2015
Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data
Kroll J, Kim J, Ohno-Machado L, de Souza S. Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. PeerJ 2015, 3: e1419. PMID: 26618088, PMCID: PMC4655094, DOI: 10.7717/peerj.1419.Peer-Reviewed Original ResearchAlternative splicing eventsSequencing dataAlternative splicing analysisNext-generation DNA sequencing technologiesTranscriptome sequencing dataUCSC Genome BrowserDNA sequencing technologiesRNA-seq dataNext-generation sequencing dataDNA sequencing platformsSoftware suiteHuman Body MapEukaryotic speciesSplicing eventsTranscriptome dataGene coordinatesSplicing analysisGenome browserUNIX-like systemsNext-generation DNA sequencing platformsSequencing technologiesBioinformatics skillsAvailable speciesExpression profilesBioinformatics background
2011
Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells
Kamberov Y, Kim J, Mazitschek R, Kuo W, Whitman M. Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells. BMC Research Notes 2011, 4: 381. PMID: 21974968, PMCID: PMC3197508, DOI: 10.1186/1756-0500-4-381.Peer-Reviewed Original ResearchIntegrated stress responseStress responseExtracellular matrix gene expressionGlobal expression profilesEpithelial cellsMicroarray expression analysisMatrix gene expressionMammary epithelial cellsTranscriptional controlTranscriptional responseExpression analysisGene expressionExpression profilesMicroarray profilingTGFβ signalingCell differentiationCell typesECM componentsPotent regulatorAmelioration of fibrosisTh17 cell differentiationSignal inhibitionCommon mechanismEffect of halofuginoneBiological effects