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
2025
The human and non-human primate developmental GTEx projects
Bell T, Blanchard T, Hernandez R, Linn R, Taylor D, VonDran M, Ahooyi T, Beitra D, Bernieh A, Delaney M, Faith M, Fattahi E, Footer D, Gilbert M, Guambaña S, Gulino S, Hanson J, Hattrell E, Heinemann C, Kreeb J, Leino D, Mcdevitt L, Palmieri A, Pfeiffer M, Pryhuber G, Rossi C, Rasool I, Roberts R, Salehi A, Savannah E, Stachowicz K, Stokes D, Suplee L, Van Hoose P, Wilkins B, Williams-Taylor S, Zhang S, Ardlie K, Getz G, Lappalainen T, Montgomery S, Aguet F, Anderson L, Bernstein B, Choudhary A, Domenech L, Gaskell E, Johnson M, Liu Q, Marderstein A, Nedzel J, Okonda J, Padhi E, Rosano M, Russell A, Walker B, Sestan N, Gerstein M, Milosavljevic A, Borsari B, Cho H, Clarke D, Deveau A, Galeev T, Gobeske K, Hameed I, Huttner A, Jensen M, Jiang Y, Li J, Liu J, Liu Y, Ma J, Mane S, Meng R, Nadkarni A, Ni P, Park S, Petrosyan V, Pochareddy S, Salamon I, Xia Y, Yates C, Zhang M, Zhao H, Conrad D, Feng G, Brady F, Boucher M, Carbone L, Castro J, del Rosario R, Held M, Hennebold J, Lacey A, Lewis A, Lima A, Mahyari E, Moore S, Okhovat M, Roberts V, de Castro S, Wessel B, Zaniewski H, Zhang Q, Arguello A, Baroch J, Dayal J, Felsenfeld A, Ilekis J, Jose S, Lockhart N, Miller D, Minear M, Parisi M, Price A, Ramos E, Zou S. The human and non-human primate developmental GTEx projects. Nature 2025, 637: 557-564. PMID: 39815096, DOI: 10.1038/s41586-024-08244-9.Peer-Reviewed Original ResearchConceptsChromatin accessibility dataFunctional genomic studiesWhole-genome sequencingEffects of genetic variationSpatial gene expression profilesNon-human primatesGenotype-Tissue ExpressionGene expression profilesGenomic studiesGene regulationGenetic dataGenetic variationGenomic researchDonor diversityCommunity engagementHuman evolutionEarly developmental defectsGene expressionCell statesDevelopmental programmeHuman diseasesExpression profilesAdult tissuesDevelopmental defectsSingle-cell
2001
Light Control of Arabidopsis Development Entails Coordinated Regulation of Genome Expression and Cellular Pathways[W]
Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng X. Light Control of Arabidopsis Development Entails Coordinated Regulation of Genome Expression and Cellular Pathways[W]. The Plant Cell 2001, 13: 2589-2607. PMID: 11752374, PMCID: PMC139475, DOI: 10.1105/tpc.010229.Peer-Reviewed Original ResearchMeSH KeywordsArabidopsisArabidopsis ProteinsCryptochromesDrosophila ProteinsExpressed Sequence TagsEye ProteinsFlavoproteinsGene Expression Regulation, DevelopmentalGene Expression Regulation, PlantGenome, PlantLightOligonucleotide Array Sequence AnalysisPhotoreceptor CellsPhotoreceptor Cells, InvertebratePhytochromePhytochrome APhytochrome BPlant ProteinsPlant ShootsReceptors, G-Protein-CoupledTranscription FactorsConceptsArabidopsis developmentExpression profilesGenome expressionCellular pathwaysLight-regulated genesSimilar gene expression profilesGenome expression profilesDistinct expression profilesGene expression profilesDifferent light qualitiesPhytochrome BSequence tagsCoordinated regulationPhytochrome ARegulatory pathwaysLight qualityLight conditionsDark transitionGenesPathwayLight treatmentLight controlBlue lightExpressionCryptochromes
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