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 malaria
2018
De 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
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
2011
VectorBase: 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 typesAnnotationLicePathogens
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 showDivergenceMosquitoesCentromeresGenomeSpecies
2008
VectorBase: a data resource for invertebrate vector genomics
Lawson D, Arensburger P, Atkinson P, Besansky N, Bruggner R, Butler R, Campbell K, Christophides G, Christley S, Dialynas E, Hammond M, Hill C, Konopinski N, Lobo N, MacCallum R, Madey G, Megy K, Meyer J, Redmond S, Severson D, Stinson E, Topalis P, Birney E, Gelbart W, Kafatos F, Louis C, Collins F. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Research 2008, 37: d583-d587. PMID: 19028744, PMCID: PMC2686483, DOI: 10.1093/nar/gkn857.Peer-Reviewed Original ResearchConceptsBody louse Pediculus humanusBioinformatics Resource CenterCommunity annotation systemGene expression repositoriesGenome informationInvertebrate vectorsAnopheles gambiaeInsecticide resistancePediculus humanusVectorBaseMosquito speciesHuman pathogensAedes aegyptiSoftware infrastructureCulex quinquefasciatusIxodes scapularisAnnotation systemVector genomesData resourcesResearch communityGenomeGenomicsGambiaeSpeciesMicroarray
2006
VectorBase: a home for invertebrate vectors of human pathogens
Lawson D, Arensburger P, Atkinson P, Besansky N, Bruggner R, Butler R, Campbell K, Christophides G, Christley S, Dialynas E, Emmert D, Hammond M, Hill C, Kennedy R, Lobo N, MacCallum M, Madey G, Megy K, Redmond S, Russo S, Severson D, Stinson E, Topalis P, Zdobnov E, Birney E, Gelbart W, Kafatos F, Louis C, Collins F. VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Research 2006, 35: d503-d505. PMID: 17145709, PMCID: PMC1751530, DOI: 10.1093/nar/gkl960.Peer-Reviewed Original ResearchEnsembl 2006
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez X, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard T. Ensembl 2006. Nucleic Acids Research 2006, 34: d556-d561. PMID: 16381931, PMCID: PMC1347495, DOI: 10.1093/nar/gkj133.Peer-Reviewed Original ResearchConceptsGenome variation dataHuman genome variation dataNumber of genomesChordate genomesLarge genome sequencesMammalian genomesRegulatory annotationsYeast genomeRNA genesGenome sequenceCiona intestinalisGenomeVariation dataAnnotationGenesOpossumIntestinalisIntegrated sourceSequenceRhesus macaquesImport