2023
ML Based Phenotype Analysis Using Differential Gene Expression Data in Schizophrenia
D A, KJ S, Maniappan V, B S, S D, R P, Raja K, Oviya I. ML Based Phenotype Analysis Using Differential Gene Expression Data in Schizophrenia. 2023, 00: 1-7. DOI: 10.1109/icstcee60504.2023.10585167.Peer-Reviewed Original ResearchGene expression dataGene expression patternsGene expression profilesGene orientationSNP informationExpression dataGene expressionPhenotypic analysisExpression patternsGenesExpression profilesCell phenotypeBiological mechanismsBiological mechanisms of schizophreniaMechanisms of schizophreniaEqtnSNPsTherapeutic approachesPhenotypeGenomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages
Oliveira G, Vogels C, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros C, Agarwal R, Tsetsarkin K, Harris E, Ebel G, Wohl S, Grubaugh N, Andersen K. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages. PLOS Neglected Tropical Diseases 2023, 17: e0011055. PMID: 36753510, PMCID: PMC9907835, DOI: 10.1371/journal.pntd.0011055.Peer-Reviewed Original ResearchConceptsHuman primary cellsFitness differencesVirus lineagesRapid molecular evolutionPrimary cellsShort generation timeAmino acid sitesFitness changesHigh mutation ratePhenotypic evolutionMolecular evolutionPositive selectionMutation rateLineagesPhenotypic analysisPhenotypic changesRNA virusesGeneration timeRecombinant virusesAedes aegypti mosquitoesReplicative fitnessFitnessAegypti mosquitoesMosquitoesZika virus
2022
Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila
Bosch J, Ugur B, Pichardo-Casas I, Rabasco J, Escobedo F, Zuo Z, Brown B, Celniker S, Sinclair D, Bellen H, Perrimon N. Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila. ELife 2022, 11: e82709. PMID: 36346220, PMCID: PMC9681215, DOI: 10.7554/elife.82709.Peer-Reviewed Original ResearchConceptsSmall open reading framesClasses of genesShares sequence similarityOpen reading frameSequence similarityBicistronic transcriptBiological functionsPhenotypic analysisMitochondrial functionImportant regulatorThousands of peptidesNeuronal functionGenesWealth of informationTranscriptsAnimal lethalityPeptidesRecent studiesParalogsDrosophilaSmORFsMitochondriaRegulatorRegulatesNeuronal peptides
2020
Flow Cytometric Analyses of p53-Mediated Cell Cycle Arrest and Apoptosis in Cancer Cells
Al Zouabi NN, Roberts CM, Lin ZP, Ratner ES. Flow Cytometric Analyses of p53-Mediated Cell Cycle Arrest and Apoptosis in Cancer Cells. Methods In Molecular Biology 2020, 2255: 43-53. PMID: 34033093, DOI: 10.1007/978-1-0716-1162-3_5.Peer-Reviewed Original ResearchConceptsGene of interestCell cycle arrestCycle arrestCell typesDNA damaging agentsP53-mediated cell cycle arrestCell cycle progressionTumor suppressor p53Cellular contextEctopic expressionExogenous stressCell cycle distributionDamaging agentsCycle progressionTumor suppressorSuppressor p53Stable expressionPhenotypic analysisCell survivalCell deathGenomic damageP53 functionGenesEnvironmental insultsCycle distributionImplicit bias of encoded variables: frameworks for addressing structured bias in EHR–GWAS data
Dueñas H, Seah C, Johnson J, Huckins L. Implicit bias of encoded variables: frameworks for addressing structured bias in EHR–GWAS data. Human Molecular Genetics 2020, 29: r33-r41. PMID: 32879975, PMCID: PMC7530523, DOI: 10.1093/hmg/ddaa192.Peer-Reviewed Original ResearchConceptsElectronic health recordsUse of electronic health recordsElectronic health record dataElectronic health record analysisGenome-wide association studiesHealth recordsPhenotype definitionAssociation studiesMedical recordsClinical decisionsPhenotypic characterizationPhenotypic analysisClinically useful insightsPotential biasPresentation of diseaseDegree of biasHomogeneous cohortClinicPhenotypeScalable mannerRecordsCohortBias
2017
Distribution of Lewis and Secretor polymorphisms and corresponding CA19‐9 antigen expression in a Chinese population
Guo M, Luo G, Lu R, Shi W, Cheng H, Lu Y, Jin K, Yang C, Wang Z, Long J, Xu J, Ni Q, Liu C, Yu X. Distribution of Lewis and Secretor polymorphisms and corresponding CA19‐9 antigen expression in a Chinese population. FEBS Open Bio 2017, 7: 1660-1671. PMID: 29123975, PMCID: PMC5666394, DOI: 10.1002/2211-5463.12278.Peer-Reviewed Original ResearchThe ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.Peer-Reviewed Original ResearchConceptsGene expressionFilamentous fungiCommon garden environmentBody developmentWide gene expressionGene expression phenotypesGene deletion studiesGene expression measurementsMulticellular developmentDivergent speciesSexual phenotypeGene familyEvolved increasesDivergent morphologyKnockout phenotypesAncestral levelsWhole genomeGarden environmentExpression phenotypesDeletion studiesRelevant genesPhenotypic analysisDevelopmental stagesExpression measurementsBody morphology
2015
The Transgenic RNAi Project at Harvard Medical School: Resources and Validation
Perkins LA, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K, Yang-Zhou D, Flockhart I, Binari R, Shim HS, Miller A, Housden A, Foos M, Randkelv S, Kelley C, Namgyal P, Villalta C, Liu LP, Jiang X, Huan-Huan Q, Wang X, Fujiyama A, Toyoda A, Ayers K, Blum A, Czech B, Neumuller R, Yan D, Cavallaro A, Hibbard K, Hall D, Cooley L, Hannon GJ, Lehmann R, Parks A, Mohr SE, Ueda R, Kondo S, Ni JQ, Perrimon N. The Transgenic RNAi Project at Harvard Medical School: Resources and Validation. Genetics 2015, 201: 843-852. PMID: 26320097, PMCID: PMC4649654, DOI: 10.1534/genetics.115.180208.Peer-Reviewed Original ResearchThe Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1
Turner EM, Brown RS, Laudermilch E, Tsai PL, Schlieker C. The Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1. Journal Of Virology 2015, 89: 8444-8452. PMID: 26041288, PMCID: PMC4524217, DOI: 10.1128/jvi.01143-15.Peer-Reviewed Original ResearchConceptsNuclear egressDouble knockout cell linesNuclear envelope dynamicsType II transmembrane proteinHerpes simplex virus 1HSV-1 nuclear egressKnockout cell linesSimplex virus 1Viral protein productionAAA ringGenome engineeringTransmembrane proteinLULL1CRISPR/Virus 1Unexpected roleProtein productionComprehensive geneticPhenotypic analysisHost cellsViral genomeEnvelope dynamicsEfficient growthCell linesHSV-1 production
2012
Familial renal glucosuria: a clinicogenetic study of 23 additional cases
Lee H, Han K, Park H, Shin J, Kim C, Namgung M, Kim K, Koo J, Chung W, Lee D, Kim S, Cheong H. Familial renal glucosuria: a clinicogenetic study of 23 additional cases. Pediatric Nephrology 2012, 27: 1091-1095. PMID: 22314875, DOI: 10.1007/s00467-012-2109-9.Peer-Reviewed Original ResearchConceptsHeterozygous mutationsInherited renal tubular disorderRenal tubular disorderCompound heterozygous mutationsUrinary glucose excretionGenotype-phenotype correlationAbsence of hyperglycemiaSLC5A2 mutationsSLC5A2 geneTubular disordersMulticenter studyRenal glucosuriaGlucose excretionMethodsMutation analysisNovel mutationsPediatric nephrologyPatientsMutated alleleIncomplete penetranceCoding genesAllelic heterogeneityKorean childrenSLC5A2ConclusionsThese findingsPhenotypic analysis
2011
Pinpointing the expression of piRNAs and function of the PIWI protein subfamily during spermatogenesis in the mouse
Beyret E, Lin H. Pinpointing the expression of piRNAs and function of the PIWI protein subfamily during spermatogenesis in the mouse. Developmental Biology 2011, 355: 215-226. PMID: 21539824, PMCID: PMC3443393, DOI: 10.1016/j.ydbio.2011.04.021.Peer-Reviewed Original ResearchConceptsPIWI proteinsXY bodyMouse testisAdult mouse testisEarly round spermatidsSex chromosomesGenomic sequencesPiRNAsChromatoid bodyCytological characterizationPachytene stageGerm cellsPhenotypic analysisAdult testisRound spermatidsProteinMeiosisSpermatogenesisCytoplasmDense bodiesSpermatocytesTestisPiRNAChromosomesTransposon
2010
Chemical Inducers of Targeted Protein Degradation*
Raina K, Crews CM. Chemical Inducers of Targeted Protein Degradation*. Journal Of Biological Chemistry 2010, 285: 11057-11060. PMID: 20147751, PMCID: PMC2856979, DOI: 10.1074/jbc.r109.078105.Peer-Reviewed Original ResearchConceptsProtein degradationTargeted Protein DegradationPost-translational levelSubsequent phenotypic analysisProtein functionSelective gene inactivationCellular proteinsCellular phenotypesRNA interferenceGene inactivationSpecific proteinsChemical inducersPhenotypic analysisChemical inductionGenetic mutationsProteinGenesDegradationMutationsPhenotypeDecreased productionMRNAInducerInactivationInduction
2009
Identification of exopolysaccharide‐deficient mutants of Mycoplasma pulmonis
Daubenspeck J, Bolland J, Luo W, Simmons W, Dybvig K. Identification of exopolysaccharide‐deficient mutants of Mycoplasma pulmonis. Molecular Microbiology 2009, 72: 1235-1245. PMID: 19432800, PMCID: PMC2752295, DOI: 10.1111/j.1365-2958.2009.06720.x.Peer-Reviewed Original ResearchConceptsOpen reading frameExopolysaccharide-deficient mutantsSynthesis of exopolysaccharidesTerminal beta-linked galactose residuesA549 lung cell lineHeterodimeric pairTransposon librarySecond exopolysaccharideReading frameMutantsPhenotypic analysisLung cell linesDecreased associationN-acetylglucosamineCell linesExopolysaccharideCapsular exopolysaccharideLectin affinity chromatographyGalactose residuesComplex carbohydratesNew pathwayPermeasesMouse lungMollicutesTransposon
2007
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. Advances In Genetics 2007, 57: 49-96. PMID: 17352902, PMCID: PMC3673015, DOI: 10.1016/s0065-2660(06)57002-6.Peer-Reviewed Original ResearchConceptsFunctional genomics projectsGenomics projectsFilamentous fungiFilamentous fungus NeurosporaFunctional genomic analysisNon-yeast fungiFunctional genomicsNeurospora genomeFungus NeurosporaNovel genesPositional cloningNeurospora crassaAntisense transcriptsGenomic analysisSNP mapAlternative promotersCDNA libraryExpression analysisGene replacementMutant strainSystematic disruptionExpression dataPhenotypic analysisNeurosporaConditions of growth
2006
Isolation and Characterization of Replication-Competent Human Immunodeficiency Virus Type 1 from a Subset of Elite Suppressors
Blankson J, Bailey J, Thayil S, Yang H, Lassen K, Lai J, Gandhi S, Siliciano J, Williams T, Siliciano R. Isolation and Characterization of Replication-Competent Human Immunodeficiency Virus Type 1 from a Subset of Elite Suppressors. Journal Of Virology 2006, 81: 2508-2518. PMID: 17151109, PMCID: PMC1865922, DOI: 10.1128/jvi.02165-06.Peer-Reviewed Original ResearchConceptsReplication-competent HIV-1Human immunodeficiency virus type 1Immunodeficiency virus type 1Elite suppressorsVirus type 1HIV-1Replication-Competent Human Immunodeficiency Virus Type 1Untreated human immunodeficiency virus type 1Type 1Active antiretroviral therapyUndetectable viral loadReplication-competent virusAntiretroviral therapyImmunologic controlViral loadCoculture assaysPatientsDefective virusCurrent assaysFull-length sequencingVirusIsolatesAssaysPhenotypic analysisViremia
2003
Sequence-specific modification of genomic DNA by small DNA fragments
Gruenert DC, Bruscia E, Novelli G, Colosimo A, Dallapiccola B, Sangiuolo F, Goncz KK. Sequence-specific modification of genomic DNA by small DNA fragments. Journal Of Clinical Investigation 2003, 112: 637-641. PMID: 12952908, PMCID: PMC182219, DOI: 10.1172/jci19773.Peer-Reviewed Original ResearchConceptsSmall fragment homologous replacementSequence-specific modificationSmall DNA fragmentsGenomic DNADNA fragmentsEndogenous genomic DNADuchenne muscular dystrophyTherapeutic modalitiesCystic fibrosisHomologous replacementGenomic editingMuscular dystrophyGenetic lociMouse cellsUnderlying mechanismPhenotypic analysisSpecific modificationsDNA
1987
Functional gamma chain-associated T cell receptors on cerebrospinal fluid-derived natural killer-like T cell clones.
Ang SL, Seidman JG, Peterman GM, Duby AD, Benjamin D, Lee SJ, Hafler DA. Functional gamma chain-associated T cell receptors on cerebrospinal fluid-derived natural killer-like T cell clones. Journal Of Experimental Medicine 1987, 165: 1453-1458. PMID: 3106557, PMCID: PMC2188318, DOI: 10.1084/jem.165.5.1453.Peer-Reviewed Original ResearchConceptsAnti-CD3 mAbT cell clonesCerebrospinal fluidCell clonesIndependent T cell clonesNK-like activityHuman immune responseT cell receptorWT-31IL-2T cellsImmune responseIntracellular calciumCell receptorMAbsTcR gamma proteinGamma proteinSepharose beadsCell surfacePhenotypic analysisCD8CD4PanencephalitisSubacutePatients
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