2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
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 ResearchConceptsTotal 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
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