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
2017
Mixture Modeling of 2-D Gel Electrophoresis Spots Enhances the Performance of Spot Detection
Marczyk M. Mixture Modeling of 2-D Gel Electrophoresis Spots Enhances the Performance of Spot Detection. IEEE Transactions On NanoBioscience 2017, 16: 91-99. PMID: 28278480, DOI: 10.1109/tnb.2017.2676725.Peer-Reviewed Original ResearchImproving Peak Detection by Gaussian Mixture Modeling of Mass Spectral Signal
Marczyk M, Polanska J, Polanski A. Improving Peak Detection by Gaussian Mixture Modeling of Mass Spectral Signal. 2017, 39-43. DOI: 10.1109/icfsp.2017.8097057.Peer-Reviewed Original Research
2016
Improved Detection of 2D Gel Electrophoresis Spots by Using Gaussian Mixture Model
Marczyk M. Improved Detection of 2D Gel Electrophoresis Spots by Using Gaussian Mixture Model. Lecture Notes In Computer Science 2016, 9683: 284-294. DOI: 10.1007/978-3-319-38782-6_24.Peer-Reviewed Original ResearchParallel computing capabilitiesSpot detectionGaussian mixture modelGel imagesComputing capabilitiesAutomatic methodEfficient implementationComputational timeBest overall performanceMixture modelAbstract2D gel electrophoresisOverall performanceImagesTrue positionDetectionAlgorithmDatasetSoftwareImplementationCapabilityMethodThousandsAccurate estimates
2015
Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry
Polanski A, Marczyk M, Pietrowska M, Widlak P, Polanska J. Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry. PLOS ONE 2015, 10: e0134256. PMID: 26230717, PMCID: PMC4521892, DOI: 10.1371/journal.pone.0134256.Peer-Reviewed Original ResearchConceptsGaussian mixture modelingMixture modelGaussian mixture modelPeak detectionProteomic mass spectraFeature extractionPartitioning algorithmEfficient algorithmSignal compressionSoftware packageAlgorithmMain ideaMixture modelingModeling approachModelingDatasetApplicationsDetectionPreliminary resultsDetection efficiencyProteomic datasetsMixture modeling approachModelDifferent typesHigh resolution
2014
Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF Spectra
Marczyk M, Polanska J, Polanski A. Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF Spectra. Advances In Intelligent Systems And Computing 2014, 242: 193-201. DOI: 10.1007/978-3-319-02309-0_20.Peer-Reviewed Original ResearchComparison of algorithmsPerformance of algorithmsPre-processing toolDifferent machineDifferent simulation scenariosVirtual instrumentAlignment algorithmAlgorithmSimulation scenariosTransform algorithmFast Fourier transform algorithmMajor techniquesFourier transform algorithmLow-resolution dataAlignment artifactsPeak alignmentSpectral alignmentStatistical measuresProblem of shiftsMachineResolution dataAlignmentIndispensable elementRobustnessScenariosAn Efficient Algorithm for Microarray Probes Re-annotation
Foszner P, Gruca A, Polanski A, Marczyk M, Jaksik R, Polanska J. An Efficient Algorithm for Microarray Probes Re-annotation. Lecture Notes In Computer Science 2014, 8342: 201-218. DOI: 10.1007/978-3-642-54455-2_9.Peer-Reviewed Original ResearchRe-annotation procedureComputational problemsEfficient algorithmAvailable servicesHuge sizeDNA microarray dataSuch dataChip standardsDNA microarray experimentsElaborated systemMicroarray dataStandard chipsAlgorithmSystemEffective toolToolTaskAnalysis of resultsMicroarray probesMicroarray experimentsMicroarray probe setsServicesBLATDataDatabase
2011
Efficient Algorithm for Microarray Probes Re-annotation
Foszner P, Gruca A, Polanski A, Marczyk M, Jaksik R, Polanska J. Efficient Algorithm for Microarray Probes Re-annotation. Lecture Notes In Computer Science 2011, 6923: 281-289. DOI: 10.1007/978-3-642-23938-0_29.Peer-Reviewed Original ResearchRe-annotation procedureComputational problemsEfficient algorithmAvailable servicesHuge sizeDNA microarray dataChip standardsDNA microarray experimentsElaborated systemMicroarray dataStandard chipsAlgorithmSystemAnalysis of resultsMicroarray probesMicroarray experimentsMicroarray probe setsServicesBLATDatabaseDataBioinformatics aspectsSet