2025
Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Millard N, Chen J, Palshikar M, Pelka K, Spurrell M, Price C, He J, Hacohen N, Raychaudhuri S, Korsunsky I. Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. Genome Biology 2025, 26: 36. PMID: 40001084, PMCID: PMC11863647, DOI: 10.1186/s13059-025-03479-9.Peer-Reviewed Original ResearchConceptsBatch effectsVisualization of gene expression patternsSpatial gene patternsGene expression analysis of cellsGene expression patternsGene expression analysisGene expression levelsGene colocalizationAnalysis of cellsGene patternsTranscriptome analysisLigand-receptor interactionsExpression patternsSpatial transcriptomicsSpatial transcriptomic analysisExpression levelsGenesMultiple samplesSpatial patternsTranscriptomeColocalizationAnatomical contextPatternsCount data
2020
Analysis of Cell and Nucleus Genome by Next-Generation Sequencing
Oh J, Abyzov A. Analysis of Cell and Nucleus Genome by Next-Generation Sequencing. 2020, 35-65. DOI: 10.1007/978-3-030-62532-0_3.Peer-Reviewed Original ResearchSingle-cell genomesBulk of cellsNext-generation sequencing technologiesMosaic variantsNuclear genomeNucleus genomeGenomic mosaicismAnalysis of cellsGenome analysisNext-generation sequencingCell genomeSequencing technologiesGenomeGenomic variantsSingle cellsCellsVariantsMosaicismDiscoverySequencingValuable insightsEnvironmental exposures
2015
Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review
Cunningham B, Zhang M, Zhuo Y, Kwon L, Race C. Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review. IEEE Sensors Journal 2015, 16: 3349-3366. PMID: 27642265, PMCID: PMC5021450, DOI: 10.1109/jsen.2015.2429738.Peer-Reviewed Original ResearchPhotonic crystal surfaceDetection of small moleculesCrystal surfaceAnalysis of drug-protein interactionsLabel-free high-resolution imagingDrug-protein interactionsDetection of disease biomarkersCancer biomarker detectionFluorescence enhancementLabel-free biosensingHigh-resolution imagesSmall moleculesOptical resonatorIndividual nanoparticlesBiomarker detectionPhotobleachable fluorescent dyesLife science researchDevice structureReview several recent advancesBiosensingDisease biomarkersHigh-resolution imaging of living cellsImaging of living cellsResolution imagesAnalysis of cells
2012
The Unique Paradigm of Spirochete Motility and Chemotaxis
Charon N, Cockburn A, Li C, Liu J, Miller K, Miller M, Motaleb M, Wolgemuth C. The Unique Paradigm of Spirochete Motility and Chemotaxis. Annual Review Of Microbiology 2012, 66: 349-370. PMID: 22994496, PMCID: PMC3771095, DOI: 10.1146/annurev-micro-092611-150145.Peer-Reviewed Original ResearchConceptsPeriplasmic flagellaSpirochete motilityIn situ analysis of cellsLyme disease spirochete Borrelia burgdorferiProtoplasmic cell cylinderGene regulationAnalysis of cellsOuter membraneUnique bacteriaCell cylinderExternal appendagesCryoelectron tomographyFlagellated bacteriaMotilitySpirochete Borrelia burgdorferiBacteriaChemotaxisModel systemLife cycleSpirochetesFlagellaCellsBacteriumGenesTranslocation
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