Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S.C., Falck, J.R., Peng, J., Gu, W. and Zhao, Y. (2007) Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics, 6(5): p. 812-9.

Xu, Y., Sprung, R., Kwon, S.W., Kim, S.C. and Zhao, Y. (2007). Isolation of Phosphopeptides by pI-Difference-Based Electrophoresis. J Proteome Res 6(3): p. 1153-7.

Lee, J., Xu, Y., Chen, Y., Sprung, R., Kim, S.C., Xie, S. and Zhao, Y. (2007) Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol Cell Proteomics. 6(4): p. 669-76.

Chang, B., Chen, Y., Zhao, Y. and Bruick, R.K. (2007) JMJD6 is a histone arginine demethylase. Science 318(5849): p. 444-7.

Raman, M., Earnest, S., Zhang, K., Zhao, Y. and Cobb, M.H. (2007) TAO kinases mediate activation of p38 in response to DNA damage. Embo J, 26(8): p. 2005-14.

Li, H., Zhang, Z., Wang, B., Zhang, J., Zhao, Y. and Jin, Y. (2007) The Wwp2-mediated Ubiquitination of the RNA Polymerase II Large Subunit in Mouse Embryonic Pluripotent Stem Cells. Mol Cell Biol,. 27(15): p. 5296-5305.

Ganesan, A.K., Kho, Y., Kim, S.C., Chen, Y., Zhao, Y. and White, M.A. (2007) Broad spectrum identification of SUMO substrates in melanoma cells. Proteomics, 7(13): p. 2216-2221.

Bartz, R., Zehmer, J.K., Zhu, M., Chen, Y., Anderson, R.G.W., Zhao, Y. and Liu, P. (2007) Comprehansive proteomic study of purified adiposomes/lipid droplets from Chinese hamster ovary K2 cells J Proteome Res, 6(8): p.3256-65.

Kang, J., Chen, Y., Zhao, Y. and Yu, H. (2007) Autophosphorylation-dependent activation of human Mps is required for the spindle checkp. Proc Natl Acad Sci U S A, 104(51): p.20232-7.

Chien, Y., Kim. S.C., Bumeister, R., Loo, Y., Kwon. S.W., Johnson, C.L., Balakireva, M.G., Romeo, Y., Kopelovich, L., Gale, M., Yeaman, C., Camonis, J.H., Zhao, Y., and White, W.A. RalB GTPase-Mediated Activation of the IkappaB Family Kinase TBK1 Couples Innate Immune Signaling to Tumor Cell Survival. Cell (2006), 127(1), 157-70.

Kim, S. C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Gao, J., Cheng, T., Kho, Y., Xiao, H., Grichine, N., White, M. A., Yang, X. J., and Zhao, Y. Substrate and Functional Diversity of Lysine Acetylation Revealed by a Proteomics Survey. Molecular Cell (2006), 23(4), 607-618.

Anselmo, A.N., Earnest, S., Chen, W., Juang, Y., Kim, S.C., Zhao, Y. and Cobb, M.H. WNK1 and OSR1 regulate the Na+, K+, 2Cl- cotransporter in HeLa cells. Proc Natl Acad Sci (2006), 103(29), 10883-10888.

Qiu, Y., Zhao, Y., Becker, M., John, S., Parekh, B. S., Huang, S., Martinez, E. D., Chen, Y., Lu, H., Adkins, N. L., Georgel, P. T., Schiltz, P. L., and Hager, G. L. HDAC1 Acetylation is Linked to Progressive Modulation of Steroid Receptor Induced Gene Transcription. Mol Cell (2006), 22: 669-679.

Nandi, A., Sprung, R., Barma, D. K., Zhao, Y., Kim, S. C., Falck, J. R., and Zhao, Y. Global identification of O-GlcNAc-modified proteins. Anal Chem (2006), 78: 452-458.

Kim, S.C., Chen, Y., Mirza, S., Xu, Y., Lee, J., Liu, P., and Zhao, Y., A Clean, More Efficient Method for In-Solution Digestion of Protein Mixtures without Detergent or Urea. J Proteome Res. (2006), 5(12): 3446-52.

Binns, D., Hanuszewski, T., Chen, Y., Hill, J., Markin, V., Zhao, Y., Gilpin, C., Chapman, K., Anderson, R. G. W., and Goodman, J. M. Pexopodia and Gnarls, Novel Structures that Indicate an Intimate Collaboration Between Peroxisomes and Lipid Bodies. J Cell Biology (2006), 173: 719-731.

McMahon, K. A., Zhu, M., Kwon, S. W., Liu, P., Zhao, Y., and Anderson, R. G. Detergent-free caveolae proteome suggests an interaction with ER and mitochondria. Proteomics (2006), 6: 143-152.

Jin, Y., Dai, M., Lu, S. Z., Xu, Y., Luo, Z., Zhao, Y. and Lu, H.. 14-3-3g Binds to MDMX that is phosphorylated by UV-activated Chk1, resulting in p53 activation. EMBO Journal (2006), 25(6): 1207-1218.

Radichev, I., Kwon, S.W., Zhao, Y., Depamphilis, M.L. and Vassilev A. Genetic analysis of human ORC2 reveals specific domains that are required in vivo for assembly and nuclear localization of the origin recognition complex. J Biol Chem (2006), 281(32), 23264-23273.

Sprung, R., Nandi, A., Chen, Y., Kim, S.C., Barma, D., Falck, J.R. & Zhao, Y. Tagging-via-substrate strategy for probing O-GlcNAc modified proteins, (2005) J Proteome Res 4, 950-7.

Chen, Y., Kwon, S.W., Kim, S.C. & Zhao, Y. An integrated approach for manual verification of peptides identified by searching protein sequence databases with tandem mass spectra, (2005) J. Proteome Research 4, 998-1005.

Zhou, G., Li, H., Gong, Y., Zhao, Y., Cheng, J., Lee, P., & Zhao, Y. Proteomic analysis of global alteration of protein expression in squamous cell carcinoma of the esophagus, (2005) Proteomics 5, 3814-21.

Chen, Y., Kim, S.C. & Zhao, Y. High-throughput identification of in-gel digested proteins by rapid, isocratic HPLC/MS/MS, (2005), Anal Chem 77, 8179-84.

Zhi, G., Ryder, J.W., Huang, J., Ding, P., Chen, Y., Zhao, Y., Kamm, K.E. & Stull, J.T. Myosin light chain kinase and myosin phosphorylation effect frequency-dependent potentiation of skeletal muscle contraction, (2005) Proc Natl Acad Sci U S A 102, 17519-24.

Cheng, J., Zhang, D., Kim, K., Zhao, Y. & Su, B. Mip1, an MEKK2-interacting protein, controls MEKK2 dimerization and activation, (2005) Mol Cell Biol 25, 5955-64.

Kho, Y., Kim, S. C., Jiang, C., Barma, D., Kwon, S. W., Cheng, J., Jaunbergs, J., Weinbaum, C., Tamanoi, F., Falck, J., and Zhao, Y. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins, (2004) Proc Natl Acad Sci 101, 12479-12484.

Zhao, Y., Zhang, W., Kho, Y., and Zhao, Y. Proteomic analysis of integral plasma membrane proteins, (2004) Anal Chem 76, 1817-1823.

Zhao, Y., Kwon, S. W., Anselmo, A., Kaur, K., and White, M. A. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins, (2004) J Biol Chem 279, 20999-21002.

Intine, R.V., Dundr, M., Vassilev, A., Schwartz, E., Zhao, Y., Zhao, Y., Depamphilis, M.L. and Maraia, R.J. (2004). Nonphosphorylated human La antigen interacts with nucleolin at nucleolar sites involved in rRNA biogenesis. Mol Cell Biol 24(24): p. 10894-904.

Berman, D. M., Shih Ie, M., Burke, L. A., Veenstra, T. D., Zhao, Y., Conrads, T. P., Kwon, S. W., Hoang, V., Yu, L. R., Zhou, M., Kurman, R. J., Petricoin, E. F., and Liotta, L. A. Profiling the activity of G proteins in patient-derived tissues by rapid affinity-capture of signal transduction proteins (GRASP), (2004) Proteomics 4, 812-818.

Geiman, T. M., Sankpal, U. T., Robertson, A. K., Chen, Y., Mazumdar, M., Heale, J. T., Schmiesing, J. A., Kim, W., Yokomori, K., Zhao, Y., and Robertson, K. D. Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery, (2004) Nucleic Acids Res 32, 2716-2729.

Geiman, T. M., Sankpal, U. T., Robertson, A. K., Zhao, Y., and Robertson, K. D. DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system, (2004) Biochem Biophys Res Commun 318, 544-555.

Xu, H. M., Liao, B., Zhang, Q. J., Wang, B. B., Li, H., Zhong, X. M., Sheng, H. Z., Zhao, Y. X., Zhao, Y., and Jin, Y. Wwp2, an E3 ubiquitin ligase that targets transcription factor Oct-4 for ubiquitination, (2004) J Biol Chem 279, 23495-23503.

Leak, L. V., Liotta, L. A., Krutzsch, H., Jones, M., Fusaroa, V. A., Ross, S. J., Zhao, Y., and Petricoin, E. F., 3rd. Proteomic analysis of lymph, (2004) Proteomics 4, 753-765.

Liu, P., Ying, Y., Zhao, Y., Mundy, D. I., Zhu, M., and Anderson, R. G. W. CHO K2 cell lipid droplets appear to be metabolic organelles involved in membrane traffic., (2004) J. Biol. Chem. 279, 3787 - 3792.

Kwon, S. W., Kim, S. C., Jaunbergs, J., Falck, J. R., and Zhao, Y. Selective-enrichment of thiophosphorylated polypeptides as a tool for the analysis of protein phosphorylation, (2003) Molecular and Cellular Proteomics 2, 242-247.`

Zhang, W., Zhou, G., Zhao, Y., White, M. A., and Zhao, Y. Affinity-enrichment of plasma membrane for proteomics analysis, (2003) Electrophoresis 24, 2855-2863.

Zhao, Y., Zhang, W., White, M. A., and Zhao, Y. Capillary HPLC/mass spectrometric analysis of proteins from affinity-purified plasma membrane, (2003) Analytical Chemistry 75, 3751-3757.

Ahram, M., Flaig, M. J., Gillespie, J. W., Duray, P. H., Linehan, W. M., Ornstein, D. K., Niu, S., Zhao, Y., Petricoin, E. F., 3rd, and Emmert-Buck, M. R. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications, (2003) Proteomics 3, 413-421.

Jiang, X., Kim, H. E., Shu, H., Zhao, Y., Zhang, H., Kofron, J., Donnelly, J., Burns, D., Ng, S. C., Rosenberg, S., and Wang, X. Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway, (2003) Science 299, 223-226.