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
2012
A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes
Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF, Balázsi G. A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. British Journal Of Cancer 2012, 106: 1107-1116. PMID: 22343619, PMCID: PMC3304402, DOI: 10.1038/bjc.2011.584.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsCell Line, TumorComputer SimulationDNA Copy Number VariationsEpithelial-Mesenchymal TransitionFemaleGene ExpressionGene Expression ProfilingGene Expression Regulation, NeoplasticGene Knockdown TechniquesGene Regulatory NetworksGenes, NeoplasmHumansModels, BiologicalProtein Interaction MapsReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneRNA InterferenceConceptsGenome-scale dataCore biological pathwaysTriple receptor-negative breast cancerProtein-protein interactionsCell line data setsGene knockdown experimentsGene copy number dataCopy number dataCopy number variation dataNumber variation dataMember genesGene networksTranscriptional disturbancesKnockdown experimentsBiological discoveryGene expressionFunctional specificityBiological pathwaysDifferential expressionIntegrative studyFunctional relevanceVariation dataLine data setsCell linesGenes
2011
S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer.
Pusztai L, Qi Y, Shi W, Liu C, Wang B, Liu X, Booser D, Esteva F, Symmans F, Hortobagyi G. S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer. Cancer Research 2011, 71: s6-4-s6-4. DOI: 10.1158/0008-5472.sabcs11-s6-4.Peer-Reviewed Original ResearchGene expression profilingBiological pathwaysExpression profilingHuman protein kinasesImportant regulatory genesCanonical biological pathwaysDNA copy number variationsDNA copy number alterationsArray CGHSOLiD sequencing platformTarget base pairCopy number variationsFunctional impact scoresCopy number alterationsProtein functionAffymetrix U133A chipsMAPK familyRegulatory genesBMP2KEntire genomeProtein kinaseSequence dataGerm-line variantsGenomic dataBiological functions