2020
Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule
Poulakakis N, Miller J, Jensen E, Beheregaray L, Russello M, Glaberman S, Boore J, Caccone A. Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule. Journal Of Zoological Systematics & Evolutionary Research 2020, 58: 1262-1275. DOI: 10.1111/jzs.12387.Peer-Reviewed Original ResearchGalapagos giant tortoisesGiant tortoisesPhylogeographic scenarioMitochondrial genomeProgression rulePhylogenetic relationshipsGalapagos IslandsExtinct speciesOlder islandsHuman-mediated dispersal eventsComplete mitochondrial genomeSouth American ancestorAncestral area reconstructionNon-native speciesMaximum likelihood analysisContribution of colonizationColonization historyDispersal eventsMultiple colonizationsAmerican ancestorsPhylogenetic treeAncestral formArea reconstructionSitu speciationBiogeographic approach
2016
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum R, Berv J, Dornburg A, Field D, Townsend J, Lemmon E, Lemmon A. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2016, 534: s7-s8. DOI: 10.1038/nature19417.Peer-Reviewed Original ResearchMajor avian lineagesAvian lineagesSister groupSequence dataLiving birdsCretaceous–Palaeogene mass extinctionIdentical phylogenetic treesDivergence time analysesGenomic sequence dataSuccessive sister groupsMaximum likelihood analysisNext-generation DNA sequencingHybrid enrichmentNuclear lociAvian phylogenyCrown birdsComprehensive phylogenyMajor cladesEvolutionary historyMajor radiationPhylogenetic treeCladePhylogenyLikelihood analysisDNA sequencing
2012
Likelihood‐based methods for regression analysis with binary exposure status assessed by pooling
Lyles R, Tang L, Lin J, Zhang Z, Mukherjee B. Likelihood‐based methods for regression analysis with binary exposure status assessed by pooling. Statistics In Medicine 2012, 31: 2485-2497. PMID: 22415630, PMCID: PMC3528351, DOI: 10.1002/sim.4426.Peer-Reviewed Original ResearchConceptsPopulation-based case-control study of colorectal cancerCase-control study of colorectal cancerPopulation-based case-control studyStudy of colorectal cancerExposure statusBinary outcomesRegression modelsCase-control sampleLogistic regression modelsGene-disease associationsObserved binary outcomeStudy designEpidemiological studiesColorectal cancerAssess exposureMaximum likelihood analysisRegression analysisLikelihood-based methodsExposure assessmentMaximum likelihood approachLikelihood approachCross-sectionSimulation studyOutcomesLikelihood analysis
2008
RPS4Ygene family evolution in primates
Andrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Ygene family evolution in primates. BMC Ecology And Evolution 2008, 8: 142. PMID: 18477388, PMCID: PMC2397393, DOI: 10.1186/1471-2148-8-142.Peer-Reviewed Original ResearchConceptsRPS4Y genesPositive selectionTestis-specific expression patternRibosomal protein genesRibosomal protein S4Non-synonymous substitutionsAmino acid replacementsMaximum likelihood analysisDuplication eventsFamily evolutionFunctional paralogsEvolutionary historyGene familyFunctional genesSex chromosomesProtein S4Protein functionPrimate phylogenyProtein domainsHuman lineageNew World monkeysProtein geneGene dosageAcid replacementsY chromosome
2006
Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees
Magori-Cohen R, Louzoun Y, Kleinstein SH. Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees. Bioinformatics 2006, 22: e332-e340. PMID: 16873490, DOI: 10.1093/bioinformatics/btl239.Peer-Reviewed Original ResearchConceptsLineage treesDNA sequencesDNA sequence dataSomatic hypermutationMaximum likelihood analysisTree shapeBioinformatics methodsSequence dataLethal mutationsMutation rateNumber of generationsLikelihood analysisMutation parametersB cellsSynthetic treeClonal expansionTreesSequenceMutationsHypermutationAffinity maturationCellsImportant linkClonesUnexpected locations
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