2022
Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases
Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax 2022, 78: 792-798. PMID: 36216496, PMCID: PMC10083187, DOI: 10.1136/thorax-2021-217703.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association analysisLocal genetic correlationsSingle-cell expression dataCandidate genesTranscription factorsIntegrative analysisGenomic regionsGenetic correlationsExpression dataTF target genesComplex genetic architectureTF binding sitesWide association studyPower of GWASSpecific DEGsGenetic architectureNew genesNovel genesCausal genesTarget genesGenetic basisEnrichment analysisAssociation studiesRegulatory roleAssociation analysis
2018
Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis
Vukmirovic M, Kaminski N. Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis. Frontiers In Medicine 2018, 5: 87. PMID: 29670881, PMCID: PMC5894436, DOI: 10.3389/fmed.2018.00087.Peer-Reviewed Original ResearchTranscriptomic studiesImpact of transcriptomicsGenome-scale profilingSingle-cell RNAseqRole of microRNAsIdiopathic pulmonary fibrosisNovel genesTranscriptomic analysisEpithelial genesIPF lungsRNA transcriptsDevelopmental pathwaysWnt pathwayBulk tissueMolecular analysisPulmonary fibrosisSpatial heterogeneityAnimal modelsTranscriptomicsGenesLethal fibrotic lung diseaseHuman IPF lungsImpact of lungPathwayFibrotic lung disease
2009
FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development
Stuckenholz C, Lu L, Thakur P, Kaminski N, Bahary N. FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development. Gastroenterology 2009, 137: 1321-1332. PMID: 19563808, PMCID: PMC2785077, DOI: 10.1053/j.gastro.2009.06.050.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedCell SeparationChromosomes, Human, Pair 8Digestive System NeoplasmsFlow CytometryGastrointestinal TractGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Expression Regulation, NeoplasticGene Regulatory NetworksGreen Fluorescent ProteinsHumansIn Situ HybridizationLarvaMicroRNAsOligonucleotide Array Sequence AnalysisOrganogenesisReproducibility of ResultsTime FactorsZebrafishZebrafish ProteinsConceptsFluorescence-activated cell sortingNovel genesGreen fluorescent proteinGene networksPutative transcription factorTransgenic zebrafish lineZebrafish Danio rerioPhosphatidylinositol-3-kinase (PI3K) pathwayExcellent model systemDevelopmental time pointsChromosome arm 8qGastrointestinal developmentZebrafish lineHuman orthologDanio rerioTranscription factorsKinase pathwayMicroarray profilingFluorescent proteinGFP expressionGenesNovel pathwayGFP cellsCell sortingOrganogenesis