2023
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Lin Y, Cao Y, Willie E, Patrick E, Yang J. Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications 2023, 14: 4272. PMID: 37460600, PMCID: PMC10352351, DOI: 10.1038/s41467-023-39923-2.Peer-Reviewed Original ResearchAlgorithmsCOVID-19Exome SequencingGene Expression ProfilingHumansSequence Analysis, RNASingle-Cell Analysis
2022
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
Lin Y, Wu T, Wan S, Yang J, Wong W, Wang Y. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning. Nature Biotechnology 2022, 40: 703-710. PMID: 35058621, PMCID: PMC9186323, DOI: 10.1038/s41587-021-01161-6.Peer-Reviewed Original ResearchMeSH KeywordsChromatin Immunoprecipitation SequencingExome SequencingMachine LearningRNA-SeqSequence Analysis, RNASingle-Cell AnalysisConceptsData modalitiesTransfer learning methodDifferent data modalitiesSingle-cell multiomics dataTransfer learningUnlabeled dataMultimodal datasetLeverage informationNeural networkLearning methodsData compositionLabel transferLabel accuracyJoint visualizationHeterogeneous collectionPromising resultsUnprecedented paceVisualizationFrameworkMultiomics dataScRNA-seq dataDatasetNetworkScATAC-seq dataCell atlases
2020
Investigating higher-order interactions in single-cell data with scHOT
Ghazanfar S, Lin Y, Su X, Lin D, Patrick E, Han Z, Marioni J, Yang J. Investigating higher-order interactions in single-cell data with scHOT. Nature Methods 2020, 17: 799-806. PMID: 32661426, PMCID: PMC7610653, DOI: 10.1038/s41592-020-0885-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsComputational BiologyDatabases, Nucleic AcidHepatocytesLiverMiceOligonucleotide Array Sequence AnalysisSequence Analysis, RNASingle-Cell AnalysisSoftwareConceptsSingle-cell dataCell fate choiceSingle-cell genomicsDifferential expression testingGene-gene correlationsFate choiceHigher-order interactionsKey genesTranscriptomic dataEmbryonic developmentCoordinated changesExpression testingGenesSubtle changesMouse liverMouse olfactory bulbCellsGenomicsSchotPseudotimeInteractionOlfactory bulbHigher-order measurementsCovariationVariabilityCiteFuse enables multi-modal analysis of CITE-seq data
Kim H, Lin Y, Geddes T, Yang J, Yang P. CiteFuse enables multi-modal analysis of CITE-seq data. Bioinformatics 2020, 36: 4137-4143. PMID: 32353146, DOI: 10.1093/bioinformatics/btaa282.Peer-Reviewed Original ResearchMeSH KeywordsEpitopesGene Expression ProfilingRNASequence Analysis, RNASingle-Cell AnalysisSoftwareTranscriptomeConceptsCITE-seq dataLigand-receptor interaction analysisCell surface proteinsMulti-modal profilingProtein expression analysisLigand-receptor interactionsCell hashingDifferential RNATranscriptome dataDistinct speciesCellular indexingExpression analysisDoublet detectionIntegrative analysisMolecular biologyStreamlined packageTranscriptomeSingle cellsInteractive web-based visualizationSupplementary dataRNAR packageProfilingEpitope profilesSuite of tools
2019
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets
Lin Y, Ghazanfar S, Wang K, Gagnon-Bartsch J, Lo K, Su X, Han Z, Ormerod J, Speed T, Yang P, Yang J. scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 9775-9784. PMID: 31028141, PMCID: PMC6525515, DOI: 10.1073/pnas.1820006116.Peer-Reviewed Original ResearchConceptsMultiple single-cell RNA-seq datasetsSingle-cell RNA-seq datasetsRNA-seq datasetsSingle-cell RNA sequencing dataRNA sequencing dataFurther biological insightsBiological discoveryBiological insightsSequencing dataStable expressionConcerted examinationRobust data integrationLarge collectionIndividual datasetsGenesMultiple collectionsPseudoreplicatesExpression