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
mirTarRnaSeq: 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
Vaginal 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 influences
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 Research
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 approachEdUVariantsLociRNANucleotidesBioinformaticsSequencingTwo 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 PMID: 24894444, PMCID: PMC4207099, DOI: 10.3791/51513.Peer-Reviewed Original Research
2013
A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process
Yuan H, Qin F, Movassagh M, Park H, Golden W, Xie Z, Zhang P, Sklar J, Li H. A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process. Cancer Discovery 2013, 3: 1394-1403. PMID: 24089019, DOI: 10.1158/2159-8290.cd-13-0186.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineForkhead Box Protein O1Forkhead Transcription FactorsGene Expression Regulation, DevelopmentalGene FusionHumansMesenchymal Stem CellsMuscle DevelopmentMusclesMyoD ProteinMyogeninOncogene Proteins, FusionPaired Box Transcription FactorsPAX3 Transcription FactorRhabdomyosarcoma, AlveolarTranslocation, GeneticConceptsPAX3-FOXO1Chimeric RNAsChromosomal translocationsMuscle differentiation processChimeric fusion RNAsChimeric gene productsNormal cellsNormal non-cancer cellsPluripotent cellsNormal fetal muscleNon-cancer cellsGene productsChromosomal rearrangementsPosttranscriptional mechanismsDevelopmental roleFusion RNAGene fusionsDifferentiation processRNA characteristicsSame lineageMyogenesis processChimeric productsNormal developmentRhabdomyosarcoma cellsRNA