2024
Gene trajectory inference for single-cell data by optimal transport metrics
Qu R, Cheng X, Sefik E, Stanley III J, Landa B, Strino F, Platt S, Garritano J, Odell I, Coifman R, Flavell R, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nature Biotechnology 2024, 1-11. PMID: 38580861, PMCID: PMC11452571, DOI: 10.1038/s41587-024-02186-3.Peer-Reviewed Original ResearchGene dynamicsGene programTrajectory inferenceBiological processesCell-cell graphDynamics of genesCell trajectory inferenceSingle-cell RNA sequencingSingle-cell dataCell state transitionsMyeloid lineage maturationDynamics of biological processesGene distributionRNA sequencingPseudotemporal orderingGene processingTrajectories of cellsGenesActivity of biological processesTechnical noiseGroups of cellsLineage maturationCellsConstruct cellsSequence
2023
Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms
Zyla J, Papiez A, Zhao J, Qu R, Li X, Kluger Y, Polanska J, Hatzis C, Pusztai L, Marczyk M. Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms. Computational And Structural Biotechnology Journal 2023, 21: 4663-4674. PMID: 37841335, PMCID: PMC10568495, DOI: 10.1016/j.csbj.2023.09.035.Peer-Reviewed Original ResearchSingle-cell RNA-seq platformsSingle-cell RNA sequencingBulk RNA-seq dataRNA-seq platformsNumber of transcriptsLow-expression genesRNA-seq dataSingle-cell dataExpression levelsLow sequencing depthDiscordant genesRNA sequencingSequencing technologiesExpression shiftsPathway levelBiological pathwaysGene levelSequencing depthTranscriptomic platformsGenesIndividual cellsSingle cellsRNA integrityPathwayCells
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