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
2010
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.
Pitzer E, Kim J, Patel K, Galante P, Ohno-Machado L. PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. AMIA Joint Summits On Translational Science Proceedings 2010, 2010: 25-9. PMID: 21347141, PMCID: PMC3041550.Peer-Reviewed Original ResearchParallel sequencing technologiesShort DNA sequencesTranscriptome studiesGenomic positionsDNA sequencesSequencing technologiesGenomic tagsExpression technologySequencing readsRapid AnnotationGene levelMicroarray probesShort readsCustom annotationsAbundance valuesAnnotationNovel alignment algorithmReadsBiological referenceTagsIlluminaAffymetrixSequenceMore insightProbe