2024
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Wei H, Justet A, Adams T, Homer R, Amei A, Rosas I, Kaminski N, Wang Z, Yan X. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 2024, 25: 271. PMID: 39402626, PMCID: PMC11475911, DOI: 10.1186/s13059-024-03416-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression ProfilingHumansMachine LearningRegression AnalysisRNA-SeqSequence Analysis, RNASingle-Cell AnalysisSoftwareTranscriptome
2017
A Dirichlet process mixture model for clustering longitudinal gene expression data
Sun J, Herazo‐Maya J, Kaminski N, Zhao H, Warren JL. A Dirichlet process mixture model for clustering longitudinal gene expression data. Statistics In Medicine 2017, 36: 3495-3506. PMID: 28620908, PMCID: PMC5583037, DOI: 10.1002/sim.7374.Peer-Reviewed Original ResearchConceptsLongitudinal gene expression profilesDirichlet process prior distributionRegression coefficientsExtensive simulation studyLongitudinal gene expression dataBayesian settingPrior distributionClustering methodFactor analysis modelDimensionality challengeStatistical methodsSimulation studyNovel clustering methodHigh dimensionality challengeSubgroup identificationImportant problemGene expression dataInteresting subgroupsClusteringCoefficientAnalysis modelModelExpression data
2015
A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Huang Y, Ma SF, Vij R, Oldham JM, Herazo-Maya J, Broderick SM, Strek ME, White SR, Hogarth DK, Sandbo NK, Lussier YA, Gibson KF, Kaminski N, Garcia JG, Noth I. A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis. BMC Pulmonary Medicine 2015, 15: 147. PMID: 26589497, PMCID: PMC4654815, DOI: 10.1186/s12890-015-0142-8.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPrognostic indexIPF patientsPulmonary fibrosisValidation cohortTraining cohortMultivariate Cox regression survival analysisPrognostic modelPeripheral blood mononuclear cellsUnivariate Cox regression analysisCox regression survival analysisLow-risk patientsWeighted gene co-expression network analysisCox regression analysisBlood mononuclear cellsCourse of diseaseIndependent validation cohortRegression survival analysisNovel prognostic modelPredictor genesT cell biologyT cell receptorCurrent prognostic toolsFunctional pathway analysisFold change
2013
Serum lysyl oxidase-like 2 levels and idiopathic pulmonary fibrosis disease progression.
Chien JW, Richards TJ, Gibson KF, Zhang Y, Lindell KO, Shao L, Lyman SK, Adamkewicz JI, Smith V, Kaminski N, O'Riordan T. Serum lysyl oxidase-like 2 levels and idiopathic pulmonary fibrosis disease progression. European Respiratory Journal 2013, 43: 1430-8. PMID: 24177001, DOI: 10.1183/09031936.00141013.Peer-Reviewed Original ResearchConceptsIPF disease progressionDisease progressionIdiopathic pulmonary fibrosis patientsCarbon monoxide diffusion capacityPulmonary fibrosis patientsDisease progression eventsGAP subjectsIPF studiesPathological stromaVital capacityLOXL2 levelsProgression eventsDiffusion capacityFibrosis patientsSpirometric dataDisease severityPhysiological surrogatesProgressionPatientsRiskMultiple limitationsSubjectsLevelsProteomic analysisCohort
1990
Effects of Perfusion Pressure and Renal Flow upon Albumin Excretion in Isolated Perfused Kidneys
Raz E, Kaminski N, Brezis M. Effects of Perfusion Pressure and Renal Flow upon Albumin Excretion in Isolated Perfused Kidneys. Nephron 1990, 56: 396-398. PMID: 2079998, DOI: 10.1159/000186182.Peer-Reviewed Original ResearchConceptsGlomerular filtration rateAlbumin excretionPerfusion pressureRenal flowWhole-kidney hemodynamicsUrinary albumin excretionMicrograms/minIsolated Perfused KidneyRenal hemodynamicsAngiotensin IIKidney hemodynamicsPerfused KidneyFiltration rateRenal excretionFractional clearanceRat kidneyExcretionKidneySequential changesHemodynamicsMinAlbuminHg