2024
SANTO: a coarse-to-fine alignment and stitching method for spatial omics
Li H, Lin Y, He W, Han W, Xu X, Xu C, Gao E, Zhao H, Gao X. SANTO: a coarse-to-fine alignment and stitching method for spatial omics. Nature Communications 2024, 15: 6048. PMID: 39025895, PMCID: PMC11258319, DOI: 10.1038/s41467-024-50308-x.Peer-Reviewed Original Research
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 Research
2022
Scalable workflow for characterization of cell-cell communication in COVID-19 patients
Lin Y, Loo L, Tran A, Lin D, Moreno C, Hesselson D, Neely G, Yang J. Scalable workflow for characterization of cell-cell communication in COVID-19 patients. PLOS Computational Biology 2022, 18: e1010495. PMID: 36197936, PMCID: PMC9534414, DOI: 10.1371/journal.pcbi.1010495.Peer-Reviewed Original ResearchConceptsCOVID-19 patientsSevere patientsDisease severityDysfunctional immune responseDistinct disease outcomesHigher mortality riskSARS-CoV-2Different disease statesImmune cellsLung tissueDisease outcomeImmune responseMortality riskPatientsCell-cell interactionsPathogenic outcomesCritical symptomsCell-cell interaction patternsDisease statesSeverityOutcomesCellsLungSymptomsscFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction
Cao Y, Lin Y, Patrick E, Yang P, Yang J. scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinformatics 2022, 38: 4745-4753. PMID: 36040148, PMCID: PMC9563679, DOI: 10.1093/bioinformatics/btac590.Peer-Reviewed Original ResearchHumansSoftware
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 ResearchConceptsType 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
2019
Evaluating stably expressed genes in single cells
Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin D, Speed T, Yang J, Yang P. Evaluating stably expressed genes in single cells. GigaScience 2019, 8: giz106. PMID: 31531674, PMCID: PMC6748759, DOI: 10.1093/gigascience/giz106.Peer-Reviewed Original ResearchConceptsSingle-cell levelScRNA-seq datasetsHousekeeping genesExpression stabilitySingle-cell RNA-seq profilingSingle cellsSingle-cell transcriptomesRNA-seq profilingSubset of genesDiverse biological systemsBioconductor R packageCell population levelEssential functionsStable expressionGenesIndividual cellsData normalizationTissue typesCell populationsDifferent cellsPopulation levelR packageBiological systemsCellsPotential rolescMerge 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