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
2021
Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies
Marczyk M, Macioszek A, Tobiasz J, Polanska J, Zyla J. Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies. Frontiers In Genetics 2021, 12: 767358. PMID: 34956320, PMCID: PMC8696167, DOI: 10.3389/fgene.2021.767358.Peer-Reviewed Original ResearchGenome-wide association studiesOver-Representation AnalysisSingle nucleotide polymorphismsMeta-Analysis Gene-set EnrichmentSame geneTypical genome-wide association studyEnrichment analysisAssociation studiesGene-set analysisLD correctionGene set enrichmentGene expression dataGSEA-SNPCancer Genome Atlas (TCGA) databaseRelevant single nucleotide polymorphismsTranscriptomic levelGene levelExpression dataVariant associationsNonrandom associationGenesAssociation of SNPsMore lociAtlas databaseBreast cancer samples