Li, Y., Evers, J., Luo, A., Erber, L., Postler, Z. & Chen, Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiometry Analysis of Ubiquitination. Angew Chem Int Ed Engl. 58(2):537-541 (2019)
Erber, L., Luo, A. & Chen, Y. Targeted and Interactome Proteomics Revealed the Role of PHD2 in Regulating BRD4 Proline Hydroxylation. Mol. Cell. Proteomics 18(9):1772-1781 (2019).
Zhou, T., Erber, L., Liu, B., Gao, Y., Ruan, H.B. & Chen, Y. Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. Oncotarget 7, 79154-79169 (2016).
Zhou, T., Chung, Y., Chen, J. & Chen, Y. Site-specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells. J Proteome Res 15, 1103-1113. (2016)
Park, J.*, Chen, Y.*, Tishkoff, D.X., Peng, C., Tan, M., Dai, L., Xie, Z., Zhang, Y., Zwaans, B.M.M., Skinner, M.E., Lombard, D.B. & Zhao, Y. Sirt5-mediated Lys desuccinylation regulates diverse metabolic pathways. Mol Cell 50, 919-930 (2013)
Chen, Y., Zhao, W., Yang, J.S., Cheng, Z., Luo, H., Lu, Z., Tan, M., Gu, W. & Zhao, Y. Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol Cell Proteomics 11, 1048-1062 (2012).
Chen, Y., Chen, W., Cobb, M.H. & Zhao, Y. PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc Natl Acad Sci U S A 106, 761-766 (2009).
Tang, Y., Zhao, W., Chen, Y., Zhao, Y. & Gu, W. Acetylation is indispensable for p53 activation. Cell 133, 612-626 (2008).
Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S.C., Falck, J.R., Peng, J., Gu, W. & Zhao, Y. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 6, 812-819 (2007).
Kim, S.C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., Grishin, N.V., White, M., Yang, X.J. & Zhao, Y. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23, 607-618 (2006).
Chen, Y., Kwon, S.W., Kim, S.C. & Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J Proteome Res 4, 998-1005 (2005).
