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
2019
A statistical framework for cross-tissue transcriptome-wide association analysis
Hu Y, Li M, Lu Q, Weng H, Wang J, Zekavat SM, Yu Z, Li B, Gu J, Muchnik S, Shi Y, Kunkle BW, Mukherjee S, Natarajan P, Naj A, Kuzma A, Zhao Y, Crane PK, Lu H, Zhao H. A statistical framework for cross-tissue transcriptome-wide association analysis. Nature Genetics 2019, 51: 568-576. PMID: 30804563, PMCID: PMC6788740, DOI: 10.1038/s41588-019-0345-7.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association analysisAssociation analysisGene-trait associationsGene expression dataGene expression levelsGenetic architectureComplex traitsMore genesGene expressionSingle tissueExpression dataAssociation resultsExpression levelsPowerful approachImputation modelHuman tissuesImputation accuracyGenotypesStatistical frameworkTissueGenesKey componentTraitsPowerful metricExpression