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
2019
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Zyla J, Marczyk M, Domaszewska T, Kaufmann SHE, Polanska J, Weiner J. Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics 2019, 35: 5146-5154. PMID: 31165139, PMCID: PMC6954644, DOI: 10.1093/bioinformatics/btz447.Peer-Reviewed Original ResearchConceptsReal-world datasetsEvaluation metricsCernoNovel algorithmReproducible scienceOnline implementationComputational timeFalse positive ratePractical reproducibilityFast algorithmSupplementary dataAlgorithmRelated dataNovel approachDatasetR packageEnrichment algorithmPositive rateMetricsImplementationEssential partGS sizeRepositoryPackage