2022
Proteotype coevolution and quantitative diversity across 11 mammalian species
Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.Peer-Reviewed Original ResearchConceptsMammalian speciesRNA metabolic processesCommon mammalian speciesUbiquitin-proteasome systemEvolutionary profilingMammalian lineagesProteomic methodsProtein degradationProtein abundanceGene expressionProtein expression levelsHigh interspeciesMetabolic processesCovariation analysisFunctional roleNucleotide levelExpression levelsQuantitative diversityCoevolutionMammalsSpeciesRemarkable variationExpressionTranscriptomeBiological variability
2020
Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: msb199170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.Peer-Reviewed Original ResearchConceptsProtein degradationGenome-wide correlation analysisGene dosage variationProtein abundance levelsStable isotope-labeled amino acidsIndividual protein isoformsSpecific biological processesAlternative splicing isoformsData-independent acquisition mass spectrometryIsotope-labeled amino acidsAcquisition mass spectrometryProtein degradation ratesIntron retentionCellular functionsProtein isoformsSplicing isoformsCellular organellesTranscriptome variabilitySame geneTurnover controlRegulatory mechanismsBiological processesSpecific mRNAsTight associationAbundance levels
2019
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
Shao W, Guo T, Toussaint N, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser C, Poyet C, Ljubicic J, Rupp N, Rüschoff J, Zhong Q, Beyer A, Ji J, Collins B, Liu Y, Rätsch G, Wild P, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 2019, 10: 2524. PMID: 31175306, PMCID: PMC6555818, DOI: 10.1038/s41467-019-10513-5.Peer-Reviewed Original ResearchConceptsProtein degradationMass spectrometric methodDegradation of mRNAAnalysis of mRNASpectrometric methodStability of proteinsMass spectrometryRNA-seqIndicator of sample qualitySWATH mass spectrometryDegree of protein degradationMRNA degradationClinical sample cohortsProteomic analysisClinical tissuesProteinMRNAMolecular measurementsConfounding conclusions
2017
Proteotyping Gene Dosage Effects in Genetic Diseases
Liu Y, Aebersold R. Proteotyping Gene Dosage Effects in Genetic Diseases. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.926.3.Peer-Reviewed Original ResearchGene dosage imbalanceCopy number variationsProtein degradationDosage imbalanceGenetic diseasesSubstantial post-transcriptional regulationHeteromeric protein complexesDivergent expression levelsPost-transcriptional regulationCorresponding protein abundanceDNA copy number variationsComponents of pathwaysTurnover analysisPatient-derived induced pluripotent stem cellsInduced pluripotent stem cellsSWATH mass spectrometryPluripotent stem cellsGene dosage effectProtein turnover ratesPluripotent stateTranscript profilingSILAC experimentsProtein complexesTranslational regulationRNA-seq
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