2024
Challenges and perspectives in computational deconvolution of genomics data
Garmire L, Li Y, Huang Q, Xu C, Teichmann S, Kaminski N, Pellegrini M, Nguyen Q, Teschendorff A. Challenges and perspectives in computational deconvolution of genomics data. Nature Methods 2024, 21: 391-400. PMID: 38374264, DOI: 10.1038/s41592-023-02166-6.Peer-Reviewed Original Research
2012
An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection
Wang X, Kang DD, Shen K, Song C, Lu S, Chang LC, Liao SG, Huo Z, Tang S, Ding Y, Kaminski N, Sibille E, Lin Y, Li J, Tseng GC. An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection. Bioinformatics 2012, 28: 2534-2536. PMID: 22863766, PMCID: PMC3463115, DOI: 10.1093/bioinformatics/bts485.Peer-Reviewed Original ResearchConceptsDifferent operation systemsMulti-core parallel computingUser-friendly softwareParallel computingPathway detectionSoftware suiteFlexible inputFast implementationOperation systemVisualization plotsSupplementary dataNew algorithmMetapathsNew challengesSummary outputMarker detectionPathway databasesLittle effortMeta-analysis pipelineRapid advancesHigh-throughput genomic technologiesGenomic dataSystematic pipelineComputingPipeline
2011
Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes
Kass DJ, Kaminski N. Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes. Clinical And Translational Science 2011, 4: 372-379. PMID: 22029812, PMCID: PMC3229869, DOI: 10.1111/j.1752-8062.2011.00287.x.Peer-Reviewed Original ResearchConceptsGenomic technologiesIdiopathic pulmonary fibrosisPathogenesis of diseaseGenomic discoveriesSystems biology approachGene expression profilingContribution of microRNAsMost human diseasesGenomic approachesGene networksBiology approachHuman genomeEpigenetic researchGenomic dataExpression profilingHuman diseasesPulmonary fibrosisDiagnosis of IPFGenesLarge collaborative studiesProgressive scarringPeripheral bloodClinical severityLung parenchymaTherapeutic goals