2021
SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Prashant N, Alomran N, Chen Y, Liu H, Bousounis P, Movassagh M, Edwards N, Horvath A. SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data. BMC Genomics 2021, 22: 689. PMID: 34551708, PMCID: PMC8459565, DOI: 10.1186/s12864-021-07974-8.Peer-Reviewed Original ResearchMeSH KeywordsPolymorphism, Single NucleotideRNARNA, Small CytoplasmicSequence Analysis, RNASingle-Cell AnalysisSoftwareConceptsSomatic mutationsNovel somatic mutationsBackgroundRecent studiesVariant allele fractionIntra-tumoral heterogeneityVariant allelesNeuroblastoma samplesCell-level expressionCancer studiesExpression signaturesAllele fractionRegions of KRASNormal cellsType of studySmall proportionCellsExpression
2018
Systematic pan-cancer analysis of somatic allele frequency
Spurr L, Li M, Alomran N, Zhang Q, Restrepo P, Movassagh M, Trenkov C, Tunnessen N, Apanasovich T, Crandall K, Edwards N, Horvath A. Systematic pan-cancer analysis of somatic allele frequency. Scientific Reports 2018, 8: 7735. PMID: 29769535, PMCID: PMC5956099, DOI: 10.1038/s41598-018-25462-0.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputational BiologyGene Expression Regulation, NeoplasticGene FrequencyHigh-Throughput Nucleotide SequencingHumansMutationNeoplasm ProteinsNeoplasmsPolymorphism, Single NucleotideTranscriptomeConceptsTotal gene expressionCancer-implicated genesSomatic allelesGene expressionHigh allele frequencyNonsense-mediated mRNA decayAllele frequenciesSomatic variantsKey cancer genesDNA sequencing dataSingle nucleotide variantsPan-cancer analysisTumor somatic variantsMRNA decayCancer Genome AtlasSequencing dataCGC genesNormal RNACancer genesNucleotide variantsGenesTumor transcriptomeGenetic variantsGenome AtlasImbalanced expression
2016
RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data
Movassagh M, Alomran N, Mudvari P, Dede M, Dede C, Kowsari K, Restrepo P, Cauley E, Bahl S, Li M, Waterhouse W, Tsaneva-Atanasova K, Edwards N, Horvath A. RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data. Nucleic Acids Research 2016, 44: e161-e161. PMID: 27576531, PMCID: PMC5159535, DOI: 10.1093/nar/gkw757.Peer-Reviewed Original Research