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 statesSeverityOutcomesCellsLungSymptoms
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