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
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Lin Y, Cao Y, Kim H, Salim A, Speed T, Lin D, Yang P, Yang J. scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Molecular Systems Biology 2020, 16: msb199389. PMID: 32567229, PMCID: PMC7306901, DOI: 10.15252/msb.20199389.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCellsCluster AnalysisDatabases as TopicHumansLeukocytes, MononuclearMachine LearningMicePancreasSample SizeSoftwareConceptsType hierarchyKey computational challengeType identificationMultiple referencesType classification methodMultiscale classificationEnsemble learningCell type hierarchyClassification frameworkClassification methodPairs of referenceJoint classificationComputational challengesAccurate classificationLarge collectionTesting dataArt methodologiesDatasetLevel of complexityExperimental datasetsCell type identificationClassificationSingle-cell atlasesNovel applicationScalability