2022
A genomic meta-analysis of clinical variables and their association with intrinsic molecular subsets in systemic sclerosis
Franks JM, Toledo DM, Martyanov V, Wang Y, Huang S, Wood TA, Spino C, Chung L, Denton C, Derrett-Smith E, Gordon JK, Spiera R, Domsic R, Hinchcliff M, Khanna D, Whitfield ML. A genomic meta-analysis of clinical variables and their association with intrinsic molecular subsets in systemic sclerosis. Rheumatology 2022, 62: 19-28. PMID: 35751592, PMCID: PMC9788818, DOI: 10.1093/rheumatology/keac344.Peer-Reviewed Original ResearchMeSH KeywordsGenomicsHumansMaleOligonucleotide Array Sequence AnalysisRNAScleroderma, SystemicSkinTranscriptomeConceptsMolecular subsetsIntrinsic subsetInflammatory subsetBaseline demographicsSSc patientsWhite/Caucasian patientsBaseline clinical demographicsAverage disease durationRodnan skin scoreAfrican American/BlackASSET trialUnique gene expression signatureDisease durationGene expression signaturesClinical demographicsParticipant seraSkin scoreSystemic sclerosisValidation cohortClinical variablesCaucasian patientsSpecific therapyAmerican/BlackSkin biopsiesDisease pathogenesisMassively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nature Biomedical Engineering 2022, 6: 257-266. PMID: 35301450, PMCID: PMC9089460, DOI: 10.1038/s41551-022-00855-9.Peer-Reviewed Original ResearchMeSH KeywordsAllelesHigh-Throughput Nucleotide SequencingHumansMutationOligonucleotide Array Sequence AnalysisSequence Analysis, DNAConceptsLow-frequency mutationsDuplex SequencingNumber of lociLow-frequency allelesWhole-genome sequencingHuman cell linesSingle nucleotide polymorphismsGenomic DNAWhole-exome sequencingMutation enrichmentParallel enrichmentBreast tumor samplesSequencingLociMutationsDistinct mutationsCell linesDNADetection of mutationsReads
2021
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin
Wang G, Kitaoka T, Crawford A, Mao Q, Hesketh A, Guppy FM, Ash GI, Liu J, Gerstein MB, Pitsiladis YP. Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. Scientific Reports 2021, 11: 21705. PMID: 34737331, PMCID: PMC8568984, DOI: 10.1038/s41598-021-00608-9.Peer-Reviewed Original ResearchMeSH KeywordsErythropoiesisErythropoietinGene ExpressionGene Expression ProfilingHigh-Throughput Nucleotide SequencingHumansOligonucleotide Array Sequence AnalysisRNARNA-SeqSequence Analysis, RNATranscriptomeConceptsRNA-seqDifferential gene expressionPathway enrichment analysisRNA biologyTranscriptomic profilingTarget genesEnrichment analysisGene expressionEPO biologyMicroarray platformGene correlateCross-platform comparisonGenesBiologyImmune regulationHuman erythropoietinTissue protectionProfilingRegulationErythropoietinRecombinant human erythropoietinExpressionImportant toolErythropoiesisOxygen transportA novel signature predicts recurrence risk and therapeutic response in breast cancer patients
Tran QH, Than VT, Luu PL, Clarke D, Lam HN, Nguyen T, Nguyen D, Duy PQ, Phung D, Nguyen MN. A novel signature predicts recurrence risk and therapeutic response in breast cancer patients. International Journal Of Cancer 2021, 148: 2848-2856. PMID: 33586202, DOI: 10.1002/ijc.33512.Peer-Reviewed Original ResearchMeSH KeywordsAcetylserotonin O-MethyltransferaseBreast NeoplasmsDatabases, GeneticFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansNeoplasm GradingOligonucleotide Array Sequence AnalysisRetrospective StudiesSequence Analysis, RNASurvival AnalysisTamoxifenTreatment OutcomeUp-RegulationConceptsBreast cancer patientsAcetylserotonin O-methyltransferaseEndocrine therapyCancer patientsASMT expressionRelapse-free survival outcomesMetastasis-free survival timeLonger metastasis-free survival timesLow-risk casesBreast cancer progressionBreast cancer tumorsAdjuvant chemotherapyOverall survivalTamoxifen treatmentEndocrine resistanceDistance recurrenceMRNA array dataRetrospective studySurvival outcomesTherapeutic responseBreast cancerSurvival timePatientsRecurrence riskSynthesis of melatonin
2020
Investigating higher-order interactions in single-cell data with scHOT
Ghazanfar S, Lin Y, Su X, Lin D, Patrick E, Han Z, Marioni J, Yang J. Investigating higher-order interactions in single-cell data with scHOT. Nature Methods 2020, 17: 799-806. PMID: 32661426, PMCID: PMC7610653, DOI: 10.1038/s41592-020-0885-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsComputational BiologyDatabases, Nucleic AcidHepatocytesLiverMiceOligonucleotide Array Sequence AnalysisSequence Analysis, RNASingle-Cell AnalysisSoftwareConceptsSingle-cell dataCell fate choiceSingle-cell genomicsDifferential expression testingGene-gene correlationsFate choiceHigher-order interactionsKey genesTranscriptomic dataEmbryonic developmentCoordinated changesExpression testingGenesSubtle changesMouse liverMouse olfactory bulbCellsGenomicsSchotPseudotimeInteractionOlfactory bulbHigher-order measurementsCovariationVariabilityTechnical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue
Lau R, Du L, Chen E, Fu C, Gould R, Marczyk M, Sinn BV, Layman R, Bedrosian I, Valero V, Symmans WF. Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue. Clinical Chemistry 2020, 66: 934-945. PMID: 32613237, DOI: 10.1093/clinchem/hvaa105.Peer-Reviewed Original ResearchConceptsQuantiGene PlexConcordance correlation coefficientBreast cancer tissuesParaffin-embedded tissue sectionsEndocrine therapyResection samplesBreast cancerTumor sectionsCancer tissuesStage IIParaffin blocksLin's concordance correlation coefficientTissue sectionsCustomized assayTherapyAnalytical sensitivityFFPE samplesNanoStringFFPE tissuesExpression indexWeekly testsAssaysTissueTechnical validitySeasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults
Avey S, Mohanty S, Chawla DG, Meng H, Bandaranayake T, Ueda I, Zapata HJ, Park K, Blevins TP, Tsang S, Belshe RB, Kaech SM, Shaw AC, Kleinstein SH. Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults. The Journal Of Immunology 2020, 204: 1661-1673. PMID: 32060136, PMCID: PMC7755271, DOI: 10.4049/jimmunol.1900922.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge FactorsAgedAgingAntibodies, ViralCohort StudiesFemaleGene Expression ProfilingHemagglutination Inhibition TestsHumansImmunogenicity, VaccineInfluenza A virusInfluenza VaccinesInfluenza, HumanMaleNK Cell Lectin-Like Receptor Subfamily BOligonucleotide Array Sequence AnalysisSeasonsTranscriptomeVaccinationVaccines, InactivatedYoung AdultConceptsVaccine-induced Ab responsesOlder adultsInfluenza vaccinationDays postvaccinationInfluenza vaccineAb responsesMore effective influenza vaccinesImportant public health toolInactivated influenza vaccinationSeasonal influenza vaccineVaccine-induced immunityEffective influenza vaccinesMolecular signaturesEffects of immunosenescencePublic health toolImmune signaturesVaccination seasonVaccine responsesVaccine compositionSubset of individualsAge groupsHealth toolsSingle age groupAdultsPostvaccination
2019
Genome‐wide association study of cognitive performance in U.S. veterans with schizophrenia or bipolar disorder
Harvey PD, Sun N, Bigdeli TB, Fanous AH, Aslan M, Malhotra AK, Lu Q, Hu Y, Li B, Chen Q, Mane S, Miller P, Rajeevan N, Sayward F, Cheung K, Li Y, Greenwood TA, Gur RE, Braff DL, on the Genetics of Schizophrenia C, Brophy M, Pyarajan S, O'Leary TJ, Gleason T, Przygodszki R, Muralidhar S, Gaziano JM, Concato J, Zhao H, Siever LJ. Genome‐wide association study of cognitive performance in U.S. veterans with schizophrenia or bipolar disorder. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2019, 183: 181-194. PMID: 31872970, DOI: 10.1002/ajmg.b.32775.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAllelesBipolar DisorderCognitionCognition DisordersFemaleGenome-Wide Association StudyGenotypeHumansMaleMiddle AgedNeuropsychological TestsOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSchizophreniaUnited StatesUnited States Department of Veterans AffairsVeteransGlutathione deficiency-elicited reprogramming of hepatic metabolism protects against alcohol-induced steatosis
Chen Y, Manna SK, Golla S, Krausz KW, Cai Y, Garcia-Milian R, Chakraborty T, Chakraborty J, Chatterjee R, Thompson DC, Gonzalez FJ, Vasiliou V. Glutathione deficiency-elicited reprogramming of hepatic metabolism protects against alcohol-induced steatosis. Free Radical Biology And Medicine 2019, 143: 127-139. PMID: 31351176, PMCID: PMC6848780, DOI: 10.1016/j.freeradbiomed.2019.07.025.Peer-Reviewed Original ResearchMeSH KeywordsAcetyl Coenzyme AAlcohol DrinkingAMP-Activated Protein KinasesAnimalsEthanolFatty AcidsFatty LiverGlucuronic AcidGlutamate-Cysteine LigaseGlutamatesGlutathioneHomeostasisLipogenesisLiverMaleMiceMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisOxidation-ReductionOxidative StressPentose Phosphate PathwayProtective AgentsTranscription, GeneticConceptsGlutamate-cysteine ligase modifier subunit geneProtein kinase pathwayAcetyl-CoA fluxMultiple cellular pathwaysAlcohol-induced steatosisCellular stressNucleotide biosynthesisLiver microarray analysisGlobal profilingSubunit geneCellular pathwaysMetabolic reprogrammingKinase pathwayMicroarray analysisMolecular mechanismsGSH poolCellular responsesMetabolic pathwaysLower GSHMolecular pathwaysMetabolic homeostasisAmino acidsDepletion of glutathioneCritical pathogenic eventGlucuronate pathwayA Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection
Zhang W, Yi Z, Keung KL, Shang H, Wei C, Cravedi P, Sun Z, Xi C, Woytovich C, Farouk S, Huang W, Banu K, Gallon L, Magee CN, Najafian N, Samaniego M, Djamali A, Alexander SI, Rosales IA, Smith RN, Xiang J, Lerut E, Kuypers D, Naesens M, O'Connell PJ, Colvin R, Menon MC, Murphy B. A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection. Journal Of The American Society Of Nephrology 2019, 30: 1481-1494. PMID: 31278196, PMCID: PMC6683710, DOI: 10.1681/asn.2018111098.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBiomarkersBiopsyFemaleGene Expression ProfilingGenomicsGraft RejectionGraft SurvivalHumansImmunosuppressive AgentsInflammationKaplan-Meier EstimateKidney Failure, ChronicKidney TransplantationMaleMiddle AgedOligonucleotide Array Sequence AnalysisProspective StudiesRisk FactorsSequence Analysis, RNAConceptsSubclinical acute rejectionKidney transplant recipientsAcute cellular rejectionAcute rejectionTransplant recipientsSurveillance biopsiesACR 3Graft functionHigh riskIndependent cohortPeripheral blood gene expression signaturesClinical acute rejectionFuture graft lossOngoing acute rejectionStable graft functionBlood gene expression signaturesCellular rejectionGraft lossGraft outcomeGraft survivalBorderline changesGene expression signaturesCox analysisHistologic featuresPeripheral bloodTranscriptome-wide piRNA profiling in human gastric cancer
Lin X, Xia Y, Hu D, Mao Q, Yu Z, Zhang H, Li C, Chen G, Liu F, Zhu W, Shi Y, Zhang H, Zheng J, Sun T, Xu J, Chao HH, Zheng X, Luo X. Transcriptome-wide piRNA profiling in human gastric cancer. Oncology Reports 2019, 41: 3089-3099. PMID: 30896887, PMCID: PMC6448102, DOI: 10.3892/or.2019.7073.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsTransposable elementsHuman gastric cancerProtein-coding genesNon-coding RNAsCancer risk SNPsPiRNA expressionNearest geneWhole transcriptomeCancer stem cellsDNA variantsIndefinite capacityDifferential expressionAdjacent non-tumorous tissuesStem cellsHuman stomachRegulatory effectsGenesRNANon-tumorous tissuesExpressionMolecular featuresBiological systemsGastric cancerTranscriptomeBAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis
Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2019, 199: 622-630. PMID: 30141961, PMCID: PMC6396865, DOI: 10.1164/rccm.201712-2551oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAirway basal cellsChronic obstructive pulmonary diseaseObstructive pulmonary diseasePulmonary diseaseBAL cellsBasal cellsPulmonary fibrosisControl subjectsCell gene expressionIndependent IPF cohortsNine-gene signatureIPF cohortDerivation cohortClinical parametersRetrospective studyUnivariate analysisUnpredictable courseCell involvementDiscovery cohortGene expressionHealthy volunteersCox modelStage IIIFatal diseasePatterning Nanoparticles with DNA Molds
Liu L, Zheng M, Li Z, Li Q, Mao C. Patterning Nanoparticles with DNA Molds. ACS Applied Materials & Interfaces 2019, 11: 13853-13858. PMID: 30793605, DOI: 10.1021/acsami.8b22691.Peer-Reviewed Original ResearchMeSH KeywordsDNAGoldMetal NanoparticlesMicroscopy, Atomic ForceNucleic Acid HybridizationOligonucleotide Array Sequence AnalysisOvalbuminPolylysineSilicon DioxideSurface PropertiesConceptsSelf-assembled DNA nanostructuresAtomic force microscopyGold nanoparticlesNonspecific adsorptionDNA nanostructuresPatterned nanoparticlesForce microscopyNanoparticlesAccessible cavitiesSpecific recognitionStructural templateNanostructuresHexagonal arrayTemplateAdsorptionGeneral methodSubstrateDNA arraysHereinDNA templateFourier transform analysisMicroscopyArrayDirect interactionLarge array
2018
scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling
Dura B, Choi JY, Zhang K, Damsky W, Thakral D, Bosenberg M, Craft J, Fan R. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling. Nucleic Acids Research 2018, 47: e16-e16. PMID: 30462277, PMCID: PMC6379653, DOI: 10.1093/nar/gky1173.Peer-Reviewed Original ResearchAnimalsCell LineFreezingGene Expression ProfilingHigh-Throughput Nucleotide SequencingHuman Umbilical Vein Endothelial CellsHumansLupus Erythematosus, SystemicMaleMelanoma, ExperimentalMiceOligonucleotide Array Sequence AnalysisRNA, MessengerSequence Analysis, RNASingle-Cell AnalysisT-LymphocytesWorkflowIn utero electroporation-based translating ribosome affinity purification identifies age-dependent mRNA expression in cortical pyramidal neurons
Huang T, Nguyen L, Lin TV, Gong X, Zhang L, Kim GB, Sarkisian MR, Breunig JJ, Bordey A. In utero electroporation-based translating ribosome affinity purification identifies age-dependent mRNA expression in cortical pyramidal neurons. Neuroscience Research 2018, 143: 44-52. PMID: 29857015, PMCID: PMC6265126, DOI: 10.1016/j.neures.2018.05.006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainDisks Large Homolog 4 ProteinDoublecortin ProteinElectroporationEmbryonic DevelopmentFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGreen Fluorescent ProteinsMaleMiceOligonucleotide Array Sequence AnalysisProtein BiosynthesisPyramidal CellsRecombinant Fusion ProteinsRibosomal Protein L10Ribosomal ProteinsRNA, MessengerSomatosensory CortexSynapsinsConceptsSpecific neuronal populationsRibosomal protein L10aRibosome affinity purificationSelective biological processesNeuronal genesMolecular profileSpecific developmental patternsTarget genesAffinity purificationBiological processesGenesUtero electroporationNeuronal populationsEmbryonic day 14Molecular profilingDevelopmental patternsMRNA expressionTopical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner
Gopinath S, Kim MV, Rakib T, Wong PW, van Zandt M, Barry NA, Kaisho T, Goodman AL, Iwasaki A. Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner. Nature Microbiology 2018, 3: 611-621. PMID: 29632368, PMCID: PMC5918160, DOI: 10.1038/s41564-018-0138-2.Peer-Reviewed Original ResearchMeSH KeywordsAdministration, TopicalAminoglycosidesAnimalsAnti-Bacterial AgentsDisease Models, AnimalGene Expression ProfilingGene Expression RegulationGerm-Free LifeHumansInfluenza A virusMiceMicrobiotaOligonucleotide Array Sequence AnalysisSimplexvirusToll-Like Receptor 3Transcription FactorsVirus DiseasesVirus ReplicationZika VirusConceptsToll-like receptor 3Aminoglycoside treatmentInterferon-stimulated genesViral infectionReceptor 3ISG inductionAminoglycoside antibioticsMicrobiota-independent mannerGerm-free miceAdapter-inducing interferonInterferon regulatory factor 3Herpes simplex virusTopical mucosal applicationRegulatory factor 3Dendritic cellsAntibiotic useAntiviral effectAminoglycoside applicationHost resistanceSimplex virusAntiviral resistanceVaginal mucosaMarked upregulationMucosal applicationTopical applicationMicroRNA signatures discriminate between uterine and ovarian serous carcinomas
Hui P, Gysler SM, Uduman M, Togun TA, Prado DE, Brambs CE, Nallur S, Schwartz PE, Rutherford TJ, Santin AD, Weidhaas JB, Ratner ES. MicroRNA signatures discriminate between uterine and ovarian serous carcinomas. Human Pathology 2018, 76: 133-140. PMID: 29518404, DOI: 10.1016/j.humpath.2018.02.019.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorCarcinomaDiagnosis, DifferentialFemaleGene Expression ProfilingGenetic Predisposition to DiseaseHumansMicroRNAsMiddle AgedNeoplasm GradingNeoplasms, Cystic, Mucinous, and SerousOligonucleotide Array Sequence AnalysisOvarian NeoplasmsPhenotypePredictive Value of TestsReproducibility of ResultsRetrospective StudiesTranscriptomeUterine NeoplasmsConceptsHigh-grade serous carcinomaOvarian serous carcinomaSerous carcinomaOvarian malignancyPrimary ovarian high-grade serous carcinomaOvarian high-grade serous carcinomaMiRNA signatureEndometrial serous carcinomaHigh-grade ovarian serous carcinomaUterine serous carcinomaEndometrial counterpartOvarian primaryTaqMan Low Density Array technologySynchronous primariesEndometrial cancerMetastatic tumorsCarcinomaPrimary siteSignature panelPathological determinationMicroRNA signatureSignificant discriminatory powerCancer cellsMalignancyLineage characteristicsAgreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time
Forest M, O'Donnell KJ, Voisin G, Gaudreau H, MacIsaac JL, McEwen LM, Silveira PP, Steiner M, Kobor MS, Meaney MJ, Greenwood CMT. Agreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time. Epigenetics 2018, 13: 19-32. PMID: 29381404, PMCID: PMC5837078, DOI: 10.1080/15592294.2017.1411443.Peer-Reviewed Original ResearchBrain-Derived Neurotrophic FactorCanadaCatechol O-MethyltransferaseDNA MethylationDried Blood Spot TestingEpigenesis, GeneticFemaleHumansMaleMouth MucosaNetherlandsOligonucleotide Array Sequence AnalysisReceptors, Dopamine D2Receptors, Dopamine D4Receptors, OxytocinReproducibility of ResultsSerotonin Plasma Membrane Transport ProteinsTime Factors
2017
Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs
Voss S, Murrugarra D, Jensen TB, Monaghan JR. Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs. Comparative Biochemistry And Physiology Part C Toxicology & Pharmacology 2017, 208: 53-63. PMID: 29107037, PMCID: PMC5920805, DOI: 10.1016/j.cbpc.2017.10.010.Peer-Reviewed Original ResearchConceptsAxolotl limbsDynamic transcriptional regulationSimilar transcriptional patternsCell cycle transcriptsDifferentiated muscle cellsProximal-distal limb axisExtracellular matrix moleculesMemory genesTranscriptional regulationTranscript abundanceTranscriptional patternsExpression patternsLimb regenerationGene expressionBlastema cellsPositional memoryArm cellsCell adhesionGenesMatrix moleculesCell surfaceEpithelial proteinsPositional informationTissue remodelingTranscriptional correlatesValidation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study
Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N. Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study. The Lancet Respiratory Medicine 2017, 5: 857-868. PMID: 28942086, PMCID: PMC5677538, DOI: 10.1016/s2213-2600(17)30349-1.Peer-Reviewed Original ResearchMeSH KeywordsAgedCohort StudiesFemaleGene Expression ProfilingGenetic MarkersGenetic TestingHumansIdiopathic Pulmonary FibrosisLeukocytes, MononuclearLinear ModelsMaleMiddle AgedOligonucleotide Array Sequence AnalysisPrognosisProportional Hazards ModelsRisk AssessmentRisk FactorsTime FactorsVital CapacityConceptsIdiopathic pulmonary fibrosisTransplant-free survivalRisk profilePulmonary fibrosisAntifibrotic drugsPeripheral blood mononuclear cellsCox proportional hazards modelClinical prediction toolGroup of patientsBlood mononuclear cellsHigh-risk groupProportional hazards modelPulmonary Fibrosis FoundationPittsburgh cohortUntreated patientsCohort studyClinical courseIPF diagnosisBlood InstituteProspective studyVital capacityMononuclear cellsPeripheral bloodUS National InstitutesNational Heart
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