2024
Knowledge-guided learning methods for integrative analysis of multi-omics data
Li W, Ballard J, Zhao Y, Long Q. Knowledge-guided learning methods for integrative analysis of multi-omics data. Computational And Structural Biotechnology Journal 2024, 23: 1945-1950. PMID: 38736693, PMCID: PMC11087912, DOI: 10.1016/j.csbj.2024.04.053.Peer-Reviewed Original ResearchAnalysis of multi-omics dataIntegrative analysis of multi-omics dataMulti-omics dataMulti-omics data integration methodBiological knowledgeMulti-omics data integrationMulti-omics data analysisMulti-omics studiesIntegrated analysisFunctional genomicsFunctional proteomicsData integration methodsComplex diseasesMolecular mechanismsAlzheimer's diseaseComprehensive insightGenomeProteomicsGenesAnalytical challengesPathwayAlzheimerBayesian mixed model inference for genetic association under related samples with brain network phenotype
Tian X, Wang Y, Wang S, Zhao Y, Zhao Y. Bayesian mixed model inference for genetic association under related samples with brain network phenotype. Biostatistics 2024, kxae008. PMID: 38494649, DOI: 10.1093/biostatistics/kxae008.Peer-Reviewed Original ResearchSample relatednessGenetic studiesGenetic association studiesRisk genetic variantsImaging genetics studiesPopulation structureAssociation studiesQuantitative phenotypesQuantitative geneticsGenetic basisGenetic variantsGenetic associationGenetic contributionPhenotypeRelatednessConnectivity traitsNetwork phenotypesConnectivity phenotypesMarkov chain Monte CarloMixed-effects modelsPedigreeGeneticsBiological structuresTraitsHuman Connectome ProjectHeterogeneity Analysis on Multi-State Brain Functional Connectivity and Adolescent Neurocognition
Wang S, Constable T, Zhang H, Zhao Y. Heterogeneity Analysis on Multi-State Brain Functional Connectivity and Adolescent Neurocognition. Journal Of The American Statistical Association 2024, 119: 851-863. DOI: 10.1080/01621459.2024.2311363.Peer-Reviewed Original ResearchBayesian semi-parametric inference for clustered recurrent events with zero inflation and a terminal event
Tian X, Ciarleglio M, Cai J, Greene E, Esserman D, Li F, Zhao Y. Bayesian semi-parametric inference for clustered recurrent events with zero inflation and a terminal event. Journal Of The Royal Statistical Society Series C (Applied Statistics) 2024, 73: 598-620. PMID: 39072299, PMCID: PMC11271983, DOI: 10.1093/jrsssc/qlae003.Peer-Reviewed Original ResearchSemi-parametric inferenceRecurrent eventsAccelerated failure time modelFailure time modelEfficient sampling algorithmFrailty distributionDirichlet processPosterior inferenceSampling algorithmTime modelTerminal eventSurvival processesComplex data structuresDirichletInferenceData structureFall injury preventionAlgorithmHomological Landscape of Human Brain Functional Sub-Circuits
Duong-Tran D, Kaufmann R, Chen J, Wang X, Garai S, Xu F, Bao J, Amico E, Kaplan A, Petri G, Goni J, Zhao Y, Shen L. Homological Landscape of Human Brain Functional Sub-Circuits. Mathematics 2024, 12: 455. DOI: 10.3390/math12030455.Peer-Reviewed Original ResearchFunctional sub-circuitsHuman brain functional connectivityWhole-brain functional connectivity networksNon-local propertiesWorking memory taskWhole-brain levelBrain functional connectivityNon-localFunctional connectivity networksMemory taskEmotional tasksLimbic networkMode networkFunctional connectivityBrain connectomeWhole-brainFormalismLocal structureMotor tasksConnectivity networksSubject domainSub-circuitsTask
2023
Identifying Shared Neuroanatomic Architecture Between Cognitive Traits Through Multiscale Morphometric Correlation Analysis
Wen Z, Bao J, Yang S, Risacher S, Saykin A, Thompson P, Davatzikos C, Huang H, Zhao Y, Shen L. Identifying Shared Neuroanatomic Architecture Between Cognitive Traits Through Multiscale Morphometric Correlation Analysis. Lecture Notes In Computer Science 2023, 14394: 227-240. PMID: 38584725, PMCID: PMC10993314, DOI: 10.1007/978-3-031-47425-5_21.Peer-Reviewed Original Research
2022
Simulating time-to-event data subject to competing risks and clustering: A review and synthesis
Meng C, Esserman D, Li F, Zhao Y, Blaha O, Lu W, Wang Y, Peduzzi P, Greene E. Simulating time-to-event data subject to competing risks and clustering: A review and synthesis. Statistical Methods In Medical Research 2022, 32: 305-333. PMID: 36412111, DOI: 10.1177/09622802221136067.Peer-Reviewed Original ResearchSex-specific genetic association between psychiatric disorders and cognition, behavior and brain imaging in children and adults
Gui Y, Zhou X, Wang Z, Zhang Y, Wang Z, Zhou G, Zhao Y, Liu M, Lu H, Zhao H. Sex-specific genetic association between psychiatric disorders and cognition, behavior and brain imaging in children and adults. Translational Psychiatry 2022, 12: 347. PMID: 36028495, PMCID: PMC9418275, DOI: 10.1038/s41398-022-02041-6.Peer-Reviewed Original ResearchConceptsCognitive functionFluid intelligenceCognitive traitsAdolescent Brain Cognitive Development (ABCD) studyPsychiatric disordersCognitive Development StudyMediation effectMost psychiatric disordersPolygenic risk scoresBrain functionBrain structuresBrain imagingEarly etiologySex differencesDevelopment studiesPsychiatric traitsChildrenIntelligenceDisordersSchizophreniaGenetic riskAdultsTraitsCognitionAutismBayesian network mediation analysis with application to the brain functional connectome
Zhao Y, Chen T, Cai J, Lichenstein S, Potenza M, Yip S. Bayesian network mediation analysis with application to the brain functional connectome. Statistics In Medicine 2022, 41: 3991-4005. PMID: 35795965, PMCID: PMC10131252, DOI: 10.1002/sim.9488.Peer-Reviewed Original ResearchConceptsStochastic block modelBayesian paradigmBrain functional connectomeBlock modelConnectivity weightsFunctional connectomeNetwork measurementsEffect componentApproach applicationBlock allocationOpioid abstinenceAnalytic approachNetwork neurosciencePractical illustrationTherapeutic interventionsMediation analysisNeural circuitsNetwork structureBrain functioningMediatorsFunctional networksFeature selectionApplicationsModelNetworkPursuing sources of heterogeneity in modeling clustered population.
Li Y, Yu C, Zhao Y, Yao W, Aseltine RH, Chen K. Pursuing sources of heterogeneity in modeling clustered population. Biometrics 2022, 78: 716-729. PMID: 33527347, DOI: 10.1111/biom.13434.Peer-Reviewed Original ResearchUsing machine learning to predict heavy drinking during outpatient alcohol treatment
Roberts W, Zhao Y, Verplaetse T, Moore KE, Peltier MR, Burke C, Zakiniaeiz Y, McKee S. Using machine learning to predict heavy drinking during outpatient alcohol treatment. Alcohol Clinical And Experimental Research 2022, 46: 657-666. PMID: 35420710, PMCID: PMC9180421, DOI: 10.1111/acer.14802.Peer-Reviewed Original ResearchConceptsAlcohol use disorderHeavy drinkingTreatment outcomesInvasive assessment methodsOutpatient AUD treatmentLast monthOutpatient alcohol treatmentMultisite clinical trialAccurate clinical predictionsHeavy alcohol useSex differencesBi-weekly sessionsAlcohol treatment outcomesPatient characteristicsClinical outcomesClinical trialsClinical dataStratified analysisEffective treatmentPsychiatric disordersUse disordersAUD treatmentSubstantial sex differencesAlcohol treatmentFirst monthA comparison of analytical strategies for cluster randomized trials with survival outcomes in the presence of competing risks
Li F, Lu W, Wang Y, Pan Z, Greene EJ, Meng G, Meng C, Blaha O, Zhao Y, Peduzzi P, Esserman D. A comparison of analytical strategies for cluster randomized trials with survival outcomes in the presence of competing risks. Statistical Methods In Medical Research 2022, 31: 1224-1241. PMID: 35290139, PMCID: PMC10518064, DOI: 10.1177/09622802221085080.Peer-Reviewed Original ResearchBayesian Interaction Selection Model for Multimodal Neuroimaging Data Analysis
Zhao Y, Wu B, Kang J. Bayesian Interaction Selection Model for Multimodal Neuroimaging Data Analysis. Biometrics 2022, 79: 655-668. PMID: 35220581, PMCID: PMC9418386, DOI: 10.1111/biom.13648.Peer-Reviewed Original ResearchIdentifying imaging genetic associations via regional morphometricity estimation.
Bao J, Wen Z, Kim M, Saykin AJ, Thompson PM, Zhao Y, Shen L. Identifying imaging genetic associations via regional morphometricity estimation. Biocomputing 2022, 27: 97-108. PMID: 34890140, PMCID: PMC8730533.Peer-Reviewed Original ResearchIdentifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data.
Bao J, Wen Z, Kim M, Zhao X, Lee BN, Jung SH, Davatzikos C, Saykin AJ, Thompson PM, Kim D, Zhao Y, Shen L, . Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data. Biocomputing 2022, 27: 109-120. PMID: 34890141, PMCID: PMC8730532.Peer-Reviewed Original Research
2021
Identifying highly heritable brain amyloid phenotypes through mining Alzheimer’s imaging and sequencing biobank data
Bao J, Wen Z, Kim M, Zhao X, Lee B, Jung S, Davatzikos C, Saykin A, Thompson P, Kim D, Zhao Y, Shen L. Identifying highly heritable brain amyloid phenotypes through mining Alzheimer’s imaging and sequencing biobank data. 2021, 109-120. DOI: 10.1142/9789811250477_0011.Peer-Reviewed Original ResearchA Novel Bayesian Semi-parametric Model for Learning Heritable Imaging Traits
Zhao Y, Zhao X, Kim M, Bao J, Shen L. A Novel Bayesian Semi-parametric Model for Learning Heritable Imaging Traits. Lecture Notes In Computer Science 2021, 12905: 678-687. PMID: 35299630, PMCID: PMC8922551, DOI: 10.1007/978-3-030-87240-3_65.Peer-Reviewed Original ResearchBayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data
Zhao Y, Chang C, Hannum M, Lee J, Shen R. Bayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data. Scientific Reports 2021, 11: 5146. PMID: 33664338, PMCID: PMC7933297, DOI: 10.1038/s41598-021-84514-0.Peer-Reviewed Original ResearchConceptsMolecular dataJoint posterior distributionHigh-dimensional settingsVariational Bayes approachSingle-cell dataArt clustering methodsPosterior distributionMolecular profiling dataComputational efficiencyCanonical oncogenicTranscriptomic alterationsBiological discoveryModel inferenceBayes approachCell decompositionStemness phenotypeProfiling dataSingle cellsComputational methodsBulk tumorPathway alterationsNebulaClustering methodAnalysis settingsCell dataPolygenic mediation analysis of Alzheimer's disease implicated intermediate amyloid imaging phenotypes.
Yingxuan E, Yao X, Liu K, Risacher SL, Saykin AJ, Long Q, Zhao Y, Shen L. Polygenic mediation analysis of Alzheimer's disease implicated intermediate amyloid imaging phenotypes. AMIA Annual Symposium Proceedings 2021, 2020: 422-431. PMID: 33936415, PMCID: PMC8075527.Peer-Reviewed Original Research
2020
Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes
Zhao Y, Li T, Zhu H. Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes. Biostatistics 2020, 23: 467-484. PMID: 32948880, PMCID: PMC9308456, DOI: 10.1093/biostatistics/kxaa035.Peer-Reviewed Original ResearchConceptsHeritability analysisHuman complex traitsLarge-scale phenotypeQuantitative geneticsComplex traitsPhenotypic variationTrait selectionGenetic datasetsSingle phenotypeDownstream analysisGenetic contributionHeritability estimationPhenotypeTraitsCentral roleNeuroimaging phenotypesUnited Kingdom BiobankHierarchical selectionPhenotypic methodsGeneticsHeritabilitySelectionVariationBrain variation