2022
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Raredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.Peer-Reviewed Original ResearchConceptsCell-cell interactionsCell-cell signalingSingle-cell resolutionSingle-cell dataLocal cellular microenvironmentSingle-cell levelSpatial transcriptomics dataCell clustersExtracellular signalingTranscriptomic dataGene expression valuesSpatial transcriptomicsSignaling mechanismCellular microenvironmentNicheExpression valuesSupplementary dataSignalingTranscriptomicsComprehensive visualizationBioinformaticsInteraction
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
2017
Transcriptome profiles in sarcoidosis and their potential role in disease prediction
Schupp JC, Vukmirovic M, Kaminski N, Prasse A. Transcriptome profiles in sarcoidosis and their potential role in disease prediction. Current Opinion In Pulmonary Medicine 2017, 23: 487-492. PMID: 28590292, PMCID: PMC5637542, DOI: 10.1097/mcp.0000000000000403.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGenome-wide expression studiesWide expression studiesTranscriptome profilesTranscriptomic dataRNA sequencingExpression studiesGene expressionMolecular mechanismsLarge prospective followTh1 immune responseTranscriptomeNonnecrotizing granulomasProspective followSystemic diseaseDisease progressionTreatment outcomesImmune responseSarcoidosisPotential roleControl tissuesProgressive sarcoidosisKey roleDiseaseTranscriptomicsGranulomas