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
2016
Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions
Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Research 2016, 44: 8714-8725. PMID: 27439714, PMCID: PMC5062970, DOI: 10.1093/nar/gkw568.Peer-Reviewed Original ResearchConceptsMulti-locus interactionsDNA FISHGene regulationChromosome conformation capture techniquesFunctional importancePairwise chromatin interactionsChromatin interactionsTranscriptional outputRegulatory elementsEnhancer elementsBiological settingsSame cellsSimultaneous interactionFishNew insightsEnhancerRegulationReceptor enhancerCapture techniquesInteractionTCRB