Seth Redmond, BSc, MSc, PhD
he/him/his
Associate Research Scientist in Epidemiology (Microbial Diseases)Cards
About
Research
Publications
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 way