2021
Bayesian information sharing enhances detection of regulatory associations in rare cell types
Wu A, Peng J, Berger B, Cho H. Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics 2021, 37: i349-i357. PMID: 34252956, PMCID: PMC8275330, DOI: 10.1093/bioinformatics/btab269.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremGene Expression ProfilingInformation DisseminationSequence Analysis, RNASingle-Cell AnalysisSoftwareConceptsScRNA-seq datasetsRegulatory associationsCell typesRegulatory networksCell type-specific gene regulatory networksCell-type specific gene regulationSingle-cell RNA sequencing technologyCell-type specific networksBenchmark scRNA-seq datasetsDiverse cellular contextsGene regulatory network inference methodRNA sequencing technologyGene regulatory networksRare cell typesSingle-cell datasetsSpecific cell typesNetwork inference methodsDynamic biological processesTranscriptional statesGene regulationCellular contextNetwork inference algorithmsComplex rewiringBiological processesGene associationsAssessing single-cell transcriptomic variability through density-preserving data visualization
Narayan A, Berger B, Cho H. Assessing single-cell transcriptomic variability through density-preserving data visualization. Nature Biotechnology 2021, 39: 765-774. PMID: 33462509, PMCID: PMC8195812, DOI: 10.1038/s41587-020-00801-7.Peer-Reviewed Original Research
2019
Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
Hie B, Cho H, DeMeo B, Bryson B, Berger B. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. Cell Systems 2019, 8: 483-493.e7. PMID: 31176620, PMCID: PMC6597305, DOI: 10.1016/j.cels.2019.05.003.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsData AnalysisDatasets as TopicGenetic HeterogeneityHumansMacrophagesRNA-SeqSingle-Cell AnalysisTranscriptomeConceptsSingle-cell transcriptomic landscapeSingle-cell RNA sequencing studiesSingle-cell omicsCell typesSeq data integrationSingle-cell data analysisRare cell typesRNA sequencing studiesScRNA-seq dataTranscriptional diversityTranscriptomic landscapeBiological cell typesTranscriptomic heterogeneitySequencing studiesRare subpopulationAnalysis pipelineCellsUmbilical cord bloodEssential stepInflammatory macrophagesOmicsComprehensive visualizationDiversityGeometric sketchHundreds of thousands
2018
Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks
Cho H, Berger B, Peng J. Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks. Cell Systems 2018, 7: 185-191.e4. PMID: 29936184, PMCID: PMC6469860, DOI: 10.1016/j.cels.2018.05.017.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCluster AnalysisComputer GraphicsGenomicsHumansNeural Networks, ComputerSequence Analysis, RNASingle-Cell AnalysisSoftwareStochastic Processes