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
2012
SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins.
de Souza J, Galante P, de Almeida R, da Cunha J, Ohara D, Ohno-Machado L, Old L, de Souza S. SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins. Cancer Immunology Research 2012, 12: 15. PMID: 23390370, PMCID: PMC3554024.Peer-Reviewed Original ResearchConceptsCell surface proteinsSurface proteinsProtein-protein interactionsUCSC Genome BrowserImportant data repositoryUser-friendly web interfaceGene annotationProtein domainsGenome browserHuman genesGene expressionGene namesGenesSomatic mutationsProteinExcellent targetAnnotationTherapeutic reagentsWeb interfaceNCBIMutationsExpressionDomainTarget