2020
Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue
Lau R, Du L, Chen E, Fu C, Gould R, Marczyk M, Sinn BV, Layman R, Bedrosian I, Valero V, Symmans WF. Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue. Clinical Chemistry 2020, 66: 934-945. PMID: 32613237, DOI: 10.1093/clinchem/hvaa105.Peer-Reviewed Original ResearchConceptsQuantiGene PlexConcordance correlation coefficientBreast cancer tissuesParaffin-embedded tissue sectionsEndocrine therapyResection samplesBreast cancerTumor sectionsCancer tissuesStage IIParaffin blocksLin's concordance correlation coefficientTissue sectionsCustomized assayTherapyAnalytical sensitivityFFPE samplesNanoStringFFPE tissuesExpression indexWeekly testsAssaysTissueTechnical validity
2017
Ranking metrics in gene set enrichment analysis: do they matter?
Zyla J, Marczyk M, Weiner J, Polanska J. Ranking metrics in gene set enrichment analysis: do they matter? BMC Bioinformatics 2017, 18: 256. PMID: 28499413, PMCID: PMC5427619, DOI: 10.1186/s12859-017-1674-0.Peer-Reviewed Original Research
2013
Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays
Jaksik R, Marczyk M, Polanska J, Rzeszowska-Wolny J. Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays. Sensors 2013, 14: 532-548. PMID: 24385030, PMCID: PMC3926573, DOI: 10.3390/s140100532.Peer-Reviewed Original ResearchBase CompositionOligonucleotide Array Sequence AnalysisAdaptive filtering of microarray gene expression data based on Gaussian mixture decomposition
Marczyk M, Jaksik R, Polanski A, Polanska J. Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition. BMC Bioinformatics 2013, 14: 101. PMID: 23510016, PMCID: PMC3637832, DOI: 10.1186/1471-2105-14-101.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsGene Expression ProfilingHumansNormal DistributionOligonucleotide Array Sequence AnalysisConceptsGaussian mixture decompositionFalse discoveriesMicroarray gene expression dataNon-informative genesAdaptive filteringSample meanAdaptive methodSample varianceGaussian componentsMixture decompositionGene filteringEarlier paperGene expression dataFilteringOptimal threshold valuePrevious methodsMicroarray experimentsNew methodTwo-step procedureThreshold valueCorrection methodPower of detectionImportant parametersSecond stepMicroarray data