2024
DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specific
2021
High Throughput Single-Cell Simultaneous Genotyping and Chromatin Accessibility Reveals Genotype to Phenotype Relationship in Human Myeloproliferation
Myers R, Izzo F, Prieto T, Mimitou E, Raviram R, Chaligne R, Hoffman R, Stahl M, Abdel-Wahab O, Marcellino B, Smibert P, Landau D. High Throughput Single-Cell Simultaneous Genotyping and Chromatin Accessibility Reveals Genotype to Phenotype Relationship in Human Myeloproliferation. Blood 2021, 138: 678. DOI: 10.1182/blood-2021-149226.Peer-Reviewed Original ResearchChromatin accessibilityMotif accessibilityFitness advantageTranscription factor (TFGenotype to phenotype relationshipsSomatic mutationsGenotype-to-phenotype mapCopy number inferenceChromatin accessibility profilesSingle-cell multi-omicsCell-type specific effectsPseudo-temporal orderingCell line identityTarget gene transcriptionTranscription factor activityMyeloproliferative neoplasmsJAK2 V617FCell fractionClonal outgrowthStages of erythroid maturationEntity's Board of DirectorsGenome coverageGenotyping accuracyGenomic locationsMPN samples
2016
A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
Moser LA, Ramirez-Carvajal L, Puri V, Pauszek SJ, Matthews K, Dilley KA, Mullan C, McGraw J, Khayat M, Beeri K, Yee A, Dugan V, Heise MT, Frieman MB, Rodriguez LL, Bernard KA, Wentworth DE, Stockwell TB, Shabman RS. A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses. MSystems 2016, 1: e00039-15. PMID: 27822536, PMCID: PMC5069770, DOI: 10.1128/msystems.00039-15.Peer-Reviewed Original ResearchNext-generation sequencingRNA virusesComplete genome coverageGenomic sequence informationViral genomic researchNext-generation sequencing protocolHigh-throughput sequencingSequence-independent methodRNA virus familiesViral genomic RNAViral RNASelect agentsInfectious viral RNABarcoding approachGenome coverageCDNA libraryGenomic RNACellular RNASequence informationGenomic researchGenomeSpecific viral sequencesSequencing protocolLibrary constructionVirion preparations
2012
Genetic Analysis of Cytomegalovirus in Malignant Gliomas
Bhattacharjee B, Renzette N, Kowalik T. Genetic Analysis of Cytomegalovirus in Malignant Gliomas. Journal Of Virology 2012, 86: 6815-6824. PMID: 22496213, PMCID: PMC3393585, DOI: 10.1128/jvi.00015-12.Peer-Reviewed Original ResearchConceptsDNA copy numberViral DNA copy numberPresence of intact open reading framesCopy numberLong regionMalignant gliomasHigh amino acid sequence conservationAmino acid sequence conservationIntact open reading framesViral populationsHuman cytomegalovirusOpen reading frameAmino acid changesSingle gene productsGenome coverageGlioblastoma multiformeSequence conservationReading framePhylogenetic analysisHCMV prevalenceCore genesSequence analysisShort regionLow-grade tumorsGenetic analysis
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