2024
Mapping the gene space at single-cell resolution with gene signal pattern analysis
Venkat A, Leone S, Youlten S, Fagerberg E, Attanasio J, Joshi N, Perlmutter M, Krishnaswamy S. Mapping the gene space at single-cell resolution with gene signal pattern analysis. Nature Computational Science 2024, 4: 955-977. PMID: 39706866, DOI: 10.1038/s43588-024-00734-0.Peer-Reviewed Original ResearchConceptsSingle-cell dataGene spaceGene representationSimulated single-cell dataGene co-expression modulesCell-cell graphCharacterization of genesGene-gene interactionsCo-expression modulesCell-cell communicationCellular state spaceSingle-cell resolutionSingle-cell sequencing analysisSequence analysisGenesBiological tasksSpatial transcriptomicsGraph signal processing approachSignal pattern analysisPattern analysisSignal processing approachComputational methodsTranscriptome
2023
Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data
Venkat A, Bhaskar D, Krishnaswamy S. Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data. Trends In Immunology 2023, 44: 551-563. PMID: 37301677, DOI: 10.1016/j.it.2023.05.003.Peer-Reviewed Original ResearchGeodesic Sinkhorn For Fast and Accurate Optimal Transport on Manifolds
Huguet G, Tong A, Zapatero M, Tape C, Wolf G, Krishnaswamy S. Geodesic Sinkhorn For Fast and Accurate Optimal Transport on Manifolds. 2023, 00: 1-6. DOI: 10.1109/mlsp55844.2023.10285995.Peer-Reviewed Original ResearchOptimal transport distanceHeat kernelHigh-dimensional single-cell dataGraph LaplacianOptimal transportSinkhornChebyshev polynomialsEfficient computationSuch computationsManifold graphComputationSingle-cell dataBarycenterGround distanceKernelData scienceManifoldPolynomialsLaplacianCell dataGraphDistributionDistanceDatapointsTransport distance
2014
Conditional density-based analysis of T cell signaling in single-cell data
Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP. Conditional density-based analysis of T cell signaling in single-cell data. Science 2014, 346: 1250689. PMID: 25342659, PMCID: PMC4334155, DOI: 10.1126/science.1250689.Peer-Reviewed Original ResearchConceptsSingle-cell dataMitogen-activated protein kinase ERK2High-dimensional single-cell technologiesProtein kinase ERK2Single-cell technologiesNaïve cellsKinase ERK2Protein speciesCellular circuitsCell variationMolecular circuitsProteinMass cytometryAbundanceCellsCell subtypesComputational approachERK2Computational methodsSpeciesPERKCascadeFunctionT cellsPS6
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