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 packageAbundancePaenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study
Morton S, Hehnly C, Burgoine K, Ssentongo P, Ericson J, Kumar M, Hagmann C, Fronterre C, Smith J, Movassagh M, Streck N, Bebell L, Bazira J, Kumbakumba E, Bajunirwe F, Mulondo R, Mbabazi-Kabachelor E, Nsubuga B, Natukwatsa D, Nalule E, Magombe J, Erickson T, Ngonzi J, Ochora M, Olupot-Olupot P, Onen J, Ssenyonga P, Mugamba J, Warf B, Kulkarni A, Lane J, Whalen A, Zhang L, Sheldon K, Meier F, Kiwanuka J, Broach J, Paulson J, Schiff S. Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study. The Lancet Microbe 2023, 4: e601-e611. PMID: 37348522, PMCID: PMC10529524, DOI: 10.1016/s2666-5247(23)00106-4.Peer-Reviewed Original ResearchConceptsMother-newborn pairsPostinfectious hydrocephalusCerebrospinal fluidNeonatal sepsisSpp infectionUgandan infantsMaternal bloodObservational case-control studyHospital OfficeInfant's cerebrospinal fluidBurden of morbidityCase-control studyRoute of infectionSubset of participantsMaternal feverCranial ultrasoundNeonatal infectionSepsis cohortOptimise treatmentTransplacental transmissionCord bloodObservational studyPlacental samplesSepsisHydrocephalusNeonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda
Ericson J, Burgoine K, Kumbakumba E, Ochora M, Hehnly C, Bajunirwe F, Bazira J, Fronterre C, Hagmann C, Kulkarni A, Kumar M, Magombe J, Mbabazi-Kabachelor E, Morton S, Movassagh M, Mugamba J, Mulondo R, Natukwatsa D, Kaaya B, Olupot-Olupot P, Onen J, Sheldon K, Smith J, Ssentongo P, Ssenyonga P, Warf B, Wegoye E, Zhang L, Kiwanuka J, Paulson J, Broach J, Schiff S. Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda. Clinical Infectious Diseases 2023, 77: 768-775. PMID: 37279589, PMCID: PMC10495130, DOI: 10.1093/cid/ciad337.Peer-Reviewed Original ResearchConceptsNeonatal sepsisPostinfectious hydrocephalusCerebrospinal fluidSigns of sepsisFull-term neonatesOptimal antibiotic treatmentUgandan referral hospitalQuantitative polymerase chain reactionNeonatal characteristicsClinical sepsisTerm neonatesUnderdiagnosed causeAntibiotic choiceMedian ageReferral hospitalUgandan hospitalNeurodevelopmental impairmentAdverse outcomesSpecimen typesAntibiotic treatmentPolymerase chain reactionClinical signsUnusual pathogensSepsisHigh risk
2022
1328. Paenibacillosis: An Emerging Cause of Neonatal Sepsis and Postinfectious Hydrocephalus
Ericson J, Burgoine K, Hehnly C, Kumbakumba E, Ochora M, Bajunirwe F, Bazira J, Fronterre C, Hagmann C, Kulkarni A, Kumar M, Magombe J, Mbabazi-Kabachelor E, Morton S, Movassagh M, Mugamba J, Mulondo R, Muwanguzi A, Natukwatsa D, Kaaya B, Olupot-Olupot P, Onen J, Sheldon K, Smith J, Ssentongo P, Ssenyonga P, Warf B, Wegoye E, Zhang L, Broach J, Kiwanuka J, Paulson J, Schiff S. 1328. Paenibacillosis: An Emerging Cause of Neonatal Sepsis and Postinfectious Hydrocephalus. Open Forum Infectious Diseases 2022, 9: ofac492.1158. PMCID: PMC9752957, DOI: 10.1093/ofid/ofac492.1158.Peer-Reviewed Original ResearchNeonatal sepsisPostinfectious hydrocephalusPolymerase chain reactionSigns of sepsisCommon presenting signsAntibiotic susceptibility testingQuantitative polymerase chain reactionUnderrecognized causeIntravenous ampicillinMedian agePresenting signUgandan hospitalNeurodevelopmental impairmentBest regimenNeonatal mortalityRRNA sequencingAdverse outcomesBirth characteristicsMost neonatesOptimal treatmentClinical signsSepsisBeta-lactamase genesCerebrospinal fluidAdditional survivorB.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 systemDisentangling the genetic basis of rhizosphere microbiome assembly in tomato
Oyserman B, Flores S, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson J, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión V, Ligterink W, Snoek B, Medema M, Raaijmakers J. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nature Communications 2022, 13: 3228. PMID: 35710629, PMCID: PMC9203511, DOI: 10.1038/s41467-022-30849-9.Peer-Reviewed Original ResearchConceptsMicrobiome assemblyGenetic basisRhizosphere microbiome assemblyMetagenome-assembled genomesGene content analysisQuantitative trait lociDomestication sweepsDomesticated tomatoRhizosphere microbiomePutative plantPlant geneticsTrait lociBacterial genesPlant growthHybrid populationsQuantitative traitsBreeding programsMbp regionGenetic variation associatesPlant polysaccharidesDifferential recruitmentTomatoStreptomycesTraitsPivotal rolemirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis
Movassagh M, Morton S, Hehnly C, Smith J, Doan T, Irizarry R, Broach J, Schiff S, Bailey J, Paulson J. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics 2022, 23: 439. PMID: 35698050, PMCID: PMC9191533, DOI: 10.1186/s12864-022-08558-w.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionLung epithelial cellsEpithelial cellsHuman lung epithelial cellsSARS-CoV-2NK cellsStatistical PackageEBV miRNAsT cellsImmune pathwaysB cellsClinical relevanceSample cohortCD34 cellsStomach adenocarcinomaEndothelial cellsTime pointsInfectionCOVID-19CellsCD4AdenocarcinomaPatientsCD19Cytokines
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 proportionCellsExpressionVaginal microbiome topic modeling of laboring Ugandan women with and without fever
Movassagh M, Bebell L, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar S, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga B, Weeks A, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts D, Meier F, Irizarry R, Broach J, Schiff S, Paulson J. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. Npj Biofilms And Microbiomes 2021, 7: 75. PMID: 34508087, PMCID: PMC8433417, DOI: 10.1038/s41522-021-00244-1.Peer-Reviewed Original ResearchConceptsIntrapartum feverClinical variablesHigh prevalenceVaginal microbiomeUgandan womenLonger labour durationMaternal clinical featuresYoung maternal ageDuration of pregnancyOnset of laborMicrobial communitiesVaginal microbial communitiesAfebrile mothersFebrile mothersPeripartum courseMaternal feverNeonatal outcomesLabor durationClinical featuresMaternal ageVaginal microbesFeverOutcome riskVeillonella genusMicrobiome influencesImmune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection
Isaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Sinnar S, Ericson J, Mbabazi-Kabachelor E, Ssenyonga P, Onen J, Mulondo R, Hornig M, Warf B, Broach J, Townsend R, Limbrick D, Paulson J, Schiff S. Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection. IScience 2021, 24: 102351. PMID: 33912816, PMCID: PMC8065213, DOI: 10.1016/j.isci.2021.102351.Peer-Reviewed Original ResearchNeonatal sepsisBrain infectionImmune activationInnate immune system responseRisk of hydrocephalusDominant bacterial pathogenHost immune responsePlatelet-activating factorImmune system responseOxidative stress reactionSecondary sequelaeAdjunctive treatmentImmune response networkNeutrophil activityIL-12Hydrocephalic infantsAfrican infantsIL-13IL-4JAK/STAT pathwayAntigen-presenting complexImmune responseHydrocephalusPotential targetNeuroinflammation
2019
Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia
Movassagh M, Oduor C, Forconi C, Moormann A, Bailey J. Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia. Scientific Reports 2019, 9: 20321. PMID: 31889055, PMCID: PMC6937232, DOI: 10.1038/s41598-019-56472-1.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusEBV positivityEBV microRNAsAdult acute myeloid leukemia patientsAdult acute myelocytic leukemiaAcute myeloid leukemia patientsIndependent risk factorMyeloid leukemia patientsAcute myelocytic leukemiaPoor patient outcomesSpectrum of cancersMessenger RNAAdult patientsClinical outcomesBarr virusImmune impairmentAML tumorsRisk factorsPatient outcomesLeukemia patientsPediatric AMLMyelocytic leukemiaPrognostic biomarkerCancer spectrumNumerous human cancers
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 contentCo-Occurrence of COMT and BRCA1/2 Variants in a Population
Movassagh M, Mudvari P, Horvath A. Co-Occurrence of COMT and BRCA1/2 Variants in a Population. New England Journal Of Medicine 2017, 376: 2090-2091. PMID: 28538113, DOI: 10.1056/nejmc1701592.Peer-Reviewed Original ResearchHuman and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma
Oduor C, Movassagh M, Kaymaz Y, Chelimo K, Otieno J, Ong'echa J, Moormann A, Bailey J. Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma. Frontiers In Microbiology 2017, 8: 501. PMID: 28400759, PMCID: PMC5368269, DOI: 10.3389/fmicb.2017.00501.Peer-Reviewed Original ResearchEndemic Burkitt lymphomaEpstein-Barr virusEBV miRNAsPredictive biomarkersPatient outcomesBurkitt's lymphomaAggressive B-cell lymphomasInitial patient outcomesB-cell lymphomaPatient tumor samplesTumor resilienceTumor cell survivalClinical presentationJaw tumorsPoor outcomeDisease progressionAnatomical presentationCell lymphomaSignificant associationEvasion of apoptosisMYC proto-oncogeneTumor samplesMiR-10aTarget genesLymphoma
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
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 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 featuresTwo Methods for Establishing Primary Human Endometrial Stromal Cells from Hysterectomy Specimens
Jividen K, Movassagh M, Jazaeri A, Li H. Two Methods for Establishing Primary Human Endometrial Stromal Cells from Hysterectomy Specimens. Journal Of Visualized Experiments 2014 DOI: 10.3791/51513-v.Peer-Reviewed Original Research