Featured Publications
Multi-omic measurements of heterogeneity in HeLa cells across laboratories
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology 2019, 37: 314-322. PMID: 30778230, DOI: 10.1038/s41587-019-0037-y.Peer-Reviewed Original ResearchConceptsCell linesGenome-wide copy numberMulti-omic measurementsHuman cultured cellsProtein turnover ratesPhenotypic responsesGenomic variabilityDifferent cell linesHeLa variantsSpecific cell linesCopy numberHeLa cellsCultured cellsHeLa cell linePhenotypic variabilityProgressive divergenceTurnover rateCellsBiological variationTechnical variationUniform conditionsTranscriptomeProteomeSuccessive passagesLines
2020
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R. A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Systems 2020, 10: 133-155.e6. PMID: 32027860, PMCID: PMC7042714, DOI: 10.1016/j.cels.2020.01.001.Peer-Reviewed Original ResearchConceptsSEC-SWATHHundreds of complexesThousands of proteinsAssembly state changesMitotic proteomeProtein complexesProteomic studiesGlobal screenHuman cellsComplex remodelingHigher-level organizationBiological researchKey hallmarksBiochemical reactionsInteractive exploration toolProteinFunctional stateSpecific changesComplexesProteomeCellsMitosisHallmarkRemodelingInterphase
2017
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells
Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications 2017, 8: 1212. PMID: 29089484, PMCID: PMC5663699, DOI: 10.1038/s41467-017-01422-6.Peer-Reviewed Original ResearchConceptsSWATH mass spectrometryPost-transcriptional effectsMitochondrial proteomeProteome remodelingProteomic resourceTranscriptomic dataProteomic dataProtein abundanceProtein turnoverEntire chromosome 21ProteomeProtein expressionPhenotypic manifestationsChromosome 21Fibroblast cellsStoichiometric complexSignificant downregulationMonozygotic twin pair discordantTwin pair discordantMass spectrometryMajor determinantChromosomesProteinPair discordantAbundanceImpact of Alternative Splicing on the Human Proteome
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports 2017, 20: 1229-1241. PMID: 28768205, PMCID: PMC5554779, DOI: 10.1016/j.celrep.2017.07.025.Peer-Reviewed Original ResearchConceptsProteomic diversityAlternative splicingAlternative splicing eventsDifferential transcript usageIntron retentionSplicing eventsHuman transcriptomeHuman proteomeTranscript usageRNA sequencingProtein abundanceTranscript levelsHuman diseasesProteomeSWATH-MSSplicingQuantitative snapshotIntegrative approachCritical determinantDiversityTranscriptomeSequencingAbundanceMRNAQuantitative manner
2011
A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer
Luo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. Journal Of Proteomics 2011, 74: 528-538. PMID: 21262398, DOI: 10.1016/j.jprot.2011.01.011.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCellular proteomeCell lung cancerCancer secretomeLung cancerOne-dimensional gel electrophoresisA549 cellsBiomarker discoveryProteomic dataGene expressionSecretory proteinsIntracellular contaminationNovel promising biomarkerNovel serum biomarkersEnzyme-linked immunosorbent assaySecretomeProteinSerum proteomic dataClinical stagingProteomeSerum biomarkersGel electrophoresisC4BP levelsPromising biomarkerImmunosorbent assay