2025
Partially characterized topology guides reliable anchor-free scRNA-integration
He C, Filippidis P, Kleinstein S, Guan L. Partially characterized topology guides reliable anchor-free scRNA-integration. Communications Biology 2025, 8: 561. PMID: 40185996, PMCID: PMC11971424, DOI: 10.1038/s42003-025-07988-y.Peer-Reviewed Original ResearchConceptsBatch effectsRare cell typesSingle-cell RNA sequencingCell typesDownstream statistical analysisScRNA-seqBiological insightsRNA sequencingBatch correctionCell phenotypeCellular resolutionBiological signalsState-of-the-art methodsAdaptive lossDomain adaptation lossState-of-the-artDiverse setBatch integrationHeterogeneous cell distributionReconstruction lossSequenceTriplet lossPhenotypeSignalCell distribution
2024
Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes
Long E, Yin J, Shin J, Li Y, Li B, Kane A, Patel H, Sun X, Wang C, Luong T, Xia J, Han Y, Byun J, Zhang T, Zhao W, Landi M, Rothman N, Lan Q, Chang Y, Yu F, Amos C, Shi J, Lee J, Kim E, Choi J. Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes. Nature Communications 2024, 15: 7995. PMID: 39266564, PMCID: PMC11392933, DOI: 10.1038/s41467-024-52356-9.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGenome-wide association study lociSusceptibility genesLung cancer susceptibility genesTranscription factor footprintsChromatin accessibility mapsCis-regulatory elementsRisk-associated variantsRare cell typesRegulate gene expressionCell typesCell type-specificCancer susceptibility genesCausal variantsAssociation studiesGene regulationGene functionMultiomics approachTarget genesLociGene expressionGenesType-specificHuman lung cellsCCREs
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
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
2008
Reprogramming of Pancreatic β Cells into Induced Pluripotent Stem Cells
Stadtfeld M, Brennand K, Hochedlinger K. Reprogramming of Pancreatic β Cells into Induced Pluripotent Stem Cells. Current Biology 2008, 18: 890-894. PMID: 18501604, PMCID: PMC2819222, DOI: 10.1016/j.cub.2008.05.010.Peer-Reviewed Original ResearchConceptsEmbryonic stem cellsPluripotent stem cellsCell typesIPS cellsStem cellsC-MycTranscription factors Oct4Rare cell typesInduced pluripotent stem cellsCertain cell typesAdult stem cellsInducible lentivirusVitro reprogrammingFactors OCT4Pluripotent cellsEctopic expressionGenetic proofPancreatic β-cellsGerm layersDifferentiated cellsChimeric animalsPluripotency markersDifferentiation stageBeta cellsPancreatic beta cells
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