas A, Machado C, Cazares-Raga F, González-Cerón L, Hernández-Martínez S, López M. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 2012, 13: 207. PMID: 22646700, PMCID: PMC3442982, DOI: 10.1186/1471-2164-13-207.Peer-Reviewed Original ResearchConceptsMalaria vectorsProtein-coding transcriptsAvailable genomic informationPlasmodium-mosquito interactionsHigh-quality assemblyImportant malaria vectorAnopheles albimanusFemale transcriptomesPutative orthologsDivergence timesPlasmodium lifecycleEukaryotic genomesTranscriptome projectsEvolutionary biologyInterPro annotationProtein familyMosquito biologyInsect vectorsGenomic informationNeotropical vectorsCDNA libraryIllumina sequencesAnopheline mosquito vectorsGenus AnophelesFat body
2011
An expression map for Anopheles gambiae
MacCallum R, Redmond S, Christophides G. An expression map for Anopheles gambiae. BMC Genomics 2011, 12: 620. PMID: 22185628, PMCID: PMC3341590, DOI: 10.1186/1471-2164-12-620.Peer-Reviewed Original ResearchConceptsPeptidoglycan recognition proteinsGene familyAnopheles gambiaeGene expressionA. gambiaeIndividual gene clustersMosquito Anopheles gambiaeDistinct biological contextsImmunity-related genesHouse-keeping roleSystems-level viewEvolutionary historyMolecular functionsGene clusterMost organismsTranscriptome dataIndividual genesDistinct functional groupsDNA replicationRecognition proteinsExpression mapProtein degradationPathogen recognitionBiological contextProtein productsVectorBase: improvements to a bioinformatics resource for invertebrate vector genomics
Megy K, Emrich S, Lawson D, Campbell D, Dialynas E, Hughes D, Koscielny G, Louis C, MacCallum R, Redmond S, Sheehan A, Topalis P, Wilson D, . VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Research 2011, 40: d729-d734. PMID: 22135296, PMCID: PMC3245112, DOI: 10.1093/nar/gkr1089.Peer-Reviewed Original ResearchConceptsBioinformatics resourcesHigh-throughput dataPopulation geneticsTaxonomic coverageInsecticide resistance dataGenome browserGenomic variationInvertebrate vectorsGenomic featuresBiology resourcesExpression dataHuman pathogensTsetse fliesGenomeBody liceTimely releaseVectorBaseGenomicsGeneticsBioinformaticsFliesMultiple typesAnnotationLicePathogensThe Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data
Jung S, Menda N, Redmond S, Buels R, Friesen M, Bendana Y, Sanderson L, Lapp H, Lee T, MacCallum B, Bett K, Cain S, Clements D, Mueller L, Main D. The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database 2011, 2011: bar051. PMID: 22120662, PMCID: PMC3225077, DOI: 10.1093/database/bar051.Peer-Reviewed Original Research
2010
SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes
Neafsey D, Lawniczak M, Park D, Redmond S, Coulibaly M, Traoré S, Sagnon N, Costantini C, Johnson C, Wiegand R, Collins F, Lander E, Wirth D, Kafatos F, Besansky N, Christophides G, Muskavitch M. SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes. Science 2010, 330: 514-517. PMID: 20966254, PMCID: PMC4811326, DOI: 10.1126/science.1193036.Peer-Reviewed Original ResearchConceptsGenomic differentiationGenome-wide monitoringGreater genetic divergenceVector mosquito populationsMalaria vector mosquitoesAfrican malaria vector mosquitoesReproductive isolationBehavioral diversificationGenetic divergenceGenomic regionsNatural selectionPopulation structurePolymorphic inversionsSelective eventsSNP genotypingVector control effortsMosquito populationsVector mosquitoesDifferentiationComplex showDivergenceMosquitoesCentromeresGenomeSpeciesWidespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences
Lawniczak M, Emrich S, Holloway A, Regier A, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang S, Minx P, Nelson J, Kyung K, Walenz B, Garcia-Hernandez E, Aguiar M, Viswanathan L, Rogers Y, Strausberg R, Saski C, Lawson D, Collins F, Kafatos F, Christophides G, Clifton S, Kirkness E, Besansky N. Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences. Science 2010, 330: 512-514. PMID: 20966253, PMCID: PMC3674514, DOI: 10.1126/science.1195755.Peer-Reviewed Original ResearchConceptsSpeciation processGenome sequencePrevious genome-wide scanHeterogeneous genomic divergenceAnopheles gambiae speciesGenome-wide scanUnknown genetic mechanismsWhole genome sequencesGene flowGenomic divergenceLarval ecologyGambiae speciesAnopheles gambiae sensu strictoPericentromeric regionGambiae sensu strictoGenetic mechanismsWidespread divergenceSensu strictoReproductive behaviorMajor vectorDivergenceSpeciationSequenceAppreciable levelsMolecular forms