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
2023
Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression
Lin C, Liu W, Jiang W, Zhao H. Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression. Biology Methods And Protocols 2023, 8: bpad024. PMID: 37901453, PMCID: PMC10599978, DOI: 10.1093/biomethods/bpad024.Peer-Reviewed Original ResearchExpression quantitative trait lociGenome-wide association studiesComplex traitsGene expression regulationGenetic association signalsQuantitative trait lociScore regressionDisease-associated variantsSNP annotationGene annotationExpression regulationGWAS resultsTrait lociTrait heritabilityEQTL effectsAssociation signalsGene expressionAssociation studiesGene effectsSNP effectsHuman diseasesHeritabilityTraitsBiological realityAnnotation
2020
Statistical Methods in Genome-Wide Association Studies
Sun N, Zhao H. Statistical Methods in Genome-Wide Association Studies. Annual Review Of Biomedical Data Science 2020, 3: 1-24. DOI: 10.1146/annurev-biodatasci-030320-041026.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesTraits of interestGenetic architectureIdentification of variantsGWAS dataStatistical methodologyStatistical challengesGenetic risk prediction modelsGenetic markersStatistical methodsHuman diseasesPhenotype informationGenetic variantsTraitsGenotype informationScientific goalsRecent progressGenesVariantsTens of thousandsHundreds of thousandsPrediction modelPathwayThousands
2017
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
Lu Q, Powles RL, Abdallah S, Ou D, Wang Q, Hu Y, Lu Y, Liu W, Li B, Mukherjee S, Crane PK, Zhao H. Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease. PLOS Genetics 2017, 13: e1006933. PMID: 28742084, PMCID: PMC5546707, DOI: 10.1371/journal.pgen.1006933.Peer-Reviewed Original ResearchConceptsTissue typesNon-coding elementsNon-coding genomeComplex human diseasesLate-onset Alzheimer's diseaseIndividual cell typesRelevant tissue typesGWAS traitsTranscriptomic annotationGenome annotationFunctional annotationDNA elementsHeritability enrichmentHuman genomeLarge international consortiaVariety of cellsGenomeHuman diseasesAnnotation dataCell typesGenetic variantsOrgan system categoriesComplex diseasesSimilar localizationAnnotation
1997
Strategies to Identify Genes for Complex Diseases
Zhang H, Zhao H, Merikangas K. Strategies to Identify Genes for Complex Diseases. Annals Of Medicine 1997, 29: 493-498. PMID: 9562515, DOI: 10.3109/07853899709007473.Peer-Reviewed Original ResearchConceptsComplex diseasesNumerous human diseasesDisease-susceptible genesComplex human disordersHuman genomeGenetic basisHuman disordersHuman diseasesMolecular biologyGenesGenetic epidemiological studiesGenetic factorsComplex patternsDisease pathophysiologyGenomeBiologyTraitsInheritanceMultiple sclerosisBreast cancerEpidemiological studies
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