2022
Normalizing and denoising protein expression data from droplet-based single cell profiling
Mulè M, Martins A, Tsang J. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nature Communications 2022, 13: 2099. PMID: 35440536, PMCID: PMC9018908, DOI: 10.1038/s41467-022-29356-8.Peer-Reviewed Original ResearchConceptsProtein expression dataSingle-cell profiling methodsExpression dataSingle-cell profilingOligo-conjugated antibodiesTechnical noiseProtein populationCITE-seqCellular heterogeneityComprehensive dissectionDownstream analysisCell profilingDSBsSingle cellsProtein levelsProtein expressionCell populationsOpen-source R packageProfiling methodProtein countsEmpty dropletsR packageComputational analysisCellsBiological variation
2017
Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network
Martins A, Narayanan M, Prüstel T, Fixsen B, Park K, Gottschalk R, Lu Y, Andrews-Pfannkoch C, Lau W, Wendelsdorf K, Tsang J. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Systems 2017, 4: 379-392.e12. PMID: 28365150, PMCID: PMC8392141, DOI: 10.1016/j.cels.2017.03.002.Peer-Reviewed Original ResearchConceptsGene networksCellular adaptationCell variationSingle-cell transcriptomic studiesGene-gene correlationsUnderlying regulatory mechanismsDegree of phosphorylationPhenotypic diversityTranscriptomic studiesEnvironmental adaptationMultiple molecular parametersGene expressionRegulatory mechanismsCellular heterogeneityDistinct environmentsSingle cellsHuman macrophagesQuantitative tuningCell populationsNatural perturbationsGenesDifferent environmentsSuch variationCellsStochastic simulation analysis
2016
Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling
Narayanan M, Martins A, Tsang J. Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling. PLOS Computational Biology 2016, 12: e1005016. PMID: 27438699, PMCID: PMC4954693, DOI: 10.1371/journal.pcbi.1005016.Peer-Reviewed Original ResearchConceptsSingle-cell expression levelsExpression levelsNovel biological informationSingle cellsKey inflammatory genesExpression variationGene expressionCellular heterogeneityBiological informationRandom poolSingle populationHuman macrophagesBiological conditionsCell populationsGenesMultiplexed technologiesK cellsInflammatory genesCellsBiological varianceQuantifying differencesSensitive technologyContinuous variationRobust inferenceProfiling