2022
B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressome
Isaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressome. Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2022, 49: s5-s5. DOI: 10.1017/cjn.2022.98.Peer-Reviewed Original ResearchProteins/genesGene pathwaysDifferential expressionIntegration of proteomicsGene networksOxidative stressGene setsProteogenomicsMolecular mechanismsPaenibacillus sppMolecular identificationPost-infectious hydrocephalusGenesDNA sequencingNovel insightsPathogenetic bacteriaProteomicsRNAseqViral pathogensPathwayHost responseExpressionExpressomeCerebrospinal fluidImmune system
2021
C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH Expressome
Isaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH Expressome. Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2021, 48: s18-s19. DOI: 10.1017/cjn.2021.279.Peer-Reviewed Original ResearchProteins/genesGene pathwaysDifferential expressionIntegration of proteomicsGene networksOxidative stressGene setsProteogenomicsMolecular mechanismsPaenibacillus sppMolecular identificationPost-infectious hydrocephalusGenesDNA sequencingNovel insightsPathogenetic bacteriaProteomicsRNAseqViral pathogensPathwayHost responseExpressionExpressomeCerebrospinal fluidImmune systemSCReadCounts: 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 ResearchConceptsSomatic mutationsNovel somatic mutationsBackgroundRecent studiesVariant allele fractionIntra-tumoral heterogeneityVariant allelesNeuroblastoma samplesCell-level expressionCancer studiesExpression signaturesAllele fractionRegions of KRASNormal cellsType of studySmall proportionCellsExpression
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