YCI Laboratory for Next-Generation Proteomics

For the full list of publication, please go to PubMed.


First-author publication

  1. Wu Y*, Williams E*, Aebersold R. Application of SWATH Proteomics to Mouse Biology. Curr Protoc Mouse Biol. 2017 Jun 19;7(2):130-143.
  2. Terfve C*, Sabidó E*, Wu Y*, Bautista L, Porstmann T, Chang V, Clough T, Vaga S, Saez-Rodriguez J, Vitek O, Stoffel M, Aebersold R. System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects. J Proteome Res. 2017 Feb 3;16(2):831-841.
  3. Williams E*, Wu Y*, Jha P, Dubuis S, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J. Systems proteomics illuminates genetic mechanisms linking mitochondrial function and metabolism. Science. 2016 Jun 10;352(6291).
  4. Wu Y*, Williams E*, Dubuis S, Mottis A, Jovaisaite V, Houten S, Argmann C, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R. Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell. 2014 Sep 11;158(6).
  5. Wu Y, Dai J, Yang X, Li S, Zhao S, Tang J, Zheng G, Li Y, Wu J, Zeng R. Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression. Mol Cell Proteomics. 2009 Dec; 8(12):2809-26.
  6. Williams E*, Wu Y*, Ryu D, Kim J, Wolski W, Jha P, Halter C, Auwerx J, Aebersold R. Variation in the mitochondrial proteome: quantifying and localizing proteins across five tissues in mice. In submission.



  1. Zhang H, Ryu D, Wu Y, Gariani K, Wang X, Luan P, D’Amico D, Ropelle E, Lutolf M, Aebersold R, Schoonjans K, Menzies K, Auwerx J. NAD⁺ repletion improves mitochondrial and stem cell function and enhances life span in mice. Science. 2016 Jun 17;352(6292).
  2. Sabidó E, Wu Y, Bautista L, Porstmann T, Chang C, Vitek O, Stoffel M, Aebersold R. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Mol Syst Biol. 2013 Jul 16;9:681.
  3. Subasic D, Brümmer A, Wu Y, Pinto S, Keller M, Jovanovic M, Imig J, Nasso S, Götze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner M. Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Research. 2015 Jul 31. pii: gr.183160.114.
  4. Wu S, Ma L, Wu Y, Zeng R, Zhu X. Nudel is crucial for the WAVE complex assembly in vivo by selectively promoting subcomplex stability and formation through direct interactions. Cell Res. 2012 Aug;22(8):1270-84.
  5. Ding Y, Wu Y, Zeng R, Liao K. Proteomic profiling of lipid droplet-associated proteins in primary adipocytes of normal and obese mouse. Acta Biochim Biophys Sin (Shanghai). 2012 May;44(5):394-406.
  6. Sheng Q, Dai J, Wu Y, Tang H, Zeng R. BuildSummary: Using group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics. J Proteome Res. 2012 Mar 2;11(3):1494-502.
  7. Dai J, Wang L, Wu Y, Sheng Q, Wu J, Shieh C, Zeng R. (2009). Fully automatic separation and identification of phosphopeptides by continuous pH-gradient anion exchange online coupled with reversed-phase liquid chromatography mass spectrometry. J Proteome Res. 2009 Jan;8(1):133-41.