2024
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis
Liu T, Long W, Cao Z, Wang Y, He C, Zhang L, Strittmatter S, Zhao H. CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. Briefings In Bioinformatics 2024, 26: bbae626. PMID: 39592241, PMCID: PMC11596696, DOI: 10.1093/bib/bbae626.Peer-Reviewed Original Research
2022
A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data
Zhu B, Li H, Zhang L, Chandra SS, Zhao H. A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data. Briefings In Bioinformatics 2022, 23: bbac166. PMID: 35514182, PMCID: PMC9487630, DOI: 10.1093/bib/bbac166.Peer-Reviewed Original ResearchConceptsDE genesSeq dataSingle-cell RNA sequencing technologyDifferential expressionSingle-cell RNA-seq dataIdentification of genesRNA sequencing technologySpecific differential expressionSingle-cell resolutionRNA-seq dataMarkov random field modelMarkov random field model-based approachSimilar cell typesNovel statistical modelRandom field modelComplex biological systemsBiological pathwaysGene detectionGenesCell typesStatistical modelMouse datasetsField modelBiological systemsReal data
2018
EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells
Zhang L, Ettou S, Khalid M, Taglienti M, Jain D, Jung YL, Seager C, Liu Y, Ng KH, Park PJ, Kreidberg JA. EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells. Development 2018, 145: dev157149. PMID: 29945864, PMCID: PMC6514390, DOI: 10.1242/dev.157149.Peer-Reviewed Original ResearchConceptsNephron progenitor cellsGene expressionProgenitor cellsNephron differentiationSelf-renewing stem cellsThousands of nephronsRole of PRC2Expression of genesDifferentiation of stemMutant micePolycomb groupH3K27me3 marksProgenitor stateEpigenetic regulationPRC2 complexHistone H3Progenitor populationsEnhancer sitesRenal vesiclesNonredundant componentMammalian kidneyCrucial rolePhysiological homeostasisGenesStem cells