2023
Shared genetic architecture of blood eosinophil counts and asthma in UK Biobank
Li B, Wang Y, Wang Z, Li X, Kay S, Chupp G, Zhao H, Gomez J. Shared genetic architecture of blood eosinophil counts and asthma in UK Biobank. ERJ Open Research 2023, 9: 00291-2023. PMID: 37650091, PMCID: PMC10463033, DOI: 10.1183/23120541.00291-2023.Peer-Reviewed Original ResearchGenome-wide association studiesGenetic architectureGenetic correlation analysisUK BiobankGWAS resultsTranscription factorsInterleukin-4 SignalingBlood eosinophil countsAssociation studiesDoctor-diagnosed asthmaSignificant variantsEosinophil countEuropean ancestryTraitsPathwayGenetic linkType 2 immune responsesType 2 inflammationSignalingCritical associationImmune responseHeterogeneous diseaseTAGCSevere asthmaTherapeutic interventions
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
Dissecting Pathway Disturbances Using Network Topology and Multi-platform Genomics Data
Zhang Y, Linder M, Shojaie A, Ouyang Z, Shen R, Baggerly K, Baladandayuthapani V, Zhao H. Dissecting Pathway Disturbances Using Network Topology and Multi-platform Genomics Data. Statistics In Biosciences 2017, 10: 86-106. PMID: 37388623, PMCID: PMC10309155, DOI: 10.1007/s12561-017-9193-0.Peer-Reviewed Original ResearchMolecular regulatory elementsCopy number variantsRegulatory elementsMRNA moleculesPathway-based analysisBRAF pathwayCancer Genome Atlas (TCGA) projectMultiple tumor lineagesTumor-specific aberrationsRegulatory topologyRelevant copy number variantsDiverse cancer typesMultiple omicsGenomic dataMajor geneCancer typesGene expressionSingle-platform analysisOncogenic pathwaysNumber variantsMethylationComplex diseasesTumor lineageAtlas projectPathway
2015
Gene-based and pathway-based genome-wide association study of alcohol dependence
Lingjun Z, ZHANG CK, SAYWARD FG, CHEUNG KH, Kesheng W, KRYSTAL JH, Hongyu Z, Xingguang L. Gene-based and pathway-based genome-wide association study of alcohol dependence. General Psychiatry 2015, 27: 111-118. PMID: 26120261, PMCID: PMC4466852, DOI: 10.11919/j.issn.1002-0829.215031.Peer-Reviewed Original ResearchGenome-wide association studiesRisk genesAssociation studiesBiological signaling processesPXN geneGene pathwaysSignaling processesGlycan degradationInteraction pathwayGenetic markersTransporter pathwaysGenesDiscovery samplePathwayReplication sampleAfrican American casesRisk pathwaysMultiple testingBonferroni correctionNew evidence
2014
Graphical Modeling of Biological Pathways in Genome-wide Association Studies
Chen M, Cho J, Zhao H. Graphical Modeling of Biological Pathways in Genome-wide Association Studies. 2014, 294-317. DOI: 10.1093/acprof:oso/9780198709022.003.0012.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesAbstract Genome-wide association studiesBiological pathwaysDisease-associated genesPrior biological knowledgeNeighboring genesPathway topologyAssociation analysisBiological knowledgeGenesSpecific pathwaysPathwayCrohn's disease cohortDiscoveryExchangeable set
2011
Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies
Chen M, Cho J, Zhao H. Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies. PLOS Genetics 2011, 7: e1001353. PMID: 21490723, PMCID: PMC3072362, DOI: 10.1371/journal.pgen.1001353.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesBiological pathwaysSingle gene-based methodsMarkov random field modelGene-based methodsPrior biological knowledgeRandom field modelGWAS analysisAssociation signalsMultiple genesPathway topologyGene associationsAssociation analysisGenesBiological knowledgeField modelGenetic variantsSpecific pathwaysReal data examplePathwayStatistical inferenceConditional modes algorithmExchangeable setRegression form
2001
Light Control of Arabidopsis Development Entails Coordinated Regulation of Genome Expression and Cellular Pathways
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. The Plant Cell 2001, 13: 2589. DOI: 10.2307/3871521.Peer-Reviewed Original ResearchLight 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