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
2013
A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process
Yuan H, Qin F, Movassagh M, Park H, Golden W, Xie Z, Zhang P, Sklar J, Li H. A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process. Cancer Discovery 2013, 3: 1394-1403. PMID: 24089019, DOI: 10.1158/2159-8290.cd-13-0186.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineForkhead Box Protein O1Forkhead Transcription FactorsGene Expression Regulation, DevelopmentalGene FusionHumansMesenchymal Stem CellsMuscle DevelopmentMusclesMyoD ProteinMyogeninOncogene Proteins, FusionPaired Box Transcription FactorsPAX3 Transcription FactorRhabdomyosarcoma, AlveolarTranslocation, GeneticConceptsPAX3-FOXO1Chimeric RNAsChromosomal translocationsMuscle differentiation processChimeric fusion RNAsChimeric gene productsNormal cellsNormal non-cancer cellsPluripotent cellsNormal fetal muscleNon-cancer cellsGene productsChromosomal rearrangementsPosttranscriptional mechanismsDevelopmental roleFusion RNAGene fusionsDifferentiation processRNA characteristicsSame lineageMyogenesis processChimeric productsNormal developmentRhabdomyosarcoma cellsRNA