2025
Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies
Zhang X, Wang L, Zhao J, Zhao H. Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies. American Journal Of Human Genetics 2025 PMID: 40902598, PMCID: PMC12412983, DOI: 10.1016/j.ajhg.2025.08.007.Peer-Reviewed Original ResearchTranscriptome-wide association studyExpression quantitative trait lociGenome-wide association studiesGene-trait pairsFalse discovery rateAssociation studiesTranscriptome-wide association study approachTranscriptome-wide association study methodExpression quantitative trait loci dataGenes associated with complex traitsGenetic variantsGenome-wide association study summary statisticsSusceptibility genesGene-trait associationsSusceptibility gene identificationQuantitative trait lociParametric bootstrap samplingGene expression levelsGenomic regionsGenetic elementsComplex traitsGene identificationTrait lociFalse discovery rate levelKnockoff procedure
2023
Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda
Saarman N, Son J, Zhao H, Cosme L, Kong Y, Li M, Wang S, Weiss B, Echodu R, Opiro R, Aksoy S, Caccone A. Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda. Infection Genetics And Evolution 2023, 114: 105501. PMID: 37709241, PMCID: PMC10593118, DOI: 10.1016/j.meegid.2023.105501.Peer-Reviewed Original ResearchConceptsGenome-wide association analysisNovel vector control strategiesAnimal African trypanosomiasisSex chromosome aneuploidyNatural populationsGenome assemblySex chromosomesGenomic regionsGenomic evidenceGenetic variationBp upstreamAutosomal SNPsSeq dataTrypanosome infectionTrypanosome parasitesAssociation analysisMolecular pathwaysAssembly metricsLinkage disequilibriumLecithin-cholesterol acyltransferaseAfrican trypanosomiasisMajor vectorGenomeSNPsPrimary vector
2022
Benchmarking automated cell type annotation tools for single-cell ATAC-seq data
Wang Y, Sun X, Zhao H. Benchmarking automated cell type annotation tools for single-cell ATAC-seq data. Frontiers In Genetics 2022, 13: 1063233. PMID: 36583014, PMCID: PMC9792779, DOI: 10.3389/fgene.2022.1063233.Peer-Reviewed Original ResearchCell type annotationScATAC-seq dataScRNA-seq dataScATAC-seqCell typesSingle-cell ATAC-seq dataAvailable single-cell datasetsRegulatory genomic regionsScRNA-seq data setsSingle-cell datasetsATAC-seq dataNovel cell typesSimilar cell typesSeurat v3Genomic regionsSequencing depthComplex tissuesDeep annotationAnnotationCellular compositionHuman tissuesType annotationsAnnotation toolAnnotation methodLabel transfer
2021
SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits
Zhang Y, Lu Q, Ye Y, Huang K, Liu W, Wu Y, Zhong X, Li B, Yu Z, Travers BG, Werling DM, Li JJ, Zhao H. SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits. Genome Biology 2021, 22: 262. PMID: 34493297, PMCID: PMC8422619, DOI: 10.1186/s13059-021-02478-w.Peer-Reviewed Original ResearchConceptsLocal genetic correlationsComplex traitsGenetic correlationsGenomic regionsLocal genetic correlation analysisGenome-wide association studiesLocal genomic regionsSpecific genomic regionsGenetic correlation analysisDistinct genetic signaturesGenetic similarityGenetic signaturesAssociation studiesTraitsSample overlapStatistical frameworkSummary statisticsDisequilibriumRegionAccurate estimationSimilarity
2015
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS
Wang Q, Yang C, Gelernter J, Zhao H. Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. Human Genetics 2015, 134: 1195-1209. PMID: 26340901, PMCID: PMC4630076, DOI: 10.1007/s00439-015-1596-8.Peer-Reviewed Original ResearchMeSH KeywordsArthritis, RheumatoidCentral Nervous SystemCrohn DiseaseGenetic PleiotropyGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansImmune System DiseasesMental DisordersNerve Tissue ProteinsOrgan SpecificityPolymorphism, Single NucleotideQuantitative Trait LociSchizophreniaSystems IntegrationConceptsImmune disordersPsychiatric disordersCrohn's diseaseDisorder pairsMHC regionPervasive pleiotropyIntegrative analysisGenome-wide association studiesImmune dysregulationImmunological mechanismsTreatment strategiesTraits/diseasesEpidemiological observationsPsychiatric diseasesBrain disordersSame effect directionDiseaseDisordersGenomic regionsRealm of psychiatryMost allelesStrong pleiotropyAnnotation resourcesChromosome 6Association studies
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