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
2017
Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling
Stanton KP, Jin J, Lederman RR, Weissman SM, Kluger Y. Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling. Nucleic Acids Research 2017, 45: e173-e173. PMID: 28981893, PMCID: PMC5716106, DOI: 10.1093/nar/gkx799.Peer-Reviewed Original ResearchConceptsChIP-seqNext-generation high-throughput DNA sequencing technologiesHigh-throughput DNA sequencing technologiesGenome-wide localizationGenome-wide scaleTF-binding sitesTranscription factor bindingDNA sequencing technologiesENCODE consortiumResultant readsChromatin immunoprecipitationReference genomeDiverse biological effectsModification eventsFactor bindingOmics techniquesSequencing technologiesOmics experimentsSequencing costsWide localizationPeak callingChip targetArtifactual peaksPeak callersBiological effects