2013
In silico investigation of the ATP7B gene: insights from functional prediction of non-synonymous substitution to protein structure
Squitti R, Siotto M, Bucossi S, Polimanti R. In silico investigation of the ATP7B gene: insights from functional prediction of non-synonymous substitution to protein structure. BioMetals 2013, 27: 53-64. PMID: 24253677, DOI: 10.1007/s10534-013-9686-3.Peer-Reviewed Original ResearchConceptsNon-synonymous substitutionsDisease-causing mutationsWilson disease-causing mutationsDisease-causing variantsUnknown gene variantsGenetic variantsProtein X-ray structuresSequence-based approachesCopper-transporting ATPaseNovel genetic variantsAmino acid changesUncharacterized proteinsProtein functionNovel ATP7B mutationsProtein domainsFunctional predictionCopper homeostasisBioinformatics methodsAmino acidic changeATP7B geneProtein structureAcid changesATP7B proteinGenesX-ray structure
2008
RPS4Ygene family evolution in primates
Andrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Ygene family evolution in primates. BMC Ecology And Evolution 2008, 8: 142. PMID: 18477388, PMCID: PMC2397393, DOI: 10.1186/1471-2148-8-142.Peer-Reviewed Original ResearchConceptsRPS4Y genesPositive selectionTestis-specific expression patternRibosomal protein genesRibosomal protein S4Non-synonymous substitutionsAmino acid replacementsMaximum likelihood analysisDuplication eventsFamily evolutionFunctional paralogsEvolutionary historyGene familyFunctional genesSex chromosomesProtein S4Protein functionPrimate phylogenyProtein domainsHuman lineageNew World monkeysProtein geneGene dosageAcid replacementsY chromosomeSingle locus typing of MHC class I and class II B loci in a population of red jungle fowl
Worley K, Gillingham M, Jensen P, Kennedy L, Pizzari T, Kaufman J, Richardson D. Single locus typing of MHC class I and class II B loci in a population of red jungle fowl. Immunogenetics 2008, 60: 233-247. PMID: 18389232, DOI: 10.1007/s00251-008-0288-0.Peer-Reviewed Original ResearchConceptsRed jungle fowlJungle fowlMajor histocompatibility complexClass II B lociMHC diversityExcess of non-synonymous substitutionsReference strand-mediated conformational analysisEstimates of genetic variationDomestic chickensMajor histocompatibility complex regionNon-synonymous substitutionsStrand-mediated conformational analysisStrength of selectionMultilocus measuresDiversifying selectionMeasures of diversityGene organisationIndividual lociExpression locusClass II BGenetic variationCaptive populationsWild ancestorGallus gallusB locus
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