2025
Travel-associated international spread of Oropouche virus beyond the Amazon
de Melo Iani F, Pereira F, de Oliveira E, Rodrigues J, Machado M, Fonseca V, Adelino T, Guimarães N, Tomé L, Gómez M, Nardy V, Ribeiro A, Rosewell A, Ferreira Á, de Mello A, Fernandes B, de Albuquerque C, dos Santos Pereira D, Pimentel E, Lima F, Silva F, de Carvalho Pereira G, Tegally H, Almeida J, Moreno K, Vasconcelos K, Santos L, Silva L, Frutuoso L, Lamounier L, Costa M, de Oliveira M, dos Anjos M, Ciccozzi M, Lima M, Pereira M, Rocha M, da Silva P, Rabinowitz P, de Almeida P, Lessells R, Gazzinelli R, da Cunha R, Gonçalves S, dos Santos S, de Alcântara Belettini S, Pedroso S, Araújo S, da Silva S, Croda J, Maciel E, Van Voorhis W, Martin D, Holmes E, de Oliveira T, Lourenço J, Alcantara L, Giovanetti M. Travel-associated international spread of Oropouche virus beyond the Amazon. Journal Of Travel Medicine 2025, 32: taaf018. PMID: 40037296, PMCID: PMC11955161, DOI: 10.1093/jtm/taaf018.Peer-Reviewed Original ResearchOropouche virusAmazon basinWhole-genome sequencingViral adaptationLocal ecological conditionsMonophyletic groupGenome segmentsPhylogenetic analysisGenomic analysisViral movementGenomic changesPhenotypic traitsEpidemiological metadataReassortment eventsBrazilian Amazon basinPublic health laboratoriesEcological conditionsHuman population changeGenomeCentral Public Health LaboratoryReassortmentPublic health significanceHealth laboratoriesGeographic expansionSequence
2022
Genetic Changes Driving Immunosuppressive Microenvironments in Oral Premalignancy
Rangel R, Pickering CR, Sikora AG, Spiotto MT. Genetic Changes Driving Immunosuppressive Microenvironments in Oral Premalignancy. Frontiers In Immunology 2022, 13: 840923. PMID: 35154165, PMCID: PMC8829003, DOI: 10.3389/fimmu.2022.840923.Peer-Reviewed Original ResearchConceptsOral premalignant lesionsImmunosuppressive microenvironmentProgression of OPLsOral cavity cancerGenomic alterationsImmune microenvironmentOral cancerOSCC progressionInflammatory environmentPremalignant lesionsSpecific genomic changesOral premalignancyTherapeutic approachesNovel biomarkersMalignant transformationMicroenvironmental changesCancerProgressionGenomic changesMicroenvironmentAlterationsGenetic changesPremalignancyTherapyLesions
2016
Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nature Communications 2016, 7: 12601. PMID: 27574101, PMCID: PMC5013636, DOI: 10.1038/ncomms12601.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntineoplastic AgentsCarcinogenesisCarcinoma, Squamous CellDisease ProgressionDNA Mutational AnalysisExome SequencingFemaleGene Expression ProfilingGenomicsHigh-Throughput Nucleotide SequencingHumansKeratosis, ActinicMiceMice, HairlessMolecular Targeted TherapyPrecancerous ConditionsSequence Analysis, RNASkinSkin NeoplasmsUltraviolet RaysConceptsCross-species genomic analysisCross-species identificationCross-species analysisKey genomic changesGenomic analysisGenomic changesTranscriptional driversDistinct precancerous lesionsGenomic driversPotential targetSquamous cell carcinoma developmentMolecular similarityActinic keratosisAccessible modelDiverse sitesCutaneous squamous cell carcinomaHuman samplesSquamous cell carcinomaHairless mouse modelProgression sequenceMouse modelCarcinoma developmentCell carcinomaPrecancerous lesionsCommon treatmentShifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma
Rubinstein JC, Brown TC, Christison-Lagay ER, Zhang Y, Kunstman JW, Juhlin CC, Nelson-Williams C, Goh G, Quinn CE, Callender GG, Udelsman R, Lifton RP, Korah R, Carling T. Shifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma. BMC Cancer 2016, 16: 646. PMID: 27538953, PMCID: PMC4989347, DOI: 10.1186/s12885-016-2665-7.Peer-Reviewed Original ResearchConceptsSingle nucleotide substitutionSomatic evolutionCommon ancestor cellGenomic changesNucleotide substitutionsTissue typesTissue-specific signaturesGenomic divergenceGenomic variationGenomic instabilityGenomic signaturesRisk of tumorigenesisSelective pressurePTC tumorigenesisTumor genomesAncestor cellsGenomeA transversionMethodsExome sequencingDiverse mutationsSomatic eventsMutational spectrumT transitionNovel patternTumorigenesis
2015
Expression of B and T Lymphocyte Attenuator (BTLA) Correlates with CNS Metastasis and Adverse Prognosis in Activated B-Cell Lymphoma and Acute Lymphoblastic Leukemia
Geng H, Chen Z, Anderson S, Fraser E, Lu M, Lingjing C, Collins C, Markus M, Rubenstein J. Expression of B and T Lymphocyte Attenuator (BTLA) Correlates with CNS Metastasis and Adverse Prognosis in Activated B-Cell Lymphoma and Acute Lymphoblastic Leukemia. Blood 2015, 126: 3900. DOI: 10.1182/blood.v126.23.3900.3900.Peer-Reviewed Original ResearchPatient-derived cell linesLarge B-cell lymphomaB-cell lymphomaShorter overall survivalAcute lymphoblastic leukemiaHigh BTLA expressionBTLA expressionOverall survivalHigh-resolution array-based comparative genomic hybridizationMurine modelRecurrent copy number gainsDNA copy number aberrationsArray-based comparative genomic hybridizationCell linesCNS metastasisLymphoblastic leukemiaCopy number gainsB cell receptorComparative genomic hybridizationCopy number aberrationsPrimary central nervous system lymphomaGenomic changesCentral nervous system lymphomaTranscript levelsAggressive B-cell lymphomasThe Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm
Perry E, Barrick J, Bohannan B. The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm. PLOS ONE 2015, 10: e0130639. PMID: 26114300, PMCID: PMC4482675, DOI: 10.1371/journal.pone.0130639.Peer-Reviewed Original ResearchConceptsBacteriophage T3Repeatable evolutionEscherichia coli BCoevolution experimentMutant phageFunction mutationsColi BLevel of pathwaysNucleotide levelLaboratory microcosmsPhage tail fibersSame ancestral strainBacterial ancestorAncestral phageConvergent evolutionContinuous culture deviceGenomic changesGenetic basisSingle codonNew phage typePhage interactionsDifferent genesTail fibersAncestral strainGenetic changes
2009
p53 responsive elements in human retrotransposons
Harris CR, DeWan A, Zupnick A, Normart R, Gabriel A, Prives C, Levine AJ, Hoh J. p53 responsive elements in human retrotransposons. Oncogene 2009, 28: 3857-3865. PMID: 19718052, PMCID: PMC3193277, DOI: 10.1038/onc.2009.246.Peer-Reviewed Original ResearchConceptsP53-responsive elementResponsive elementHuman genomeL1 promoterL1 elementsP53 DNA binding sitesRepetitive DNA elementsDNA binding sitesL1 mRNAP53 proteinCytosine methylationNuclear element-1DNA elementsGenomic stabilityHuman retrotransposonsP53-dependent processesGenomic changesGenomic protectionGenomeElement 1L1 mRNA expressionProteinBinding sitesPromoterL1 protein
2008
Evolutionary Genomics of Host Adaptation in Vesicular Stomatitis Virus
Remold SK, Rambaut A, Turner PE. Evolutionary Genomics of Host Adaptation in Vesicular Stomatitis Virus. Molecular Biology And Evolution 2008, 25: 1138-1147. PMID: 18353798, DOI: 10.1093/molbev/msn059.Peer-Reviewed Original ResearchConceptsGenetic architectureComplex traitsHigher fitnessVirus populationsVesicular stomatitis virus populationsParallel phenotypic changesSimilar selection pressuresRNA virus populationsHigh mutation rateEvolutionary genomicsGenome evolutionHost useComplete consensus sequenceTrue pleiotropyHost adaptationAllele substitutionGenomic changesSelection pressureVesicular stomatitis virusConsensus sequenceMutation rateEcological historyPhenotypic changesRNA virusesHeLa cells
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