2023
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfiling
2022
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Raredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.Peer-Reviewed Original ResearchConceptsCell-cell interactionsCell-cell signalingSingle-cell resolutionSingle-cell dataLocal cellular microenvironmentSingle-cell levelSpatial transcriptomics dataCell clustersExtracellular signalingTranscriptomic dataGene expression valuesSpatial transcriptomicsSignaling mechanismCellular microenvironmentNicheExpression valuesSupplementary dataSignalingTranscriptomicsComprehensive visualizationBioinformaticsInteraction
2021
Detection of differentially abundant cell subpopulations in scRNA-seq data
Zhao J, Jaffe A, Li H, Lindenbaum O, Sefik E, Jackson R, Cheng X, Flavell RA, Kluger Y. Detection of differentially abundant cell subpopulations in scRNA-seq data. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2100293118. PMID: 34001664, PMCID: PMC8179149, DOI: 10.1073/pnas.2100293118.Peer-Reviewed Original ResearchMeSH KeywordsAgingB-LymphocytesBrainCell LineageCOVID-19CytokinesDatasets as TopicDendritic CellsGene Expression ProfilingGene Expression RegulationHigh-Throughput Nucleotide SequencingHumansMelanomaMonocytesPhenotypeRNA, Small CytoplasmicSARS-CoV-2Severity of Illness IndexSingle-Cell AnalysisSkin NeoplasmsT-LymphocytesTranscriptomeConceptsDA subpopulationsIll COVID-19 patientsImmune checkpoint therapyCOVID-19 patientsSingle-cell RNA sequencing analysisCheckpoint therapyBrain tissueCell subpopulationsRNA sequencing analysisTime pointsSubpopulationsDiseased individualsDistinct phenotypesOriginal studyCell typesAbundant subpopulationSequencing analysisCellsDA measuresPhenotypeImportant differencesNonrespondersPatientsTherapy
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 ResearchMeSH KeywordsAlgorithmsAnimalsBase SequenceComputational BiologyGene Expression ProfilingGenetic MarkersMiceRNASequence Analysis, RNASingle-Cell AnalysisStochastic Processes
2006
Characterizing disease states from topological properties of transcriptional regulatory networks
Tuck DP, Kluger HM, Kluger Y. Characterizing disease states from topological properties of transcriptional regulatory networks. BMC Bioinformatics 2006, 7: 236. PMID: 16670008, PMCID: PMC1482723, DOI: 10.1186/1471-2105-7-236.Peer-Reviewed Original ResearchConceptsTranscriptional regulatory networksRegulatory networksTranscription factorsTranscriptional networksRegulated genesGene deregulationExpression profilesDiseased statesGene regulatory networksCentrality of genesGene expression experimentsGene expression profilesGene expression studiesGene centralityRegulatory linkExpression experimentsExpression studiesGene linksGenesCell typesExpression datasetsGene subsetsDifferential activityNormal cellsRemarkable degree
2003
Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions
Kluger Y, Basri R, Chang JT, Gerstein M. Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions. Genome Research 2003, 13: 703-716. PMID: 12671006, PMCID: PMC430175, DOI: 10.1101/gr.648603.Peer-Reviewed Original ResearchBreast NeoplasmsCentral Nervous System NeoplasmsCerebellar NeoplasmsDatabases, GeneticGene Expression ProfilingGene Expression Regulation, NeoplasticGenes, NeoplasmGliomaHumansLeukemia, Lymphocytic, Chronic, B-CellLymphoma, B-CellLymphoma, FollicularLymphoma, Large B-Cell, DiffuseMedulloblastomaNeoplasms, Germ Cell and EmbryonalOligonucleotide Array Sequence AnalysisPhenotypeReference ValuesTumor Cells, Cultured
2001
RNA 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