2024
Characteristics of autoantibody-positive individuals without high-risk HLA-DR4-DQ8 or HLA-DR3-DQ2 haplotypes
Redondo M, Cuthbertson D, Steck A, Herold K, Oram R, Atkinson M, Brusko T, Parikh H, Krischer J, Onengut-Gumuscu S, Rich S, Sosenko J. Characteristics of autoantibody-positive individuals without high-risk HLA-DR4-DQ8 or HLA-DR3-DQ2 haplotypes. Diabetologia 2024, 68: 588-601. PMID: 39670998, PMCID: PMC11832693, DOI: 10.1007/s00125-024-06338-7.Peer-Reviewed Original ResearchHLA-DR4-DQ8HLA-DR3-DQ2High-risk HLA haplotypesType 1 diabetesAutoantibody-positive individualsHLA haplotypesHLA-DR3-DQ2 haplotypeClinical type 1 diabetesType 1 diabetes pathogenesisPrevalence of autoantibodiesPrevalence of overweight/obesityIslet autoantibody-positive individualsAutoantibody-positive relativesHLA-DRB1Metabolic markersC-peptideIA-2DR3/DR4Aetiological heterogeneityYounger ageNon-Hispanic participantsPhenotypic differencesAssociated with phenotypic differencesPrevalenceRelatives of individualsCell-specific gene networks and drivers in rheumatoid arthritis synovial tissues
Pelissier A, Laragione T, Gulko P, Martínez M. Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues. Frontiers In Immunology 2024, 15: 1428773. PMID: 39161769, PMCID: PMC11330812, DOI: 10.3389/fimmu.2024.1428773.Peer-Reviewed Original ResearchTranscription factorsNatural killer TPhenotypic differencesGene regulatory networksCo-regulatory networkRNA-seq databaseCell typesFibroblast-like synoviocytesRNA-seqRegulatory networksGene networksTF clustersMultiple cell typesB cellsCell regulationKiller TRheumatoid arthritis synovial tissuePhenotypic groupsRA pathogenesisRA synovial tissuePathway changesTissue genesGenesCompare network propertiesComputational approach
2019
Analysis of Melanin Structure and Biochemical Composition in Conjunctival Melanocytic Lesions Using Pump–Probe Microscopy
Robles F, Deb S, Vajzovic L, Vora G, Mruthyunjaya P, Warren W. Analysis of Melanin Structure and Biochemical Composition in Conjunctival Melanocytic Lesions Using Pump–Probe Microscopy. Translational Vision Science & Technology 2019, 8: 33-33. PMID: 31183249, PMCID: PMC6549561, DOI: 10.1167/tvst.8.3.33.Peer-Reviewed Original ResearchBiochemical compositionOverall biochemical compositionSubcellular spatial resolutionPigment organizationMelanin structurePhenotypic differencesMolecular signaturesSpecific molecular informationStructure of melaninMolecular informationBiochemical heterogeneityMelaninPrincipal component analysisPowerful tool
2016
Individual differences in frontolimbic circuitry and anxiety emerge with adolescent changes in endocannabinoid signaling across species
Gee DG, Fetcho RN, Jing D, Li A, Glatt CE, Drysdale AT, Cohen AO, Dellarco DV, Yang RR, Dale AM, Jernigan TL, Lee FS, Casey BJ, Jernigan T, San Diego U, McCabe C, San Diego U, Chang L, Hawaii U, Akshoomoff N, San Diego U, Newman E, San Diego U, Dale A, San Diego U, Core M, Ernst T, Hawaii U, Dale A, San Diego U, Van Zijl P, Kuperman J, San Diego U, Murray S, Bloss C, Schork N, Appelbaum M, San Diego U, Gamst A, San Diego U, Thompson W, San Diego U, Bartsch H, San Diego U, Jernigan T, Dale A, Akshoomoff N, Chang L, Ernst T, Keating B, Amaral D, Sowell E, Kaufmann W, Van Zijl P, Mostofsky S, Casey B, Ruberry E, Powers A, Rosen B, Kenet T, Frazier J, Kennedy D, University Y, Gruen J. Individual differences in frontolimbic circuitry and anxiety emerge with adolescent changes in endocannabinoid signaling across species. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 4500-4505. PMID: 27001846, PMCID: PMC4843434, DOI: 10.1073/pnas.1600013113.Peer-Reviewed Original ResearchConceptsFatty acid amide hydrolaseAnxiety-related behaviorGene expressionFrontolimbic circuitryEndocannabinoid signalingAnxiety disordersNeural circuit maturationPostnatal day 45Phenotypic differencesFrontoamygdala circuitryAnandamide levelsGenetic effectsAEA levelsBiological stateIndividual differencesCircuit maturationGenetic alterationsFAAH genotypeMouse modelDevelopmental neurobiologyLevels of analysisAdolescent changesDevelopmental windowAmide hydrolaseBrain circuitry
2014
Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia
Brennand K, Savas J, Kim Y, Tran N, Simone A, Hashimoto-Torii K, Beaumont K, Kim H, Topol A, Ladran I, Abdelrahim M, Matikainen-Ankney B, Chao S, Mrksich M, Rakic P, Fang G, Zhang B, Yates J, Gage F. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Molecular Psychiatry 2014, 20: 361-368. PMID: 24686136, PMCID: PMC4182344, DOI: 10.1038/mp.2014.22.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsAntipsychotic AgentsCell DifferentiationCell MovementCells, CulturedFemaleGene ExpressionHumansMaleMiceMice, Inbred C57BLMice, TransgenicMitochondriaNeural Cell Adhesion MoleculesNeural Stem CellsOxidative StressPhenotypePluripotent Stem CellsProsencephalonProteomicsReactive Oxygen SpeciesSchizophreniaYoung AdultConceptsHiPSC neural progenitor cellsNeural progenitor cellsHuman-induced pluripotent stem cellsHiPSC-derived neuronsGene expressionGene expression comparisonsStable isotope labelingProteomic mass spectrometry analysisAbnormal gene expressionPluripotent stem cellsOxidative stressCytoskeletal remodelingMass spectrometry analysisCellular phenotypesExpression comparisonsDevelopmental mechanismsIsotope labelingPhenotypic differencesBrainSpan AtlasDisease predispositionAmino acidsScalable assayNPC phenotypeStem cellsProgenitor cells
2013
Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice
Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice. American Journal Of Respiratory Cell And Molecular Biology 2013, 49: 130522202035005. PMID: 23590305, PMCID: PMC3824050, DOI: 10.1165/rcmb.2012-0337oc.Peer-Reviewed Original ResearchMeSH KeywordsAcute Lung InjuryAllelesAnimalsChemical Warfare AgentsChromosome MappingElectrophoretic Mobility Shift AssayFemaleGene ExpressionGene Expression ProfilingGenomeGenome-Wide Association StudyGenomicsGenotypeIntegrinsLungMiceMice, Inbred StrainsOligonucleotide Array Sequence AnalysisPhosgenePolymorphism, Single NucleotidePromoter Regions, GeneticReelin ProteinSodium-Potassium-Exchanging ATPaseConceptsSignificant SNP associationsSNP associationsTranscriptomic analysisCompetitive electrophoretic mobility shift analysisGenome-wide association mappingFunctional genomic assessmentPutative transcription factorElectrophoretic mobility shift analysisMobility shift analysisAssociation mappingGenetic resolutionTranscription factorsCandidate genesFunctional domainsNonsynonymous SNPsGenomic assessmentPhenotypic differencesPhenotypic extremesDiverse panelGenesGenetic determinantsShift analysisPTPRTAllelesITGA9
2012
An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product
Chen HD, Jewett MW, Groisman EA. An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product. PLOS Genetics 2012, 8: e1003060. PMID: 23300460, PMCID: PMC3531487, DOI: 10.1371/journal.pgen.1003060.Peer-Reviewed Original ResearchConceptsPolymyxin B resistanceGene productsTranscription of PmrAGene regulatory circuitsB resistanceSingle amino acid differenceAmino acid differencesPmrA proteinAncestral genomesAncestral genePmrD proteinRegulatory circuitsB alleleHorizontal transferGene expressionPhenotypic differencesAcid differencesGenesBiochemical propertiesBiofilm formationPmrAAllelesSalmonella entericaS. entericaProteinThe screening and ranking algorithm to detect DNA copy number variations
Niu Y, Zhang H. The screening and ranking algorithm to detect DNA copy number variations. The Annals Of Applied Statistics 2012, 6: 1306-1326. DOI: 10.1214/12-aoas539.Peer-Reviewed Original ResearchDNA copy number variationsSource of genetic variationGenome analysis platformHigh-throughput dataCopy number variationsRanking algorithmGenetic variationNumber variationsPhenotypic differencesTheoretical propertiesThroughput dataAnalysis platformAlgorithmCharacterization algorithmGenomeComputational methodsResampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size
Rice DP, Townsend JP. Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size. G3: Genes, Genomes, Genetics 2012, 2: 905-911. PMID: 22908039, PMCID: PMC3411246, DOI: 10.1534/g3.112.003228.Peer-Reviewed Original ResearchRegulatory element copy number differences shape primate expression profiles
Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C. Regulatory element copy number differences shape primate expression profiles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12656-12661. PMID: 22797897, PMCID: PMC3411951, DOI: 10.1073/pnas.1205199109.Peer-Reviewed Original ResearchConceptsCopy number differencesExpression differencesExpression profilesLong intergenic noncoding RNAsCopy numberIntergenic noncoding RNAsGene expression differencesSignificant expression differencesGene expression profilesLevel of RNAUltraconserved elementsRegulatory regionsNoncoding RNAsSelective pressureDifferent genesRegulatory moleculesDevelopmental pathwaysPhenotypic differencesPrimate speciesGenesRNANumber differenceSpeciesExpressionPseudogenes
2009
Transcription factor function and promoter architecture govern the evolution of bacterial regulons
Perez JC, Groisman EA. Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 4319-4324. PMID: 19251636, PMCID: PMC2649204, DOI: 10.1073/pnas.0810343106.Peer-Reviewed Original ResearchConceptsRegulatory circuitsBacterial regulonsPhoP proteinRegulatory protein PhoPBacterial transcription factorsTranscription factor functionCis-regulatory elementsGene regulatory circuitsHorizontal gene transferPathogen Salmonella entericaPromoter architectureEvolutionary changeRelated organismsVirulence regulatorTranscription factorsRegulonPhenotypic differencesFactor functionGene transferYersinia pestisSalmonella entericaCore membersProteinEukaryotesPhoP
2004
Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes
Winfield MD, Groisman EA. Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 17162-17167. PMID: 15569938, PMCID: PMC534605, DOI: 10.1073/pnas.0406038101.Peer-Reviewed Original ResearchConceptsPmrD proteinPolymyxin B resistanceHomologous genesB resistancePhenotypic differencesDifferential regulationRange of nichesSpecies-specific genesPmrA/PmrBE. coliE. coli KTwo-component systemEnterica serovar TyphimuriumGene transcriptionS. enterica serovar TyphimuriumEcological consequencesColi KLPS modificationsNatural isolatesPathogenicity islandE. coli strainsGenesMolecular analysisEscherichia coliSerovar Typhimurium
2003
Phenotypic differences in transient outward K+ current of human and canine ventricular myocytes: insights into molecular composition of ventricular Ito
Akar FG, Wu RC, Deschenes I, Armoundas AA, Piacentino V, Houser SR, Tomaselli GF. Phenotypic differences in transient outward K+ current of human and canine ventricular myocytes: insights into molecular composition of ventricular Ito. AJP Heart And Circulatory Physiology 2003, 286: h602-h609. PMID: 14527940, DOI: 10.1152/ajpheart.00673.2003.Peer-Reviewed Original ResearchConceptsTransient outwardPhenotypic differencesKv channel-interacting proteinsIndependent transient outwardChannel-interacting proteinsProtein chemical techniquesSteady-state inactivationCanine ventricular myocytesWestern blot analysisElectrical remodelingChannel subunit genesMonoexponential time coursePharmacological sensitivityVentricular repolarizationCardiac diseaseElectrophysiological roleCanine ventricularHuman cardiac diseasePosttranslational modificationsVentricular myocytesSubunit genePharmacological propertiesDiseased heartPhenotypic propertiesOxidative stress
1998
Seeking the genetic basis of phenotypic differences among bacterial species
Ochman H, Groisman E. Seeking the genetic basis of phenotypic differences among bacterial species. 1998, 221-235. DOI: 10.1007/978-3-0348-8948-3_12.Peer-Reviewed Original ResearchEnteric bacteria Escherichia coliBacterial speciesSpecies-specific genesSpecies-specific charactersGene complementSole carbon sourceDNA regionsPhenotypic charactersGenetic basisAllelic variationBacteria Escherichia coliPhenotypic differencesEscherichia coliSpeciesSalmonella entericaCarbon sourceGenesMicrobesCertain compoundsColiObserved differencesPhysiologySequenceEntericaCharacter
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