2017
Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
Restrepo P, Movassagh M, Alomran N, Miller C, Li M, Trenkov C, Manchev Y, Bahl S, Warnken S, Spurr L, Apanasovich T, Crandall K, Edwards N, Horvath A. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. Scientific Reports 2017, 7: 8287. PMID: 28811643, PMCID: PMC5557904, DOI: 10.1038/s41598-017-08416-w.Peer-Reviewed Original ResearchConceptsCancer Gene CensusDNA sequence dataCancer-implicated genesSomatic allelesCancer Genome AtlasGenome regionsSequence dataCancer transcriptomeCGC genesAllele contentAllele expressionFunctional variantsGenesGenetic variantsGenome AtlasTranscriptomeFunctional elementsAllelesExpressionVariantsVariant allele fractionRNAAllele fractionOverexpressionInformation content
2014
SNPlice: variants that modulate Intron retention from RNA-sequencing data
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards N, Golestaneh N, Horvath A. SNPlice: variants that modulate Intron retention from RNA-sequencing data. Bioinformatics 2014, 31: 1191-1198. PMID: 25481010, PMCID: PMC4393518, DOI: 10.1093/bioinformatics/btu804.Peer-Reviewed Original ResearchConceptsRNA-seq datasetsExon-intron boundariesImportance of splicingRNA-sequencing dataHigh-throughput approachIntron retentionSplicing eventsAltered splicingSplice junctionsVariant lociVariant nucleotidesAllele-specific sequencingSplicingSupplementary dataLinux computerBinary packagesComputational approachEdUVariantsLociRNANucleotidesBioinformaticsSequencing