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
Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
Zeng L, Warren J, Zhao H. Phylogeny-based tumor subclone identification using a Bayesian feature allocation model. The Annals Of Applied Statistics 2019, 13: 1212-1241. DOI: 10.1214/18-aoas1223.Peer-Reviewed Original ResearchCopy number variationsCourse of evolutionSubgroup of cellsWhole-genome sequencing samplesTumor subclonesBayesian feature allocation modelPhylogenetic structureDifferent genetic alterationsPhylogeny structureSequencing depthFeature allocation modelNumber variationsSequencing samplesTree sizeDistinct genotypesGenetic alterationsSubclonesResult of competitionTumor progressionBayesian modelEstimation accuracySifADrug resistanceCellsSimulation study