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, 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
2021
Doubly Stochastic Normalization of the Gaussian Kernel Is Robust to Heteroskedastic Noise.
Landa B, Coifman RR, Kluger Y. Doubly Stochastic Normalization of the Gaussian Kernel Is Robust to Heteroskedastic Noise. SIAM Journal On Mathematics Of Data Science 2021, 3: 388-413. PMID: 34124607, PMCID: PMC8194191, DOI: 10.1137/20m1342124.Peer-Reviewed Original ResearchStochastic normalizationHeteroskedastic noiseGaussian kernelHigh-dimensional settingsMatrix convergesAmbient dimensionDifferent noise variancesEuclidean spaceData pointsNoise varianceSymmetric normalizationCertain normalizationAffinity matrixClean counterpartsPairwise distancesKernelNoiseData analysis techniqueSingle-cell RNA-sequencing dataParticular directionSpaceWidespread approachConvergesMatrixHeteroskedasticity