2024
LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information
Dong Z, Jiang W, Li H, DeWan A, Zhao H. LDER-GE estimates phenotypic variance component of gene–environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information. Briefings In Bioinformatics 2024, 25: bbae335. PMID: 38980374, PMCID: PMC11232466, DOI: 10.1093/bib/bbae335.Peer-Reviewed Original ResearchConceptsHuman complex traitsComplex traitsGene-environment interactionsGene-environmentLinkage disequilibriumPhenotypic variance componentsPhenotypic varianceProportion of phenotypic varianceSummary statisticsEuropean ancestry subjectsUK Biobank dataAssociation summary statisticsComplete linkage disequilibriumControlled type I error ratesLD informationLD matrixVariance componentsBiobank dataType I error rateEuropean ancestrySample size increaseGenetic effectsTraitsE-I pairsSimulation study
2022
WebCSEA: web-based cell-type-specific enrichment analysis of genes
Dai Y, Hu R, Liu A, Cho K, Manuel A, Li X, Dong X, Jia P, Zhao Z. WebCSEA: web-based cell-type-specific enrichment analysis of genes. Nucleic Acids Research 2022, 50: w782-w790. PMID: 35610053, PMCID: PMC10359109, DOI: 10.1093/nar/gkac392.Peer-Reviewed Original ResearchConceptsCell type-specificCell-type specificityEnrichment analysisHuman complex traitsTrait-associated genesTC-specificSingle-cell RNA sequencingCell typesComplex traitsGene listsHuman tissuesPermutation-based methodsRNA sequencingTissue-specificGenesCellular heterogeneityHuman organ systemsSignature genesDevelopmental stagesInteractive heatmapsGeneral tissueTissue-TissueSequenceSpecificityDeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Liu Q, Hua K, Zhang X, Wong H, Jiang R. DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility. Genomics Proteomics & Bioinformatics 2022, 20: 496-507. PMID: 35293310, PMCID: PMC9801045, DOI: 10.1016/j.gpb.2021.08.015.Peer-Reviewed Original ResearchConceptsChromatin accessible regionsTranscription factorsChromatin accessibilityWhole-genome sequencing data analysisDisease-associated genetic variantsChromatin accessibility signalsGenome-wide scaleHigh-throughput biological experimentsHuman complex traitsGenome-wide predictionNovel binding motifsSequencing data analysisIdentification of functional regionsCore transcription factorsCell typesSequence signaturesAnalysis of TF activityComplex traitsHuman genomeRegulatory elementsSequence informationBinding motifCellular contextDeepCAGEGenetic variants
2020
Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes
Zhao Y, Li T, Zhu H. Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes. Biostatistics 2020, 23: 467-484. PMID: 32948880, PMCID: PMC9308456, DOI: 10.1093/biostatistics/kxaa035.Peer-Reviewed Original ResearchConceptsHeritability analysisHuman complex traitsLarge-scale phenotypeQuantitative geneticsComplex traitsPhenotypic variationTrait selectionGenetic datasetsSingle phenotypeDownstream analysisGenetic contributionHeritability estimationPhenotypeTraitsCentral roleNeuroimaging phenotypesUnited Kingdom BiobankHierarchical selectionPhenotypic methodsGeneticsHeritabilitySelectionVariationBrain variation
2016
Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Lu Q, Powles RL, Wang Q, He BJ, Zhao H. Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies. PLOS Genetics 2016, 12: e1005947. PMID: 27058395, PMCID: PMC4825932, DOI: 10.1371/journal.pgen.1005947.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGWAS signalsComplex traitsFunctional annotationAssociation studiesHuman complex traitsFunctional regionsNon-coding regionsGWAS p-valuesWide association studyNovel biological insightsRelevant tissue typesEpigenetic annotationsGenomic functionsRegulatory machineryTransposable elementsHuman genomeGenoSkylineRisk lociBiological insightsIntegrative analysisGenetic studiesRegulatory miRNAPrioritization performanceSpecific annotations
2007
Linkage Disequilibrium Mapping for Complex Disease Genes
DeWan A, Klein RJ, Hoh J. Linkage Disequilibrium Mapping for Complex Disease Genes. Methods In Molecular Biology 2007, 376: 85-107. PMID: 17984540, DOI: 10.1007/978-1-59745-389-9_7.Books
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