2021
Improved methods for RNAseq-based alternative splicing analysis
Halperin RF, Hegde A, Lang JD, Raupach EA, Legendre C, Liang W, LoRusso P, Sekulic A, Sosman J, Trent J, Rangasamy S, Pirrotte P, Schork N. Improved methods for RNAseq-based alternative splicing analysis. Scientific Reports 2021, 11: 10740. PMID: 34031440, PMCID: PMC8144374, DOI: 10.1038/s41598-021-89938-2.Peer-Reviewed Original ResearchConceptsProtein-level effectsSplicing analysisSplice eventsSplice isoformsRNAseq dataAlternative splicing analysisTissue-specific splice variantsDifferential splicing analysisGene expression levelsPathogenic splicing variantProtein level expressionSequence readsSplicing variantsSplice variantsOncogenic mutationsMass spectrometry dataSplice alterationsExpression levelsRNAseqIsoformsMelanoma datasetSpectrometry dataNovel statistical approachAnalysis resourcesMass spectrometry
2014
AN INTEGRATED FRAMEWORK FOR REPORTING CLINICALLY RELEVANT BIOMARKERS FROM PAIRED TUMOR/NORMAL GENOMIC AND TRANSCRIPTOMIC SEQUENCING DATA IN SUPPORT OF CLINICAL TRIALS IN PERSONALIZED MEDICINE
Altman R, Dunker A, Hunter L, Ritchie M, Murray T, Klein T, NASSER S, KURDOGLU A, IZATT T, ALDRICH J, RUSSELL M, CHRISTOFORIDES A, TEMBE W, KIEFER J, CORNEVEAUX J, BYRON S, FORMAN K, ZUCCARO C, KEATS J, LORUSSO P, CARPTEN J, TRENT J, CRAIG D. AN INTEGRATED FRAMEWORK FOR REPORTING CLINICALLY RELEVANT BIOMARKERS FROM PAIRED TUMOR/NORMAL GENOMIC AND TRANSCRIPTOMIC SEQUENCING DATA IN SUPPORT OF CLINICAL TRIALS IN PERSONALIZED MEDICINE. Biocomputing 2014, 56-67. PMID: 25592568, DOI: 10.1142/9789814644730_0007.Peer-Reviewed Original ResearchConceptsTranscriptomic sequencing dataHigh-throughput genomic dataRelational database systemsTerabytes of dataTumor/normal samplesSingle nucleotide changeDiversity of usersReal-time mannerIndividual genomesAnnotation databasesDatabase systemsFlexible computational frameworkChromosomal rearrangementsGenomic dataGene expressionSequencing dataData structureComputational architectureGene fusionsNucleotide changesMultiple trackersBase pairsSmall insertionsTime mannerClinical genomic testing