Featured Publications
VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data
Yasumizu Y, Hara A, Sakaguchi S, Ohkura N. VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data. Bioinformatics 2020, 37: 1465-1467. PMID: 33017003, PMCID: PMC7745649, DOI: 10.1093/bioinformatics/btaa859.Peer-Reviewed Original ResearchConceptsConventional RNA-seq dataRNA-seq dataSequence dataSupplementary dataRNA transcriptsBioinformatics methodsVirus copy numberRNA sequencingCopy numberVirus RNAHuman cellsExpression profilesBioinformaticsMultiple virusesInfected cellsClinical samplesTranscriptionRNACellsVirusVirus analysisSARS-CoV-2SequenceMRNAHerpesvirus
2018
Innate Myeloid Cell Subset-Specific Gene Expression Patterns in the Human Colon are Altered in Crohn’s Disease Patients
Sekido Y, Yasumizu Y, Nishimura J, Kayama H, Matsuno H, Ogino T, Miyoshi N, Takahashi H, Haraguchi N, Hata T, Matsuda C, Doki Y, Mori M, Takeda K, Ohkura N, Sakaguchi S, Mizushima T. Innate Myeloid Cell Subset-Specific Gene Expression Patterns in the Human Colon are Altered in Crohn’s Disease Patients. Digestion 2018, 99: 194-204. PMID: 30343293, DOI: 10.1159/000490890.Peer-Reviewed Original ResearchMeSH KeywordsColonComputational BiologyCrohn DiseaseGene Expression ProfilingHumansImmunity, InnateIntestinal MucosaMyeloid CellsSequence Analysis, RNATranscriptomeConceptsGene expression patternsGO BP termsExpression patternsGene OntologyGut homeostasisMyeloid cell subsetsInnate myeloid cellsBiological processesCrohn's diseaseComprehensive gene expression profilesMaintenance of gut homeostasisCell type-specific mechanismsCell subsetsMyeloid cellsHuman colonGene expression profilesHuman intestinal lamina propriaInnate immune responseLamina propriaType-specific mechanismsTranscriptional analysisGO-BPRNA sequencingDisease patientsPathogenesis of Crohn's disease