2022
From COVID to fibrosis: lessons from single-cell analyses of the human lung
Justet A, Zhao AY, Kaminski N. From COVID to fibrosis: lessons from single-cell analyses of the human lung. Human Genomics 2022, 16: 20. PMID: 35698166, PMCID: PMC9189802, DOI: 10.1186/s40246-022-00393-0.Peer-Reviewed Original ResearchConceptsSingle-cell RNA-sequencing technologySingle-cell RNA sequencingRNA-sequencing technologyGene expression patternsMonocyte-derived macrophage populationSingle-cell analysisCell populationsLung diseaseCellular phenotypesRNA sequencingExpression patternsGene expressionAberrant repairMultiple tissuesPulmonary fibrosisMechanisms of diseaseFibrotic interstitial lung diseaseLife-threatening complicationsProgressive lung diseaseCOVID-19 pneumoniaInterstitial lung diseaseParenchymal lung diseaseAcute viral diseaseMacrophage populationsNovel cellComputation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome. Scientific Reports 2022, 12: 4187. PMID: 35264704, PMCID: PMC8906120, DOI: 10.1038/s41598-022-07959-x.Peer-Reviewed Original Research
2017
Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis
Vukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, Stefanovic B, Kaminski N. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis. BMC Pulmonary Medicine 2017, 17: 15. PMID: 28081703, PMCID: PMC5228096, DOI: 10.1186/s12890-016-0356-4.Peer-Reviewed Original ResearchConceptsPaired-end sequencingTranscript profilingHuman genomeRNA sequencingTranscriptomic profilingFFPE lung tissuesSequencing readsLung tissueTotal RNABackgroundIdiopathic pulmonary fibrosisLethal lung diseaseSequencingReadsProfilingPulmonary fibrosisLung diseaseUnknown etiologyIPF tissueGenomeHiSeqTissueTopHat2GenesIPFRNA
2010
Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension
Rajkumar R, Konishi K, Richards TJ, Ishizawar DC, Wiechert AC, Kaminski N, Ahmad F. Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension. AJP Heart And Circulatory Physiology 2010, 298: h1235-h1248. PMID: 20081107, PMCID: PMC2853417, DOI: 10.1152/ajpheart.00254.2009.Peer-Reviewed Original ResearchConceptsPulmonary arterial hypertensionIdiopathic pulmonary fibrosisPathogenesis of PAHIdiopathic pulmonary arterial hypertensionPulmonary hypertensionArterial hypertensionRegulation of actinThrombospondin type 1 motif 9Pulmonary arteriolar remodelingSecondary pulmonary hypertensionCoagulation factor II receptorDistinct pathophysiological mechanismsLife-threatening conditionDistinct gene expression signaturesEstrogen receptor 1Nuclear receptor coactivator 2RNA expression profilesPurinergic receptor P2YGenomewide microarray analysisPlatelet factor 4RNA expression profilingHigh expression levelsOncogene homolog 1Gene expression signaturesProtein ubiquitination
2005
Abnormal Vascular Phenotypes in Patients With Idiopathic Pulmonary Fibrosis and Secondary Pulmonary Hypertension
Gagermeier J, Dauber J, Yousem S, Gibson K, Kaminski N. Abnormal Vascular Phenotypes in Patients With Idiopathic Pulmonary Fibrosis and Secondary Pulmonary Hypertension. CHEST Journal 2005, 128: 601s. PMID: 16373857, DOI: 10.1378/chest.128.6_suppl.601s.Peer-Reviewed Original Research