2023
Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms
Zyla J, Papiez A, Zhao J, Qu R, Li X, Kluger Y, Polanska J, Hatzis C, Pusztai L, Marczyk M. Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms. Computational And Structural Biotechnology Journal 2023, 21: 4663-4674. PMID: 37841335, PMCID: PMC10568495, DOI: 10.1016/j.csbj.2023.09.035.Peer-Reviewed Original ResearchSingle-cell RNA-seq platformsSingle-cell RNA sequencingBulk RNA-seq dataRNA-seq platformsNumber of transcriptsLow-expression genesRNA-seq dataSingle-cell dataExpression levelsLow sequencing depthDiscordant genesRNA sequencingSequencing technologiesExpression shiftsPathway levelBiological pathwaysGene levelSequencing depthTranscriptomic platformsGenesIndividual cellsSingle cellsRNA integrityPathwayCells
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