Featured Publications
Cardiac dopamine D1 receptor triggers ventricular arrhythmia in chronic heart failure
Yamaguchi T, Sumida TS, Nomura S, Satoh M, Higo T, Ito M, Ko T, Fujita K, Sweet ME, Sanbe A, Yoshimi K, Manabe I, Sasaoka T, Taylor MRG, Toko H, Takimoto E, Naito AT, Komuro I. Cardiac dopamine D1 receptor triggers ventricular arrhythmia in chronic heart failure. Nature Communications 2020, 11: 4364. PMID: 32868781, PMCID: PMC7459304, DOI: 10.1038/s41467-020-18128-x.Peer-Reviewed Original ResearchConceptsVentricular arrhythmiasDopamine D1 receptorsD1 receptorsChronic heart failureHeart failure patientsSustained ventricular tachycardiaNormal calcium handlingFailure patientsHeart failureModel miceVentricular tachycardiaPathophysiological roleCalcium handlingTherapeutic targetDopamine systemSingle-cell resolution analysisArrhythmiasD1RCardiomyocytesReceptorsTachycardiaPatientsMice
2024
A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
Subedi S, Sumida T, Park Y. A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection. Life Science Alliance 2024, 7: e202402713. PMID: 39107066, PMCID: PMC11303850, DOI: 10.26508/lsa.202402713.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyGene Expression ProfilingHumansModels, StatisticalRNA-SeqSequence Analysis, RNASingle-Cell AnalysisConceptsCell type-specific marker genesSingle-cell RNA-seq data analysisRNA-seq data analysisSingle-cell data analysisTopic modelsSingle-cell dataProbabilistic topic modelPathway annotationScalable approximation methodsLow memory consumptionComputation timeCellular statesMarker genesDictionary matrixLatent representationSingle-cellMemory consumptionTopic assignmentsComputing unitsFrequency vectorSelection stepCellsData analysisScalable approachData matrix
2019
High-throughput single-molecule RNA imaging analysis reveals heterogeneous responses of cardiomyocytes to hemodynamic overload
Satoh M, Nomura S, Harada M, Yamaguchi T, Ko T, Sumida T, Toko H, Naito AT, Takeda N, Tobita T, Fujita T, Ito M, Fujita K, Ishizuka M, Kariya T, Akazawa H, Kobayashi Y, Morita H, Takimoto E, Aburatani H, Komuro I. High-throughput single-molecule RNA imaging analysis reveals heterogeneous responses of cardiomyocytes to hemodynamic overload. Journal Of Molecular And Cellular Cardiology 2019, 128: 77-89. PMID: 30611794, DOI: 10.1016/j.yjmcc.2018.12.018.Peer-Reviewed Original ResearchConceptsTransverse aortic constrictionHemodynamic overloadCardiomyocyte sizeExpression levelsGene expressionHeart failure stageSingle-cell RNA sequencingSingle-molecule RNAMyosin heavy chain βSingle-cell quantitative PCRFetal gene expressionFetal gene programSingle-cell analysis methodsSingle-molecule fluorescenceHeart failureSingle-cell levelPressure overloadAortic constrictionHypertrophy stageCardiac hypertrophyIsolated cardiomyocytesMyh7 expressionTemporal regulationRNA sequencingFetal genes