A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data
Li H, Zhu B, Xu Z, Adams T, Kaminski N, Zhao H. A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. BMC Bioinformatics 2021, 22: 524. PMID: 34702190, PMCID: PMC8549347, DOI: 10.1186/s12859-021-04412-0.Peer-Reviewed Original ResearchConceptsMarkov random field modelRandom field modelMean field-like approximationField modelSpecific DEGsExpectation maximizationSingle-cell sequencing technologiesProtein-coding genesRNA sequencing data setsSingle-cell RNA-seq dataCell-type levelCell typesGibbs samplerSingle-cell RNA sequencing data setsCell-cell networksDifferential expression analysisRNA-seq dataGene network informationStatistical powerType I error ratesDifferent expression levelsMRF modelI error rateModel parametersBiological networksIntegrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.Peer-Reviewed Original ResearchConceptsDifferential expression analysisPrimary lung endothelial cellsLung endothelial cellsCell typesMarker genesExpression analysisSingle-cell RNA sequencing dataCross-species analysisVenous endothelial cellsEndothelial marker genesSingle-cell atlasMarker gene setsRNA sequencing dataEndothelial cellsSubsequent differential expression analysisDifferent lung cell typesResident cell typesLung cell typesCellular diversityEndothelial cell typesCapillary endothelial cellsHuman lung endothelial cellsPhenotypic diversityEndothelial diversityIndistinguishable populations