2024
A new lineage nomenclature to aid genomic surveillance of dengue virus
Hill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.Peer-Reviewed Original ResearchConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settingsA comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Du Z, He J, Jiao W. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25: 91. PMID: 38589937, PMCID: PMC11003132, DOI: 10.1186/s13059-024-03239-1.Peer-Reviewed Original ResearchConceptsPlant genomesGenotyping methodsComplexity of plant genomesHeterozygous plant genomesGenotypic algorithmsGenotype millionsShort readsGenomic contextGenomic diversitySequencing technologiesHuman genomeGenomeGenetic variantsExcessive repeatsVariant typeGenotypesStructural variationsEnsemble pipelinePlantsConclusionsOur studyVariant genotypesGenotype performanceVariantsDeletionSequenceGiants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores
Ahuja N, Cao X, Schultz D, Picciani N, Lord A, Shao S, Jia K, Burdick D, Haddock S, Li Y, Dunn C. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biology And Evolution 2024, 16: evae048. PMID: 38502059, PMCID: PMC10980510, DOI: 10.1093/gbe/evae048.Peer-Reviewed Original ResearchConceptsK-mer spectraMitochondrial genomeGenomic diversityK-mersNuclear genomeEstimate nuclear genome sizesMitochondrial gene orderNuclear genome sizeGenome assembly projectsRearranged mitochondrial genomesK-mer countingGenome skimmingGene orderGenome sizeRead coverageSequencing depthPhylogenetic samplingIllumina sequencingCnidarian speciesGenomeAssembly projectsSiphonophoresZooplankton communityAbundant predatorsSpecies
2022
Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals
Tahir U, Katz D, Avila-Pachecho J, Bick A, Pampana A, Robbins J, Yu Z, Chen Z, Benson M, Cruz D, Ngo D, Deng S, Shi X, Zheng S, Eisman A, Farrell L, Hall M, Correa A, Tracy R, Durda P, Taylor K, Liu Y, Johnson W, Guo X, Yao J, Chen Y, Manichaikul A, Ruberg F, Blaner W, Jain D, Bouchard C, Sarzynski M, Rich S, Rotter J, Wang T, Wilson J, Clish C, Natarajan P, Gerszten R. Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals. Nature Communications 2022, 13: 4923. PMID: 35995766, PMCID: PMC9395431, DOI: 10.1038/s41467-022-32275-3.Peer-Reviewed Original ResearchConceptsGenome association studiesGenomic diversityAssociation studiesWhole-genome association studiesLocus-metabolite associationsIndividuals of European ancestryIntegrative omics approachMetabolite peaksGenetic informationCardiometabolic diseasesSpecific allelesEuropean ancestryOmics approachesSickle cell diseaseMulti-ethnic cohortTransthyretin amyloidosisAncestryHereditary diseaseIdentified metabolitesCell diseaseHuman metabolismUnknown metabolitesDiversityBlack individualsJackson Heart StudyThe Human Pangenome Project: a global resource to map genomic diversity
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison N, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D. The Human Pangenome Project: a global resource to map genomic diversity. Nature 2022, 604: 437-446. PMID: 35444317, PMCID: PMC9402379, DOI: 10.1038/s41586-022-04601-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHuman reference genomeReference genomeGenomic diversityGenomic variationHuman genomic variationGlobal genomic diversitySingle nucleotide variantsGene-disease associationsDiploid genomeGenetic resourcesGenomeGenomic researchFuture biomedical researchHigh-quality referenceStructural variantsHuman geneticsRoutine assemblyCommon variantsFunctional elementsPolymorphic regionDiversityBiomedical researchVariantsMajor updateGenetics
2017
Population genomics of the Asian tiger mosquito, Aedes albopictus: insights into the recent worldwide invasion
Kotsakiozi P, Richardson J, Pichler V, Favia G, Martins A, Urbanelli S, Armbruster P, Caccone A. Population genomics of the Asian tiger mosquito, Aedes albopictus: insights into the recent worldwide invasion. Ecology And Evolution 2017, 7: 10143-10157. PMID: 29238544, PMCID: PMC5723592, DOI: 10.1002/ece3.3514.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsGenetic structureRecent invasionRestriction site-associated DNA sequencingAsian tiger mosquitoGenomics-based approachesTiger mosquitoPopulation genomicsInvasive populationsNative rangeWorldwide invasionMultiple invasionsGenomic diversityRange populationsPopulation clustersMajor clustersDNA sequencingNucleotide polymorphismsAedes albopictusVector control strategiesInvasionMosquitoesLocal scaleDifferentiationGenomics
2015
Limits and patterns of cytomegalovirus genomic diversity in humans
Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss M, Hamprecht K, Yamamoto A, Mussi-Pinhata M, Britt W, Jensen J, Kowalik T. Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e4120-e4128. PMID: 26150505, PMCID: PMC4522815, DOI: 10.1073/pnas.1501880112.Peer-Reviewed Original ResearchConceptsGenomic diversityHuman hostGenome-wide mutationsHuman cytomegalovirusRecombination rate mapsHCMV populationsViral genomic diversityGenome beingRegulatory proteinsViral populationsDiversityPolymorphismHostPatient samplesDiverse regionsGenomeNatural infectionLociCongenitally infected infantsGenesMutationsProteinInfected infantsGlycoproteinRecombination
2011
Hunter-gatherer genomic diversity suggests a southern African origin for modern humans
Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 5154-5162. PMID: 21383195, PMCID: PMC3069156, DOI: 10.1073/pnas.1017511108.Peer-Reviewed Original ResearchConceptsHunter-gatherer populationsAfrican hunter-gatherer populationsModern humansGenome-wide linkage disequilibriumModern human populationsSex-biased migrationSevere population bottleneckLinkage disequilibriumSouthern African originHuman prehistoryAfrican populationsComplex historyPopulation differentiationPopulation bottlenecksGenetic diversityGenomic diversityEastern AfricaGenetic variationAfrican originPopulation todaySouthern AfricaGeographic patternsContinent of originAfricaSouth Africa
2010
Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB. Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families. Genome Research 2010, 20: 960-971. PMID: 20430783, PMCID: PMC2892097, DOI: 10.1101/gr.102814.109.Peer-Reviewed Original ResearchConceptsProtein familyMembrane proteinsMembrane protein familyRecent metagenomic studiesMembrane protein contentAdditional environmental featuresProtein diversityDisparate habitatsGenomic diversityPhosphate transporterProtein variationMetagenomic sequencesMetagenomic studiesEnvironmental featuresIron transporterHuman impactProteinOceanographic variablesMarine sitesEcological analysisTransportersDiversityProtein contentFamilyClimate change
2009
Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460: 894-898. PMID: 19633652, PMCID: PMC4590770, DOI: 10.1038/nature08187.Peer-Reviewed Original Research
1996
A nuclear perspective on human evolution
Kidd K, Kidd J. A nuclear perspective on human evolution. 1996, 242-264. DOI: 10.1017/cbo9780511525643.018.Peer-Reviewed Original ResearchHuman diversity studiesHuman populationDNA sequence variationHuman evolutionAbsence of recombinationRecent human evolutionHuman genome diversityY-chromosome DNAPatterns of variationEvolutionary forcesExtant diversityVariety of speciesGenome diversityGenetic diversitySex chromosomesAutosomal DNAMitochondrial DNATaxonomic issuesGenomic diversityChromosome DNADiversity studiesEvolutionary factorsRecent ancestorSequence variationNuclear perspective
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