2023
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Liu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 394. PMID: 37858060, PMCID: PMC10588114, DOI: 10.1186/s12859-023-05523-6.Peer-Reviewed Original ResearchIntegrative genetic and genomic networks identify microRNA associated with COPD and ILD
Pavel A, Garrison C, Luo L, Liu G, Taub D, Xiao J, Juan-Guardela B, Tedrow J, Alekseyev Y, Yang I, Geraci M, Sciurba F, Schwartz D, Kaminski N, Beane J, Spira A, Lenburg M, Campbell J. Integrative genetic and genomic networks identify microRNA associated with COPD and ILD. Scientific Reports 2023, 13: 13076. PMID: 37567908, PMCID: PMC10421936, DOI: 10.1038/s41598-023-39751-w.Peer-Reviewed Original ResearchConceptsSeed sequenceGene expressionShort RNA sequencingAirway differentiationIntegrative network analysisExpression networksRNA sequencingGenomic networksMiRNA regulatorsMiRNA isoformsNotch pathwayIsomiRsDistinct subclustersSNP microarraysGenesMicroRNAsMolecular heterogeneityILD pathogenesisDisease networkOverexpressionSequenceExpressionNetwork analysisDifferentiationGrb2An integrated cell atlas of the lung in health and disease
Sikkema L, Ramírez-Suástegui C, Strobl D, Gillett T, Zappia L, Madissoon E, Markov N, Zaragosi L, Ji Y, Ansari M, Arguel M, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung M, Collin A, Gay A, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos T, Kole T, Leroy S, Mayr C, Oliver A, von Papen M, Peter L, Taylor C, Walzthoeni T, Xu C, Bui L, De Donno C, Dony L, Faiz A, Guo M, Gutierrez A, Heumos L, Huang N, Ibarra I, Jackson N, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini K, Wilbrey-Clark A, Worlock K, Yoshida M, van den Berge M, Bossé Y, Desai T, Eickelberg O, Kaminski N, Krasnow M, Lafyatis R, Nikolic M, Powell J, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold M, Sheppard D, Shepherd D, Sin D, Timens W, Tsankov A, Whitsett J, Xu Y, Banovich N, Barbry P, Duong T, Falk C, Meyer K, Kropski J, Pe’er D, Schiller H, Tata P, Schultze J, Teichmann S, Misharin A, Nawijn M, Luecken M, Theis F. An integrated cell atlas of the lung in health and disease. Nature Medicine 2023, 29: 1563-1577. PMID: 37291214, PMCID: PMC10287567, DOI: 10.1038/s41591-023-02327-2.Peer-Reviewed Original ResearchConceptsCell atlasGene modulesCell typesCell type definitionsHuman Cell AtlasSingle-cell technologiesSingle-cell datasetsUndescribed cell typeMultiple lung diseasesCell statesMarker genesMonocyte-derived macrophagesDistal axisStudy of diseasesHuman tissuesAnnotationAtlasGenesSPP1DiversityExpressionTreesLimited numberCellsNew dataThe Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During Aging
Yuan Y, Khoury J, Ramachandra A, Singh I, Tellides G, Humphrey J, Kaminski N, Manning E. The Extracellular Matrix of the Human Proximal Pulmonary Artery Regulates Gene Expression of Resident Cells Responsible for Remodeling During Aging. 2023, a2680-a2680. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a2680.Peer-Reviewed Original Research
2022
Integrating Gene Expression with Genome-Wide Association Summary Statistics to Identify Genes Associated with Idiopathic Pulmonary Fibrosis Survival
Hu X, Kim J, Ma S, Huang Y, Oldham J, Allen R, Molyneaux P, Joseph C, Guillen Guio B, Hernández Beeftink T, Kropski J, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Strek M, Hubbard R, Hart S, Nicholson A, Lancaster L, Lorenzo-Salazar J, Vo V, Hirani N, Whyte M, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Wain L, Flores C, Noth I, Manichaikul A. Integrating Gene Expression with Genome-Wide Association Summary Statistics to Identify Genes Associated with Idiopathic Pulmonary Fibrosis Survival. 2022, a2326-a2326. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2326.Peer-Reviewed Original Research
2020
Genetic determinants of ammonia-induced acute lung injury in mice
Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Genetic determinants of ammonia-induced acute lung injury in mice. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2020, 320: l41-l62. PMID: 33050709, PMCID: PMC7847062, DOI: 10.1152/ajplung.00276.2020.Peer-Reviewed Original ResearchConceptsSNP associationsWide association mappingGenetic determinantsSignificant SNP associationsAcute lung injuryIntegrative functional approachAssociation mappingMolecular functionsTranscriptomic analysisCandidate genesFunctional domainsNonsynonymous SNPsPromoter regionLung injuryDiverse panelGenesSNPsMouse strainsPathophysiological roleAATFInjuryProteinLAMA3ExpressionAssembly
2019
BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications
Weathington N, O’Brien M, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie A, Jarjour N, Meyers D, Milosevic J, Moore W, Tedrow J, Trudeau J, Wong H, Wu W, Kaminski N, Wenzel S, Modena B. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. American Journal Of Respiratory And Critical Care Medicine 2019, 200: 837-856. PMID: 31161938, PMCID: PMC6812436, DOI: 10.1164/rccm.201811-2221oc.Peer-Reviewed Original ResearchMeSH KeywordsAdrenergic beta-AgonistsAdultAsthmaBronchoalveolar Lavage FluidCase-Control StudiesCyclic AMPEosinophilsEpithelial CellsFemaleGene ExpressionHumansIn Vitro TechniquesLymphocytesMacrophages, AlveolarMaleNeutrophilsSequence Analysis, RNASeverity of Illness IndexSignal TransductionTHP-1 CellsConceptsCell gene expressionGene expressionAirway epithelial cell gene expressionEpithelial cell gene expressionGlobal gene expressionCellular gene expressionCell expression profilesAsthma susceptibility lociProtein levelsSystem-wide analysisExpression networksImportant disease mechanismCoexpression networkCellular milieuExpression changesExpression profilesSusceptibility lociCellular modelDisease mechanismsBiomolecular mechanismsNew targetsRobust upregulationSample traitsGenesExpressionAlveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPF
Vukmirovic M, Brereton C, Yan X, Xylourgidis N, Deluliis G, Woolard T, Hu B, Mihaljinec A, Homer R, Maya J, Ahangari F, Fabre A, Smart D, Conforti F, Marshall B, Alzetani A, Davies D, Richeldi L, Kaminski N, Jones M. Alveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPF. 2019, a5262-a5262. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5262.Peer-Reviewed Original Research
2017
Selecting the most appropriate time points to profile in high-throughput studies
Kleyman M, Sefer E, Nicola T, Espinoza C, Chhabra D, Hagood JS, Kaminski N, Ambalavanan N, Bar-Joseph Z. Selecting the most appropriate time points to profile in high-throughput studies. ELife 2017, 6: e18541. PMID: 28124972, PMCID: PMC5319842, DOI: 10.7554/elife.18541.Peer-Reviewed Original ResearchConceptsMolecular dataMouse lung developmentHigh-throughput profilingHigh-throughput studiesDNA methylationGene expressionThroughput profilingExpression dataTime series experimentsExpression valuesLung developmentSeries experimentsBiological systemsGenesMethylationMiRNAProteinProfilingExpressionTime pointsKey design strategiesLarge setAppropriate time points
2014
Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways
Modena BD, Tedrow JR, Milosevic J, Bleecker ER, Meyers DA, Wu W, Bar-Joseph Z, Erzurum SC, Gaston BM, Busse WW, Jarjour NN, Kaminski N, Wenzel SE. Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 1363-1372. PMID: 25338189, PMCID: PMC4294630, DOI: 10.1164/rccm.201406-1099oc.Peer-Reviewed Original ResearchConceptsEpithelial cell gene expressionCell gene expressionGene expressionAirway epithelial cell gene expressionGene expression patternsSevere Asthma Research ProgramActin cytoskeletonGene clusterGenomic studiesGene transcriptionGene pathwaysMolecular basisExpression patternsAsthma phenotypesWnt pathwayMicroarray platformGenesNovel pathwayPhenotypeBiomolecular pathwaysNeuronal functionPathwayUnadjusted p-valuesExpressionBiological characteristicsRelationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis
Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DA. Relationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2014, 190: 1263-1272. PMID: 25333685, PMCID: PMC4315819, DOI: 10.1164/rccm.201408-1452oc.Peer-Reviewed Original ResearchConceptsGene expressionDNA methylationMethylation marksMethylation changesQuantitative trait lociTrans-gene expressionIntegrative genomic analysisTrait lociEpigenetic mechanismsTranscriptional changesGenomic analysisTranscription factorsCASZ1 expressionTarget genesFunctional validationExpression relationshipsMethylationGenesDMRsExpressionEnvironmental factorsTargeted analysisPathogenesis of IPFComplex interactionsTranscriptome
2013
Reconstructing dynamic microRNA-regulated interaction networks
Schulz MH, Pandit KV, Cardenas C, Ambalavanan N, Kaminski N, Bar-Joseph Z. Reconstructing dynamic microRNA-regulated interaction networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 15686-15691. PMID: 23986498, PMCID: PMC3785769, DOI: 10.1073/pnas.1303236110.Peer-Reviewed Original ResearchConceptsTranscription factorsGene expressionDynamic Regulatory Events MinerTemporal gene expressionDynamic regulatory networksSpecific developmental phasesMRNA expression dataLung developmentRegulatory networksMiRNA targetsInteraction networksImportant miRNAsExpression dataMiRNAsAdditional miRNAsLung differentiationDevelopmental phasesMiRNAPostnatal lung developmentProgression pathwaysProliferation assaysExpressionRegulationMRNA expressionMicroRNAs
2012
Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing
Brothers J, Kusko R, Liu G, Luo L, Guardela B, Tedrow J, Alekesyev Y, Yang I, Correll M, Geraci M, Quackenbush J, Sciurba F, Sebastiani P, Lenburg M, Kaminski N, Schwartz D, Spira A, Beane J. Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing. BMC Proceedings 2012, 6: p4. PMCID: PMC3467663, DOI: 10.1186/1753-6561-6-s6-p4.Peer-Reviewed Original Research
2008
Carbon Monoxide Modulates α–Smooth Muscle Actin and Small Proline Rich-1a Expression in Fibrosis
Zheng L, Zhou Z, Lin L, Alber S, Watkins S, Kaminski N, Choi AM, Morse D. Carbon Monoxide Modulates α–Smooth Muscle Actin and Small Proline Rich-1a Expression in Fibrosis. American Journal Of Respiratory Cell And Molecular Biology 2008, 41: 85-92. PMID: 19097987, PMCID: PMC2701963, DOI: 10.1165/rcmb.2007-0401oc.Peer-Reviewed Original ResearchMeSH KeywordsActinsAdministration, InhalationAnimalsBleomycinBone DevelopmentCarbon MonoxideCell DeathCell MovementCells, CulturedCornified Envelope Proline-Rich ProteinsDisease Models, AnimalDose-Response Relationship, DrugExtracellular Signal-Regulated MAP KinasesFibroblastsGene Expression ProfilingLungMaleMAP Kinase Signaling SystemMiceMice, Inbred C57BLMuscle DevelopmentOrganometallic CompoundsPulmonary FibrosisTime FactorsTransforming Growth Factor beta1UbiquitinationConceptsExtracellular signal-regulated kinase (ERK) pathwayCategories of genesSignal-regulated kinase pathwayNovel transcriptional targetMuscular system developmentGene expression profilingMurine bleomycin modelStress-inducible enzymeTranscriptional targetsAlpha-smooth muscle actin expressionExpression profilingKinase pathwayMuscle actin expressionΑ-smooth muscle actinEffects of COActin expressionGrowth factorHeme oxygenaseExpressionMuscle actinActive moleculesGenesOxygenaseProteinActin
2007
Effects of exercise training on quadriceps muscle gene expression in chronic obstructive pulmonary disease
Radom-Aizik S, Kaminski N, Hayek S, Halkin H, Cooper DM, Ben-Dov I. Effects of exercise training on quadriceps muscle gene expression in chronic obstructive pulmonary disease. Journal Of Applied Physiology 2007, 102: 1976-1984. PMID: 17483440, DOI: 10.1152/japplphysiol.00577.2006.Peer-Reviewed Original ResearchMeSH KeywordsAgedCase-Control StudiesCluster AnalysisEnergy MetabolismExerciseGene ExpressionGene Expression ProfilingHumansMaleOligonucleotide Array Sequence AnalysisOxidative StressOxygen ConsumptionProteasome Endopeptidase ComplexPulmonary Disease, Chronic ObstructiveQuadriceps MuscleReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionRNA, MessengerUbiquitinConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseaseCOPD patientsPulmonary diseaseExercise trainingAge-matched healthy menMuscle gene expressionHigh expressionSkeletal muscle functionExercise capacityGene expressionWalk testHealthy menControl subjectsNeedle biopsyMuscle functionVastus lateralisPatientsOxidative stressTraining responseFunctional parametersDiseaseTissue stressExpressionGene pathways
2005
Ha-rasval12 induces HSP70b transcription via the HSE/HSF1 system, but HSP70b expression is suppressed in Ha-rasval12-transformed cells
Stanhill A, Levin V, Hendel A, Shachar I, Kazanov D, Arber N, Kaminski N, Engelberg D. Ha-rasval12 induces HSP70b transcription via the HSE/HSF1 system, but HSP70b expression is suppressed in Ha-rasval12-transformed cells. Oncogene 2005, 25: 1485-1495. PMID: 16278678, DOI: 10.1038/sj.onc.1209193.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsCell Line, TransformedDNA-Binding ProteinsGene Expression RegulationGenes, ReporterHeat Shock Transcription FactorsHeLa CellsHSP70 Heat-Shock ProteinsHumansMiceMice, NudeNIH 3T3 CellsOncogene Protein p21(ras)Oxidation-ReductionPhosphorylationRatsTranscription FactorsTranscription, GeneticConceptsCellular protective responseHeat shock factor 1Shock factor 1Fibroblast expressionProtective responseHeat shock proteinsHSP70 expressionFactor 1Promoter-driven reporter geneSoft agarTumorsHeat shock elementShock proteinsHSF1 activationCellsDirect effectExpressionHsp70 transcriptionPoint mutationsEffects of Aerobic Training on Gene Expression in Skeletal Muscle of Elderly Men
RADOM-AIZIK S, HAYEK S, SHAHAR I, RECHAVI G, KAMINSKI N, BEN-DOV I. Effects of Aerobic Training on Gene Expression in Skeletal Muscle of Elderly Men. Medicine & Science In Sports & Exercise 2005, 37: 1680-1696. PMID: 16260967, DOI: 10.1249/01.mss.0000181838.96815.4d.Peer-Reviewed Original ResearchConceptsGene expressionGlobal gene expressionSkeletal muscleExpression of genesCatabolism genesTranscriptional responseHeme biosynthesisMonths of trainingElderly menGeneChip arraysGenesEnergy metabolismHealthy elderly menPeak O2 uptakeExpressionProtein catabolismPathwayAerobic trainingNeedle biopsyPhysical activityEnergy pathwaysVastus lateralisBeneficial effectsDephosphorylationRibosomesGene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis
Selman M, Pardo A, Barrera L, Estrada A, Watson SR, Wilson K, Aziz N, Kaminski N, Zlotnik A. Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2005, 173: 188-198. PMID: 16166619, PMCID: PMC2662988, DOI: 10.1164/rccm.200504-644oc.Peer-Reviewed Original ResearchConceptsGene expression signaturesExpression signaturesCustom oligonucleotide microarrayGene expression patternsOligonucleotide DNA microarrayStandard Affymetrix protocolGene clusterDNA microarraysExpression patternsGene expressionOligonucleotide microarraysComplementary ribonucleic acidTranscriptional signatureProbe setsCustom arrayT cell activationTissue remodelingNonspecific interstitial pneumoniaRibonucleic acidGenesMicroarrayInterstitial lung diseaseHypersensitivity pneumonitisPathogenic mechanismsExpression
2004
Increase in p21 expression independent of the p53 pathway in bleomycin-induced lung fibrosis
Blundell R, Kaminski N, Harrison D. Increase in p21 expression independent of the p53 pathway in bleomycin-induced lung fibrosis. Experimental And Molecular Pathology 2004, 77: 231-237. PMID: 15507241, DOI: 10.1016/j.yexmp.2004.07.003.Peer-Reviewed Original ResearchConceptsP21 expressionLung fibrosisFibrotic lungsAnimal mouse modelsNuclear p21 expressionCytoplasmic p21 expressionExpression of p21Bleomycin injectionLung diseaseMouse modelAnimal modelsImmuno-histochemistryDay 14P27 expressionCell cycle regulatory genesBleomycin inductionFibrosisLungBleomycinP53 pathwayP53Gene expression analysisExpressionPCNAPathogenesis
2003
Loss of integrin αvβ6-mediated TGF-β activation causes Mmp12-dependent emphysema
Morris DG, Huang X, Kaminski N, Wang Y, Shapiro SD, Dolganov G, Glick A, Sheppard D. Loss of integrin αvβ6-mediated TGF-β activation causes Mmp12-dependent emphysema. Nature 2003, 422: 169-173. PMID: 12634787, DOI: 10.1038/nature01413.Peer-Reviewed Original ResearchConceptsTGF-β activationLungs of miceActive TGF-β1Pulmonary gene expressionHeterodimeric cell-surface proteinsTransgenic expressionPulmonary emphysemaMMP12 expressionTGF-β1Functional alterationsΒ6 integrinIntegrin αvβ6Latent TGFMarked inductionEmphysemaGrowth factorMacrophage metalloelastaseCell surface proteinsActivation pathwayMiceTGFActivationCell growthIntegrinsExpression