Zhangsheng Yu
Professor Adjunct of BiostatisticsCards
About
Research
Publications
2024
HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics
Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nature Communications 2024, 15: 5700. PMID: 38972896, PMCID: PMC11228050, DOI: 10.1038/s41467-024-49846-1.Peer-Reviewed Original ResearchConceptsSpatially variable genesVariable genesSpatial expression patternsSpatial transcriptomics technologiesSpatial transcriptomics researchTranscriptome researchTranscriptomic technologiesBiological functionsExpression patternsSpatial transcriptomicsGenesState-of-the-art methodsColorectal cancer dataDeep Learning-Based Detect-Then-Track Pipeline for Treatment Outcome Assessments in Immunotherapy-Treated Liver Cancer
Zhou J, Xia Y, Xun X, Yu Z. Deep Learning-Based Detect-Then-Track Pipeline for Treatment Outcome Assessments in Immunotherapy-Treated Liver Cancer. Journal Of Digital Imaging 2024, 1-14. PMID: 38740661, DOI: 10.1007/s10278-024-01132-8.Peer-Reviewed Original ResearchHarnessing TME depicted by histological images to improve cancer prognosis through a deep learning system
Gao R, Yuan X, Ma Y, Wei T, Johnston L, Shao Y, Lv W, Zhu T, Zhang Y, Zheng J, Chen G, Sun J, Wang Y, Yu Z. Harnessing TME depicted by histological images to improve cancer prognosis through a deep learning system. Cell Reports Medicine 2024, 5: 101536. PMID: 38697103, PMCID: PMC11149411, DOI: 10.1016/j.xcrm.2024.101536.Peer-Reviewed Original ResearchColorectal cancer cohortTumor microenvironmentCancer prognosisCancer cohortCancer Genome Atlas-Breast CancerAssociated with cancer prognosisImprove cancer prognosisPrognosis prediction modelBreast cancerConcordance indexClinical availabilitySurvival modelsSpatial transcriptomicsST expressionCancer typesPrognosisCancerSurvivalHistological imagesSingle-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression
Gong Y, Xu J, Wu M, Gao R, Sun J, Yu Z, Zhang Y. Single-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression. Cell Reports Methods 2024, 4: 100742. PMID: 38554701, PMCID: PMC11045878, DOI: 10.1016/j.crmeth.2024.100742.Peer-Reviewed Original ResearchConceptsSnRNA-seq dataGene modulesAD progressionPathogenesis of Alzheimer's diseaseBiologically interpretable resultsSingle-cell data analysisGene regulatory changesFunctional gene modulesGene coexpression patternsAlzheimer's diseaseSingle-cell levelSnRNA-seqBiclustering methodsPolygenic diseaseBatch effectsDropout eventsCoexpression patternsNetwork biomarkersCell typesBiclusteringCellsGenesScRNABiologyComparative analysisPredicting long-term progression of Alzheimer’s disease using a multimodal deep learning model incorporating interaction effects
Wang Y, Gao R, Wei T, Johnston L, Yuan X, Zhang Y, Yu Z. Predicting long-term progression of Alzheimer’s disease using a multimodal deep learning model incorporating interaction effects. Journal Of Translational Medicine 2024, 22: 265. PMID: 38468358, PMCID: PMC10926590, DOI: 10.1186/s12967-024-05025-w.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseGenetic polymorphism dataProgression of Alzheimer's diseaseMild cognitive impairmentPolymorphism dataAlzheimer's Disease Neuroimaging InitiativeAD progressionArea under the receiver operating characteristic curvePrediction of AD progressionDeep learning modelsADNI-1AlzheimerPatient careLearning modelsMCI to ADInteraction effectsADNI-3Increase prediction accuracyMild cognitive impairment to ADEarly interventionCognitive impairmentClinical assessmentBayesian network-based Mendelian randomization for variant prioritization and phenotypic causal inference
Sun J, Zhou J, Gong Y, Pang C, Ma Y, Zhao J, Yu Z, Zhang Y. Bayesian network-based Mendelian randomization for variant prioritization and phenotypic causal inference. Human Genetics 2024, 1-14. PMID: 38381161, DOI: 10.1007/s00439-024-02640-x.Peer-Reviewed Original ResearchMendelian randomizationGenetic instrumental variablesGenomic dataIndividual-level dataInstrumental variablesUK BiobankFalse-positive discoveriesGenetic structureVariant prioritizationEffect estimatesMR methodsGene interactionsGenetic variantsCausal inferencePsychiatric disordersStatistical powerBlood pressureBayesian frameworkInference frameworkInferenceBiobankEstimationCausal relationshipsPleiotropyGenesA generalized calibrated Bayesian hierarchical modeling approach to basket trials with multiple endpoints
Chi X, Yuan Y, Yu Z, Lin R. A generalized calibrated Bayesian hierarchical modeling approach to basket trials with multiple endpoints. Biometrical Journal 2024, 66: e2300122. PMID: 38368277, PMCID: PMC11323483, DOI: 10.1002/bimj.202300122.Peer-Reviewed Original ResearchConceptsBayesian hierarchical modeling approachShrinkage parameterTheoretical propertiesPhase II basket trialBasket trialsSimulation studyHierarchical modelHierarchical modeling approachFunctional formGeneral hierarchical modelEfficacy endpointLatent variable approachApproach yieldsRisk-benefit profileVariable approachImmunotherapy agentsTumor responseGeneralizationTargeted therapyCancer subtypesMultiple cancer subtypesTreatment effectsMonitoring procedures
2023
Prediction of outpatient waiting time: using machine learning in a tertiary children’s hospital
Li X, Liu W, Kong W, Zhao W, Wang H, Tian D, Jiao J, Yu Z, Liu S. Prediction of outpatient waiting time: using machine learning in a tertiary children’s hospital. Translational Pediatrics 2023, 12: 2030043-2032043. PMID: 38130586, PMCID: PMC10730972, DOI: 10.21037/tp-23-58.Peer-Reviewed Original ResearchMachine learning algorithmsLearning algorithmsOutpatient waiting timesMachine learningPediatric hospitalEnhance healthcare servicesGBDT modelDepartment categoryPatient-centred careWaiting timeEffective hospital managementClassification methodWaiting time of patientsTertiary children's hospitalHealthcare servicesMedical appointmentsOptimization modelAlgorithmPredicted waiting timeHospital managementPatient anxietyMachineChildren's hospitalOutpatient clinicDay of admission