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W. Shao, E. Caron, P. Pedrioli, R. Aebersold. “The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses” Methods in Molecular Biology. 2120:173-181 (2020) （一作；通訊）

W. Shao*, T. Guo*, N. Toussaint, U. Wagner, G. Ratsch, P. Wild, R. Aebersold et al. “Comparative analysis of mRNA degradation and protein degradation in 68 pairs of adjacent prostate tissue samples indicates high stability of proteins.” Nature Communications 10, 2524.

W. Shao, P. Pedrioli, W. Wolski, C. Scurtescu, et al. “The SysteMHC Atlas project.” Nucleic Acids Research 46, 1237-1247.

W. Shao, H. Lam. “Tandem mass spectral libraries of peptides and their roles in proteomics research.” Mass Spectrometry Reviews 5, 634-648.

P. Forny*, X. Bonilla*, D. Lamparter*, W. Shao*, et al. “Integrated multi-omics reveals anaplerotic insufficiency in methylmalonyl-CoA mutase deficiency” Nature Metabolism  2023 (co-first; listed alphabetically)

Buljan, M., Banaei-Esfahani, A., Blattmann, P., Meier-Abt, F., Shao, W., Vitek, O., Tang, H., & Aebersold, R. (2023). A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nature Methods