Featured Publications
SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure
Tang D, Park S, Zhao H. SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure. Genome Biology 2022, 23: 129. PMID: 35706040, PMCID: PMC9199219, DOI: 10.1186/s13059-022-02688-w.Peer-Reviewed Original ResearchConceptsCell type-specific gene expressionType-specific gene expressionCell type proportionsDifferential expression analysisCell type-specific gene expression profilesExpression analysisGene expressionSingle-cell RNA-seq dataRNA-seq dataGene differential expression analysisGene expression profilesType proportionsExpression profilesExpressionGenesCells
2023
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo
May D, Yun S, Gonzalez D, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez L, Cockburn K, Greco V. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. ELife 2023, 12: e83444. PMID: 36880644, PMCID: PMC10027315, DOI: 10.7554/elife.83444.Peer-Reviewed Original ResearchConceptsStem cell differentiationCell differentiationStem cell compartmentCompaction changesChromatin compaction statesDynamic transcriptional statesCell compartmentChromatin architectureCell cycle statusChromatin rearrangementNascent RNATranscriptional burstingTranscriptional statesLive imagingTissue contextGene expressionDifferentiating cellsGlobal remodelingIndividual cellsCycle statusStem cellsDifferentiation statusDifferentiationCellsMorphological changes
2022
Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer
Li L, Zhang Y, Ren Y, Cheng Z, Zhang Y, Wang X, Zhao H, Lu H. Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer. Frontiers In Bioengineering And Biotechnology 2022, 10: 849798. PMID: 35646860, PMCID: PMC9136039, DOI: 10.3389/fbioe.2022.849798.Peer-Reviewed Original ResearchUpper gastrointestinal cancerCancer stem cellsPoor eating habitsTumor stem cellsChronic inflammationGastrointestinal cancerEating habitsStem cellsGastrointestinal cancer stem cellsPersistent chronic inflammationGastrointestinal cancer diagnosisCore signal pathwaysWnt pathway genesMucosa damagePoor outcomeAggressive carcinomasInflammatory genesSpecific cancer stem cellsCancer diagnosisCancerSignal pathwayInflammationWnt pathwayCell typesCells
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
2014
Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T Cells
Schenten D, Nish S, Yu S, Yan X, Lee H, Brodsky I, Pasman L, Yordy B, Wunderlich F, Brüning J, Zhao H, Medzhitov R. Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T Cells. Immunity 2014, 40: 814. DOI: 10.1016/j.immuni.2014.04.012.Peer-Reviewed Original Research