2025
Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus
Yang Y, Yan J, Olson R, Jiang X. Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus. MSystems 2025, 10: e00060-25. PMID: 40207939, PMCID: PMC12090793, DOI: 10.1128/msystems.00060-25.Peer-Reviewed Original ResearchConceptsGene clusterVibrio speciesEvolutionary analysisBiofilm dispersalBiofilm matrix proteinsVibrio cholerae</i>Genetic modificationTail proteinsVibrio genusCholera pathogenIdentified genesGene groupsVibrio cholerae</i>.Host functionsEvolutionary patternsBiofilm diversityBiofilm formationBiofilm proteinsBiofilm matrixVibrioBiofilm developmentEngineered biofilmsGenusStructural domainsAcute diarrheal disease
2024
GENETIC VARIANTS OF UNCERTAIN SIGNIFICANCE IN PATIENTS WITH PRESENTATIONS CONCERNING FOR INBORN ERRORS OF IMMUNITY
Novotny S, Yoo N, Granoth M, Chen J, Osmani L, Kang I, Shin J. GENETIC VARIANTS OF UNCERTAIN SIGNIFICANCE IN PATIENTS WITH PRESENTATIONS CONCERNING FOR INBORN ERRORS OF IMMUNITY. Annals Of Allergy Asthma & Immunology 2024, 133: s60. DOI: 10.1016/j.anai.2024.08.200.Peer-Reviewed Original ResearchInborn errors of immunityClinical presentationOrganelle biogenesisGenetic resultsT cellsAssociated with distinct clinical presentationInborn errors of immunity patientsGenetic testingClinical presentation of patientsDiagnosis of inborn errors of immunityImmune functionImmune thrombocytopenic purpuraReviewed electronic medical recordsT cell immunityErrors of immunityPresentation of patientsB cell immunityGene groupsCytomegalovirus infectionVariable immunodeficiencyThrombocytopenic purpuraRate of rheumatoid arthritisPediatric patientsGenetic variantsB cells
2022
Extensive protein dosage compensation in aneuploid human cancers
Schukken KM, Sheltzer J. Extensive protein dosage compensation in aneuploid human cancers. Genome Research 2022, 32: 1254-1270. PMID: 35701073, PMCID: PMC9341510, DOI: 10.1101/gr.276378.121.Peer-Reviewed Original ResearchConceptsDosage compensationPost-translational regulatory mechanismsProtein complex subunitsCopy numberHuman cancersCell cycle genesEffects of aneuploidyMajority of proteinsChromosome copy numberProtein expression dataKey driver genesChromosome copy number changesExpression of oncogenesCopy number changesKey cancer driversComplex subunitsCycle genesGene groupsCancer driversCancer proteomeRegulatory mechanismsTumor suppressorExpression dataDriver genesChromosome gains
2018
Systematic reconstruction of autism biology from massive genetic mutation profiles
Luo W, Zhang C, Jiang YH, Brouwer CR. Systematic reconstruction of autism biology from massive genetic mutation profiles. Science Advances 2018, 4: e1701799. PMID: 29651456, PMCID: PMC5895441, DOI: 10.1126/sciadv.1701799.Peer-Reviewed Original ResearchConceptsComplex genetic diseasesWhole-exome studiesHundreds of variantsGene functionNovel genesSubpathway levelGene groupsSame geneCanonical pathwaysPathway levelAutism-related mutationsSecond messenger systemsGenesGenetic diseasesASD biologyCAMP second messenger systemBiologyGenetic associationMutationsMultiple independent analysesMost variantsPathwayVariant levelsSynaptic functionGenetic mutation profiles
2009
Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract
Miller G, Socci N, Dhall D, D'Angelica M, DeMatteo R, Allen P, Singh B, Fong Y, Blumgart L, Klimstra D, Jarnagin W. Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract. Journal Of Experimental & Clinical Cancer Research 2009, 28: 62. PMID: 19435499, PMCID: PMC2698861, DOI: 10.1186/1756-9966-28-62.Peer-Reviewed Original ResearchConceptsOver-Representation AnalysisCGH analysisBiliary cancerGene expressionCopy numberGenome wide analysisGlobal gene expression patternsFunctional gene groupsBiliary tract cancer specimensAnatomic site of originFunctional over-representation analysisDNA copy numberGene expression patternsUnsupervised hierarchical clustering analysisTranscript mutationsAmplified regionGene groupsIdentification of therapeutic targetsWide analysisClinical-pathological correlationChromosome 1pSite of originGallbladder cancerExpression patternsExtrahepatic cholangiocarcinomaCharacterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus)
Glaberman S, Moreno M, Caccone A. Characterization and evolution of MHC class II B genes in Galápagos marine iguanas (Amblyrhynchus cristatus). Developmental & Comparative Immunology 2009, 33: 939-947. PMID: 19454336, DOI: 10.1016/j.dci.2009.03.003.Peer-Reviewed Original ResearchConceptsClass II B genesGalápagos marine iguanasB geneMarine iguanasMHC class II B genesAvian MHC evolutionInterlocus gene conversionAncestral locusEvolutionary forcesMHC evolutionBird speciesGene conversionGene groupsPositive selectionCDNA sequenceClass II genesLocus groupsVertebratesGenesMammalsShort tractsBeta 2 domainAdaptive immune systemMajor groupsSquamates
2003
Global Expression Profiling of Fibroblast Responses to Transforming Growth Factor-β1 Reveals the Induction of Inhibitor of Differentiation-1 and Provides Evidence of Smooth Muscle Cell Phenotypic Switching
Chambers RC, Leoni P, Kaminski N, Laurent GJ, Heller RA. Global Expression Profiling of Fibroblast Responses to Transforming Growth Factor-β1 Reveals the Induction of Inhibitor of Differentiation-1 and Provides Evidence of Smooth Muscle Cell Phenotypic Switching. American Journal Of Pathology 2003, 162: 533-546. PMID: 12547711, PMCID: PMC1851161, DOI: 10.1016/s0002-9440(10)63847-3.Peer-Reviewed Original ResearchMeSH KeywordsCell DivisionCell LineCell SurvivalFetusFibroblastsGene Expression ProfilingHelix-Loop-Helix MotifsHumansImmunohistochemistryInhibitor of Differentiation Protein 1Inhibitor of Differentiation ProteinsLungMuscle, SmoothNeoplasm ProteinsPhenotypeRepressor ProteinsRNA, MessengerTranscription FactorsTranscription, GeneticTransforming Growth Factor betaTransforming Growth Factor beta1ConceptsMajor functional categoriesHelix transcription factorGlobal gene expressionNumber of genesCell lineage commitmentGlobal expression profilingDominant-negative antagonistSmooth muscle cell phenotypic switchingProtein levelsSmooth muscle myosin heavy chainInduction of inhibitorMuscle myosin heavy chainTransformation of fibroblastsImmediate early genesTranscriptional regulatorsTranscriptional programsExtracellular matrix protein depositionTranscriptional programmingProtein biosynthesisGene groupsLineage commitmentCytoskeletal reorganizationTranscription factorsFunctional categoriesCell signaling
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