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 dataSingle-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 analysisBayesian 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, 143: 1081-1094. 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 relationshipsPleiotropyGenes