2022
Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases
Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax 2022, 78: 792-798. PMID: 36216496, PMCID: PMC10083187, DOI: 10.1136/thorax-2021-217703.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association analysisLocal genetic correlationsSingle-cell expression dataCandidate genesTranscription factorsIntegrative analysisGenomic regionsGenetic correlationsExpression dataTF target genesComplex genetic architectureTF binding sitesWide association studyPower of GWASSpecific DEGsGenetic architectureNew genesNovel genesCausal genesTarget genesGenetic basisEnrichment analysisAssociation studiesRegulatory roleAssociation analysisCINS: 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
2018
Reconstructing differentiation networks and their regulation from time series single-cell expression data
Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Research 2018, 28: 383-395. PMID: 29317474, PMCID: PMC5848617, DOI: 10.1101/gr.225979.117.Peer-Reviewed Original ResearchTranscription factorsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataDiverse cell populationsGene expression levelsDifferent cell typesStages of organogenesisCell fateDescendant cellsDifferentiation networkExpression similarityKey regulatorRegulatory informationExpression dataCell typesProgenitor cellsCell trajectoriesExpression levelsCell populationsDevelopmental dataCellsLineagesOrganogenesisRegulator