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 ResearchConceptsScRNA-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 associations
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