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 approachEdUVariantsLociRNANucleotidesBioinformaticsSequencingAnalysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform
Movassagh M, Mudvari P, Kokkinaki M, Edwards N, Golestaneh N, Horvath A. Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform. Journal Of Clinical Bioinformatics 2014, 4: 14. DOI: 10.1186/2043-9113-4-14.Peer-Reviewed Original ResearchRetinal pigment epitheliumNPC1 proteinLow-grade brain tumorsVariant nucleotidesFunctional NPC1 proteinTranscriptome-wide searchParallel sequencing technologiesCommon synonymous variantSingle sequencing readExon-intron boundariesDiploid genomeAllelic phaseAlternative splicingHuman transcriptomeSynonymous substitutionsBreast cancerCellular phenotypesBrain tumorsSequencing technologiesPigment epitheliumColon cancerAutosomal recessive mannerCholesterol traffickingRetinal degenerationRNA features