2019
Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data
Linderman GC, Rachh M, Hoskins JG, Steinerberger S, Kluger Y. Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data. Nature Methods 2019, 16: 243-245. PMID: 30742040, PMCID: PMC6402590, DOI: 10.1038/s41592-018-0308-4.Peer-Reviewed Original Research
2004
Lineage specificity of gene expression patterns
Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Nasr A, Halaban HR, Krause DS, Zhang X, Newburger PE, Weissman SM. Lineage specificity of gene expression patterns. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 6508-6513. PMID: 15096607, PMCID: PMC404075, DOI: 10.1073/pnas.0401136101.Peer-Reviewed Original ResearchConceptsGene expression patternsExpression patternsExpression dataGene Ontology databaseTree of relationshipsStem cellsBroad functional categoriesHematopoietic cell populationsMRNA expression dataHematopoietic programBioCarta databasesGenome databaseLineage choiceHematopoietic stem cellsKyoto EncyclopediaDifferent lineagesFunctional categoriesLineage developmentCell lineagesGene expressionLineage specificityOligonucleotide microarraysFunctional pathwaysLineage discriminationOntology database
2001
Genomic and proteomic analysis of the myeloid differentiation program
Lian Z, Wang L, Yamaga S, Bonds W, Beazer-Barclay Y, Kluger Y, Gerstein M, Newburger P, Berliner N, Weissman S. Genomic and proteomic analysis of the myeloid differentiation program. Blood 2001, 98: 513-524. PMID: 11468144, DOI: 10.1182/blood.v98.3.513.Peer-Reviewed Original ResearchConceptsNew transcription factorMammalian cell typesMurine bone marrow cellsGene expression patternsDominant-negative retinoic acid receptorGene expression changesTranscription regulatory factorsMyeloid differentiation programRetinoic acid receptorsTranscription factorsProteomic analysisDifferentiation programArray hybridizationDifferential displayExpression patternsExpression changesPromyelocytic cell lineRegulatory factorsMyeloid differentiationLevels of mRNACell typesMolecular levelExtensive catalogueMicroM retinoic acidBone marrow cellsRNA expression patterns change dramatically in human neutrophils exposed to bacteria
Subrahmanyam Y, Yamaga S, Prashar Y, Lee H, Hoe N, Kluger Y, Gerstein M, Goguen J, Newburger P, Weissman S. RNA expression patterns change dramatically in human neutrophils exposed to bacteria. Blood 2001, 97: 2457-2468. PMID: 11290611, DOI: 10.1182/blood.v97.8.2457.Peer-Reviewed Original ResearchMeSH KeywordsCells, CulturedCytokinesDNA, ComplementaryEndopeptidasesEscherichia coliExpressed Sequence TagsGene Expression ProfilingGene Expression RegulationHumansInflammationNeutrophilsOxidoreductasesProtein KinasesReceptors, CytokineRNA, MessengerRNA, RibosomalSpecies SpecificitySubtraction TechniqueTranscription, GeneticTranscriptional ActivationVirulenceYersinia pestisConceptsMembrane trafficking regulatorsRNA expression patternsGene clusterTrafficking regulatorResponse genesGene inductionExpression patternsGene expressionNonpathogenic bacteriaCell typesVariety of stimuliMessenger RNA levelsYersinia pestisDifferent bacteriaVariety of cytokinesNeutrophil physiologyHuman neutrophilsBacteriaGenesActive regulationRNA levelsPestisMRNAActivation responseCellular inflammatory response