2024
Signatures of transmission in within-host Mycobacterium tuberculosis complex variation: a retrospective genomic epidemiology study
Walter K, Cohen T, Mathema B, Colijn C, Sobkowiak B, Comas I, Goig G, Croda J, Andrews J. Signatures of transmission in within-host Mycobacterium tuberculosis complex variation: a retrospective genomic epidemiology study. The Lancet Microbe 2024, 6: 100936. PMID: 39615498, PMCID: PMC11777664, DOI: 10.1016/j.lanmic.2024.06.003.Peer-Reviewed Original ResearchWithin-host variationMycobacterium tuberculosis complexTransmission inferenceSequence dataMinority variantsGenome Epidemiology StudyMTBC diversityWhole-genome sequencing dataPairs of isolatesAvailable sequence dataPublicly available sequencing dataRetrospective population-based studyPopulation-based studyIdentical genomesPPE genesGenetic differencesWalker etCulture isolatesTuberculosis complexHousehold transmission studyIsolatesEpidemiological linkageReceiver Operating CharacteristicEpidemiological studiesCulture of sputumMassively parallel approaches for characterizing noncoding functional variation in human evolution
Rong S, Root E, Reilly S. Massively parallel approaches for characterizing noncoding functional variation in human evolution. Current Opinion In Genetics & Development 2024, 88: 102256. PMID: 39217658, PMCID: PMC11648527, DOI: 10.1016/j.gde.2024.102256.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsCis-regulatory elementsFunction of cis-regulatory elementsImpact of sequence variantsHigh-throughput approachNoncoding variationGenome functionNoncoding regionsSequence variantsPhenotypic consequencesCRISPR screensGenetic basisGenetic variantsGenetic differencesDiverse phenotypesGene expressionRegulatory functionsHuman evolutionFunctional variationGenomeUnique phenotypePhenotypeRegulatory impactModel systemVariantsGenes
2023
Bacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States
Magness L, Delesalle V, Vill A, Strine M, Chaudhry B, Lichty K, Guffey A, DeCurzio J, Krukonis G. Bacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States. PHAGE 2023, 4: 165-172. PMID: 40134792, PMCID: PMC11932521, DOI: 10.1089/phage.2023.0021.Peer-Reviewed Original ResearchPutative protein coding genesDouble-stranded DNA genomeBacillus subtilis phagePhage host rangeLow GC contentProtein coding genesDiversity of phagesAmino acid similarityPhage clusterPhage evolutionPhage genomeGC contentUnique genesBacillus phagesCoding genesDNA genomeReplication genesModel organismsPhageHost rangeMicrobial dynamicsGenetic differencesGenomeGenesDesert soils
2018
Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients
Patrick M, Stuart P, Raja K, Gudjonsson J, Tejasvi T, Yang J, Chandran V, Das S, Callis-Duffin K, Ellinghaus E, Enerbäck C, Esko T, Franke A, Kang H, Krueger G, Lim H, Rahman P, Rosen C, Weidinger S, Weichenthal M, Wen X, Voorhees J, Abecasis G, Gladman D, Nair R, Elder J, Tsoi L. Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients. Nature Communications 2018, 9: 4178. PMID: 30301895, PMCID: PMC6177414, DOI: 10.1038/s41467-018-06672-6.Peer-Reviewed Original ResearchConceptsPsoriasis patientsPredicting PsAGenetic architectureGenetic markersGenetic signaturesComputational pipelineGenetic differencesPsoriatic arthritis developmentChronic musculoskeletal conditionsCutaneous-only psoriasisArea under the receiver operating curveReceiver operating curvePSC patientsPsA riskPsoriasis subtypesPsoriatic patientsArthritis developmentPsoriatic arthritisPsoriasisPatientsConditional inference forestsShrinkage discriminant analysisPSAMusculoskeletal conditionsOperating curve
2016
Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence
Molinari E, Bar H, Pyle AM, Patrizio P. Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence. Molecular Human Reproduction 2016, 22: 866-876. PMID: 27268410, PMCID: PMC4986421, DOI: 10.1093/molehr/gaw038.Peer-Reviewed Original ResearchConceptsRNA sequencingHuman cumulus cellsCumulus cellsGEO accession numberHypoxia stress responseWhole transcriptome analysisTranscriptome analysisSomatic cellsEmbryonic developmentBioinformatics toolsGene pathwaysSpecific molecular findingsAccession numbersCell agingMolecular mechanismsStress responseVasculature developmentGenetic differencesSAMPLES/MATERIALSGenetic platformMolecular pathwaysReproductive potentialCAMP turnoverGenesSenescence
2012
Genetic variability of glutathione S-transferase enzymes in human populations: Functional inter-ethnic differences in detoxification systems
Polimanti R, Carboni C, Baesso I, Piacentini S, Iorio A, De Stefano GF, Fuciarelli M. Genetic variability of glutathione S-transferase enzymes in human populations: Functional inter-ethnic differences in detoxification systems. Gene 2012, 512: 102-107. PMID: 23043933, DOI: 10.1016/j.gene.2012.09.113.Peer-Reviewed Original ResearchConceptsGenetic association studiesGenetic variabilityAssociation studiesHuman populationFunctional genetic differencesDetoxification genesGlutathione S-transferaseCellular detoxificationEnzymatic functionGlutathione S-transferase enzymesGST genesBiological processesGenetic differencesDetoxification systemGenesGST enzymesS-transferaseFunctional impactLoF variantsFunction variantsGSTEnzymeHapMap databaseGenetic polymorphismsKey roleThe Impact of Differential Regulation on Bacterial Speciation
Groisman E. The Impact of Differential Regulation on Bacterial Speciation. 2012, 109-114. DOI: 10.1128/9781555818470.ch15.Peer-Reviewed Original ResearchBacterial speciesGene regulatory strategiesRelated bacterial speciesResistance proteinAmino acid sequenceEukaryotic speciesRelated speciesBacterial speciationRelated organismsIndividual speciesRegulatory proteinsAcid sequenceBacterial behaviorEnteric speciesGenetic differencesGenetic scenariosDifferential regulationResistance genesEscherichia coliSpeciesEconomic importanceProteinSalmonella entericaFamily EnterobacteriaceaeOrganisms
2007
Recurrent DNA copy number variation in the laboratory mouse
Egan CM, Sridhar S, Wigler M, Hall IM. Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics 2007, 39: 1384-1389. PMID: 17965714, DOI: 10.1038/ng.2007.19.Peer-Reviewed Original ResearchConceptsCopy number variationsCopy numberNumber variationsGenome-wide analysisDNA copy number variationsRecent common ancestryGenerations of inbreedingRecurrent copy number variationsHigh-resolution microarraysCommon ancestryNatural variationGenetic differencesDifferent speciesDifferent lociGenerational timeLaboratory miceNonrandom processGenomeRecurrent mutationsLociAdditional strainsInbreedingLineagesGenesDiscrete segments4.14 The Development and Evolutionary Expansion of the Cerebral Cortex in Primates
Rakic P, Kornack D. 4.14 The Development and Evolutionary Expansion of the Cerebral Cortex in Primates. 2007, 243-259. DOI: 10.1016/b0-12-370878-8/00004-5.Peer-Reviewed Original ResearchEvolutionary expansionSpecies-specific sizeSmall genetic differencesCerebral cortexEvolutionary mechanismsMammalian speciesBrain evolutionCell cycleCellular eventsSpontaneous mutationsGenetic differencesRadial unit hypothesisRodent embryosBasic organizationModern neurobiologyEmbryosNew insightsNon-human primatesCorticogenesisHuman uniquenessBiological substratesCortexNeuronal interactionsEmbryogenesisHuman cerebrum
2005
Variation in IL-1β gene expression is a major determinant of genetic differences in arthritis aggressivity in mice
Ohmura K, Johnsen A, Ortiz-Lopez A, Desany P, Roy M, Besse W, Rogus J, Bogue M, Puech A, Lathrop M, Mathis D, Benoist C. Variation in IL-1β gene expression is a major determinant of genetic differences in arthritis aggressivity in mice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 12489-12494. PMID: 16113081, PMCID: PMC1194932, DOI: 10.1073/pnas.0504325102.Peer-Reviewed Original ResearchConceptsInbred strainsWhole-genome scanQuantitation of transcriptsInterleukin-1 gene familyConventional inbred strainsWild-derived strainsComplex genetic controlSequence haplotypesGenomic regionsGenetic lociNoncoding polymorphismsCandidate genesGenetic analysisGenetic differencesBALB/c haplotypeGenetic controlGene expressionIL-1B gene expressionBreeding strategiesBreeding schemesIL1B geneGenesSerum-transfer arthritisStrainHigh-responder BALB/c
2004
Genomic regions controlling corticosterone levels in rats
Potenza MN, Brodkin ES, Joe B, Luo X, Remmers EF, Wilder RL, Nestler EJ, Gelernter J. Genomic regions controlling corticosterone levels in rats. Biological Psychiatry 2004, 55: 634-641. PMID: 15013833, DOI: 10.1016/j.biopsych.2003.11.005.Peer-Reviewed Original ResearchConceptsGenomic regionsQuantitative trait locus (QTL) analysisGenome-wide levelSpecific genomic regionsUnderstanding of susceptibilitySignificant QTLGenomic backgroundChromosome 4Locus analysisF2 progenyGenetic differencesSuggestive significanceDisease susceptibilityQTLFirst identificationCongenic animalsDeoxyribonucleic acidGenetic factorsProgenyIdentificationRegionSusceptibilityLevelsGene expression profiling in evolutionary genetics
Hartl D, Meiklejohn C, Castillo-Davis C, Cavalieri D, Ranz J, Townsend J. Gene expression profiling in evolutionary genetics. 2004, 74-93. DOI: 10.1017/cbo9780511542619.007.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNatural populationsPopulation geneticsKey model organismGenotypes of organismsGene expression profilingDNA sequencing strategyEvolutionary geneticsComparative genomicsEvolutionary timeModel organismsChain termination methodHuman genomePopulation geneticistsGenomic sequencesGenetic variationSingle speciesComplete sequenceExpression profilingMolecular geneticsGenetic differencesGenomeMolecular biologySequencing strategyMolecular levelDNA sequencing
1997
Patterns of genetic variability in colonized strains of Lutzomyia longipalpis (Diptera: Psychodidae) and its consequences.
Mukhopadhyay J, Rangel E, Ghosh K, Munstermann L. Patterns of genetic variability in colonized strains of Lutzomyia longipalpis (Diptera: Psychodidae) and its consequences. American Journal Of Tropical Medicine And Hygiene 1997, 57: 216-21. PMID: 9288819, DOI: 10.4269/ajtmh.1997.57.216.Peer-Reviewed Original ResearchConceptsLaboratory coloniesField collectionsNew World sandEnzyme lociAverage heterozygosityGenetic qualityGenetic variabilityGenetic shiftColonization processField populationsGenetic differencesLutzomyia longipalpisGeographic strainsDifferent allelesSand fliesBiological inferencesLapinha CavePhlebotomine sand fliesHeterozygosityAllelesInfrequent allelesApparent consequenceColoniesField specimensPolyacrylamide gels
1994
The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium
Ochman H, Groisman EA. The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. EXS 1994, 69: 479-493. PMID: 7994120, DOI: 10.1007/978-3-0348-7527-1_27.Peer-Reviewed Original ResearchConceptsSpecies-specific sequencesSalmonella chromosomeEscherichia coliCodon usage patternsOpen reading frameHost epithelial cellsCommon ancestorMap positionPhenotypic charactersReading frameBase compositionHorizontal transferSalmonella typhimuriumMutant strainGenetic differencesEnteric speciesBacterial speciesGenomePoint mutationsPhenotypic characteristicsSpeciesCorresponding regionChromosomesSpecies differencesEpithelial cells
1987
Intraspecific DNA divergence in Drosophila: a study on parthenogenetic D. mercatorum.
Caccone A, Amato G, Powell J. Intraspecific DNA divergence in Drosophila: a study on parthenogenetic D. mercatorum. Molecular Biology And Evolution 1987, 4: 343-350. PMID: 3447012, DOI: 10.1093/oxfordjournals.molbev.a040451.Peer-Reviewed Original ResearchConceptsDNA-DNA hybridizationIntraspecific genetic variationInsertion/deletion differencesIntraspecific DNA variationSpecies of invertebratesFurther genetic differencesDNA divergenceDNA diversityDNA variationD. mercatorumIndependent genomesIntraspecific variationDrosophila mercatorumGenetic variationDNA differencesParthenogenetic strainsBase pair mismatchesGenetic differencesInvertebratesGenomeSpeciesHybridizationDrosophilaStrainsDiversity
1985
Genetic and evolutionary relationships among Asian Macaques
Melnick1 D, Kidd K. Genetic and evolutionary relationships among Asian Macaques. International Journal Of Primatology 1985, 6: 123-160. DOI: 10.1007/bf02693650.Peer-Reviewed Original ResearchEvolutionary relationshipsGenetic distanceSpecies groupsInferred evolutionary relationshipsEffective population sizeIntraspecific genetic distancesGene frequency dataMacaque speciesDivergence timesPhylogenetic treeAllele definitionGenetic differencesPopulation sizeCavalli-SforzaAsian macaquesSpeciesTree analysisLociPopulationTreesMajor sea-level changesFrequency dataSea-level changesAsia
1983
The genetic consequences of social group fission in a wild population of rhesus monkeys (Macaca mulatta)
Melnick D, Kidd K. The genetic consequences of social group fission in a wild population of rhesus monkeys (Macaca mulatta). Behavioral Ecology And Sociobiology 1983, 12: 229-236. DOI: 10.1007/bf00290775.Peer-Reviewed Original ResearchSocial group fissionGenetic consequencesWild populationsPatterns of paternityClear genetic differencesMaternal relatednessGroup fissionCayo Santiago islandMacroevolutionary effectsGenetic differentiationGenetic structureEvolutionary historyMammalian populationsGenetic analysisPrimate populationsGenetic differencesGenetic effectsPaternityMatrilinesRelatednessDifferentiationResult of differencesFissionDemographic structureGreater genetic effect
1980
Genetics and the Origin of a Vector Population: Aedes aegypti, a Case Study
Powell J, Tabachnick W, Arnold J. Genetics and the Origin of a Vector Population: Aedes aegypti, a Case Study. Science 1980, 208: 1385-1387. PMID: 7375945, DOI: 10.1126/science.7375945.Peer-Reviewed Original ResearchConceptsEnzyme-coding genesMosquito Aedes aegyptiAedes aegyptiPopulation geneticsGenetic differencesVector populationsWorldwide distributionVector-borne diseasesGeneticsAegyptiSubspeciesGeographic regionsGenesPopulationSuch studiesMultivariate discriminant analysisOriginPopulation sampleGeneral applicability
1978
Genetic structure of the East African domestic populations of Aedes aegypti
TABACHNICK W, POWELL J. Genetic structure of the East African domestic populations of Aedes aegypti. Nature 1978, 272: 535-537. PMID: 692658, DOI: 10.1038/272535a0.Peer-Reviewed Original ResearchConceptsPopulation genetic analysesDomestic populationsSignificant genetic differencesA. aegyptiYellow fever mosquitoAedes aegyptiGenetic substructuringGenetic structurePanmictic unitFeral formsPopulation breedsGenetic analysisTropical forestsDisturbed areasBehavioral variationGenetic differencesCoconut palmsDark formGene frequenciesMosquito populationsDomestic formsAegyptiComplex speciesClose proximitySpecies
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply