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 ResearchConceptsSingle-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
2016
Reconstructing Causal Biological Networks through Active Learning
Cho H, Berger B, Peng J. Reconstructing Causal Biological Networks through Active Learning. PLOS ONE 2016, 11: e0150611. PMID: 26930205, PMCID: PMC4773135, DOI: 10.1371/journal.pone.0150611.Peer-Reviewed Original ResearchConceptsGaussian Bayesian networksBayesian networkContinuous Bayesian networksDiscrete Bayesian networksBiological networksFast convergenceGreat practical interestGene regulatory networksGraph structurePractical interestQuantitative propertiesSignificant runtime improvementsComplex biological systemsRuntime improvementCausal biological networksSystems biologyCentral problemFinal distributionPrevious approachesNetwork structureResource constraintsData setsLearning algorithmImportant modelActive learning algorithm
2015
Exploiting ontology graph for predicting sparsely annotated gene function
Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics 2015, 31: i357-i364. PMID: 26072504, PMCID: PMC4542782, DOI: 10.1093/bioinformatics/btv260.Peer-Reviewed Original ResearchConceptsFunction prediction algorithmsPrediction algorithmVariety of algorithmsFunctional labelsOntology graphCross-validation experimentsOverfitting problemGraph structurePrevious stateGene functionAlgorithmAnnotation catalogsTens of thousandsMolecular interaction networksFunction predictionOntology databasePoor predictive performanceAnnotationLabelsPredictive performanceGene Ontology databaseInformationLarge numberGO termsInteraction networks