2021
Detection of differentially abundant cell subpopulations in scRNA-seq data
Zhao J, Jaffe A, Li H, Lindenbaum O, Sefik E, Jackson R, Cheng X, Flavell RA, Kluger Y. Detection of differentially abundant cell subpopulations in scRNA-seq data. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2100293118. PMID: 34001664, PMCID: PMC8179149, DOI: 10.1073/pnas.2100293118.Peer-Reviewed Original ResearchMeSH KeywordsAgingB-LymphocytesBrainCell LineageCOVID-19CytokinesDatasets as TopicDendritic CellsGene Expression ProfilingGene Expression RegulationHigh-Throughput Nucleotide SequencingHumansMelanomaMonocytesPhenotypeRNA, Small CytoplasmicSARS-CoV-2Severity of Illness IndexSingle-Cell AnalysisSkin NeoplasmsT-LymphocytesTranscriptomeConceptsDA subpopulationsIll COVID-19 patientsImmune checkpoint therapyCOVID-19 patientsSingle-cell RNA sequencing analysisCheckpoint therapyBrain tissueCell subpopulationsRNA sequencing analysisTime pointsSubpopulationsDiseased individualsDistinct phenotypesOriginal studyCell typesAbundant subpopulationSequencing analysisCellsDA measuresPhenotypeImportant differencesNonrespondersPatientsTherapy
2013
TrAp: a tree approach for fingerprinting subclonal tumor composition
Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Research 2013, 41: e165-e165. PMID: 23892400, PMCID: PMC3783191, DOI: 10.1093/nar/gkt641.Peer-Reviewed Original ResearchConceptsGenome-wide experimentsEvolutionary relationshipsMutational profileSequencing technologiesMixed cell populationsSilico analysisTumor samplesCell subpopulationsEvolutionary frameworkNumber of subpopulationsSingle cellsEvolutionary pathCell populationsCollective signalClonal compositionMetastatic potentialNumerous cellsTumor karyotypeComputational approachSubpopulationsCellsMixed subpopulationsAbundanceDistinct metastasesTumor composition