2023
PCSK6 and Survival in Idiopathic Pulmonary Fibrosis
Oldham J, Allen R, Lorenzo-Salazar J, Molyneaux P, Ma S, Joseph C, Kim J, Guillen-Guio B, Hernández-Beeftink T, Kropski J, Huang Y, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Vo V, Strek M, Jou J, Muñoz-Barrera A, Rubio-Rodriguez L, Hubbard R, Hirani N, Whyte M, Hart S, Nicholson A, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Banovich N, Fahy W, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Flores C, Wain L, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1515-1524. PMID: 36780644, PMCID: PMC10263132, DOI: 10.1164/rccm.202205-0845oc.Peer-Reviewed Original ResearchConceptsGenome-wide significanceTransplantation-free survivalIdiopathic pulmonary fibrosisStage IIPF survivalDownstream analysisPulmonary fibrosisIPF progressionWide association studyPeripheral blood gene expressionProportional hazards regressionStage II casesLimited treatment optionsStage I casesBlood gene expressionGene expressionAssociation studiesMolecular determinantsHazards regressionTreatment optionsPlasma concentrationsLung parenchymaConsistent effect directionMolecular driversProtein
2022
CINS: Cell Interaction Network inference from Single cell expression data
Yuan Y, Cosme C, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. CINS: Cell Interaction Network inference from Single cell expression data. PLOS Computational Biology 2022, 18: e1010468. PMID: 36095011, PMCID: PMC9499239, DOI: 10.1371/journal.pcbi.1010468.Peer-Reviewed Original ResearchConceptsCell type interactionsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataScRNA-seq experimentsCell-cell interactionsExpression dataCell typesMouse datasetsNetwork inferenceCell interactionsInteraction predictionNetwork analysisInference pipelineGenesCINSProteinInteractionBayesian network analysis
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
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
2010
Have advanced research technologies made real impact on respiratory medicine?
Kjetil A, EICKELBERG O, GAULDIE J, KAMINSKI N, Martin K. Have advanced research technologies made real impact on respiratory medicine? Respirology 2010, 15: 876-880. PMID: 20646243, DOI: 10.1111/j.1440-1843.2010.01811.x.Peer-Reviewed Original ResearchConceptsGene array analysisGenetic manipulationGene expressionSystems biologyMolecular researchNovel pathwayArray analysisTremendous sophisticationDisease initiationPotential roleNovel toolAdvanced research technologiesLung diseaseRespiratory medicineHumans todayProteomicsUnique insightsGenesRNABiologyBioinformaticsProteinChronic lung diseaseTherapeutic interventionsPathway
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