2022:
· Sun, L., Yan, Y., Lv, H., Li, J., Wang, Z., Wang, K., Wang, L., Li, Y., Jiang, H., Zhang, Y. *, Rapamycin targets STAT3 and impacts c-Myc to suppress tumor growth. Cell Chem Biol 2022, 29(3):373-385.
· Si, C., Cao, Y., Zhang, Y. *, SecMS analysis of selenoproteins with selenocysteine insertion sequence and beyond, Methods in Enzymology: Selenoprotein Structure and Function 2022, 662:227-240, ISSN 0076-6879, https://doi.org/10.1016/bs.mie.2021.10.022.
· Zhang C., He H., Dai J., Li Y., He J., Yang W., Dai J., Han F., Kong W., Wang X., Zheng X., Zhou J., Pan W., Chen Z., Singhal M., Zhang Y., Guo F.*, Hu J.*, KANK4 Promotes Arteriogenesis by Potentiating VEGFR2 Signaling in a TALIN-1-Dependent Manner. Arterioscler Thromb Vasc Biol 2022, 42 (6):772-788.
· Wu X., Niu K., Wang X., Zhao J., Wang H., Li D., Wang H., Miao T., Yang Y., Ma H., Zhang Y., Pan L., Liu R., Bai H., Liu N.*, microRNA-252 and FoxO repress inflammaging by a dual inhibitory mechanism on Dawdle-mediated TGF-beta pathway in Drosophila. Genetics 2022, 220(3):iyab234.
· Huang C.#, Lu J. #, Ma X. #, Qiang J., Wang C., Liu C., Fang Y., Zhang Y., Jiang L., Li D. *, Zhang S. *, The mouse nicotinamide mononucleotide adenylyltransferase chaperones diverse pathological amyloid client proteins. J Biol Chem 2022, 298 (5):101912.
· Fan Y., Zhao Q., Xia W., Tao Y., Yu W., Chen M., Liu Y., Zhao J., Shen Y., Sun Y., Si C., Zhang S., Zhang Y., Li W., Liu C. *, Wang J. *, Li D.*, Generic amyloid fibrillation of TMEM106B in patient with Parkinson's disease dementia and normal elders. Cell Res 2022, 32 (6):585-588.
· Hou, Y., Lu, H., Li, J., Guan, Z., Zhang, J., Zhang, W., Yin, C., Sun, L., Zhang, Y., Jiang, H. *, A photoaffinity labeling strategy identified EF1A1 as a binding protein of cyclic dinucleotide 2′3′-cGAMP. Cell Chem Biol 2022, 29(1):133-144.
2021:
· Qiang, J., Xu, Z., Li, Y., Wang, H., Zhang, Y. *, Carboxypeptidase Y Assisted Disulfide-Bond Identification with Linearized Database Search. Anal Chem 2021, 93 (45), 14940-14945.
· Zhang, K. #, Wang, Q. #, Liang, Y., Yan, Y., Wang, H., Cao, X., Shan, B., Zhang, Y. *, Li, A. *, Fang, Y. *, Quantitative Proteomic Analysis of Mouse Sciatic Nerve Reveals Post-injury Upregulation of ADP-Dependent Glucokinase Promoting Macrophage Phagocytosis. Front Mol Neurosci 2021, 14, 777621.
· Wang, H.#, Zhang, Y. #, Zeng, K. #, Qiang, J. #, Cao, Y., Li, Y., Fang, Y., Zhang, Y. *, Chen, Y. *, Selective Mitochondrial Protein Labeling Enabled by Biocompatible Photocatalytic Reactions inside Live Cells. JACS Au 2021, 1(7):1066-1075.
· Ni, J. #, Ren, Y. #, Su, T., Zhou, J., Fu, C., Lu, Y., Li, D., Zhao, J., Li, Y., Zhang, Y., Fang, Y., Liu, N., Geng, Y. *, Chen, Y. *, Loss of TDP-43 function underlies hippocampal and cortical synaptic deficits in TDP-43 proteinopathies. Mol Psychiatry 2021.
· Zu, R., Yu, Z., Zhao, J., Lu, X., Liang, W., Sun, L., Si, C., Zhu, K., Zhang, T., Li, G., Zhang, M., Zhang, Y., Liu, N., Yuan, J. *, Shan, B. *, Quantitative analysis of phosphoproteome in necroptosis reveals a role of TRIM28 phosphorylation in promoting necroptosis-induced cytokine production. Cell Death Dis 2021, 12 (11), 994.
· Zhang, L., Wang, Z., Wang, Z., Luo, F., Guan, M., Xu, M., Li, Y., Zhang, Y., Wang, Z. *, Wang, W. *, A Simple and Efficient Method to Generate Dual Site-Specific Conjugation ADCs with Cysteine Residue and an Unnatural Amino Acid. Bioconjug Chem 2021, 32 (6), 1094-1104.
· Lou, M., Tang, X., Wang, G., He, J., Luo, F., Guan, M., Wang, F., Zou, H., Wang, J., Zhang, Q., Xu, M., Shi, Q., Shen, L., Ma, G., Wu, Y., Zhang, Y., Liang, A., Wang, T., Xiong, L., Wang, J., Xu, J., Wang, W. *, Long noncoding RNA BS-DRL1 modulates the DNA damage response and genome stability by interacting with HMGB1 in neurons. Nat Commun 2021, 12 (1), 4075.
· Li, S. #, Luo, H. #, Lou, R. #, Tian, C. #, Miao, C., Xia, L., Pan, C., Duan, X., Dang, T., Li, H., Fan, C., Tang, P., Zhang, Z., Liu, Y., Li, Y., Xu, F., Zhang, Y., Zhong, G. *, Hu, J. *, Shui, W. *, Multiregional profiling of the brain transmembrane proteome uncovers novel regulators of depression. Sci Adv 2021, 7 (30): eabf0634.
2020:
· Wang, Z., Liu, H., Yan, Y., Yang, X., Zhang, Y. *, Wu, L. *, Integrated proteomic and N-glycoproteomic analyses of human breast cancer. J Proteome Res 2020, 19(8):3499-3509.
· Lou, R., Tang, P., Ding, K., Li, S., Tian, C., Li, Y., Zhao, S. *, Zhang, Y. *, Shui, W. *, Hybrid Spectral Library Combining DIA-MS Data and a Targeted Virtual Library Substantially Deepens the Proteome Coverage. iScience 2020, 23(3):100903.
· Guo, L. #, Gao, J. #, Gao, Y., Zhu, Z., Zhang, Y. *, Aspirin reshapes acetylomes in inflammatory and cancer cells via CoA-dependent and -independent pathways. J Proteome Res 2020, 19(2):962-972.
· Hu, X., Wang, L., Wang, Y., Ji, J., Li, J., Wang, Z., Li, C., Zhang, Y., Zhang, Z. *, RNF126-Mediated Reubiquitination Is Required for Proteasomal Degradation of p97-Extracted Membrane Proteins. Mol Cell 2020, 79 (2), 320-331.
· Dai, J., Zhang, C., Guo, L., He, H., Jiang, K., Huang, Y., Zhang, X., Zhang, H., Wei, W., Zhang, Y., Lu, L. *, Hu, J. *, A necroptotic-independent function of MLKL in regulating endothelial cell adhesion molecule expression. Cell Death Dis 2020, 11 (4), 282.
· Ma, X., Zhu, Y., Lu, J., Xie, J., Li, C., Austin, S., Qiang, J., Liu, J., Dou, S., Xiao, Y., Wang, C., Jia, C., Long, H., Yang, J., Fang, Y., Jiang, L., Zhang, Y., Zhang, S., Zhai, RG. *, Liu, C. *, Li, D. *, Nicotinamide mononucleotide adenylyltransferase uses its NAD+ substrate-binding site to chaperone phosphorylated Tau. ELife 2020, 9:e51859.
· Sun, Y., Hou, S., Zhao, K., Long, H., Liu, Z., Gao, J., Zhang, Y., Su, X., Li, D.*, Liu, C. *, Cryo-EM structure of full-length α-synuclein amyloid fibril with Parkinson’s disease familial A53T mutation. Cell Res 2020, 30(4):360-362.
2019:
· Yang, L., Cao, Y., Zhao, J., Fang Y., Liu, N. *, Zhang, Y. *, Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila. Mol Cell Proteomics 2019, 18(10):2078-2088.
· Yang, L., Ma, Z., Wang, H., Niu, K., Cao, Y., Sun, L., Geng, Y., Yang, B., Gao, F., Chen, Z., Wu, Z., Li, Q., Shen, Y., Zhang, X., Jiang, H., Chen, Y., Liu, R., Liu, N. *, Zhang, Y. *, Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker. Nat Commun 2019, 10(1), 2191.
· Qiang, J., Ma, Z., Xie, X., Shi, L., Geng, Y., Hu, J., Liu, R., Liu, N., Zhang, Y. *, Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells. J Proteome Res 2019, 18(3), 1054-1063.
· Duan, Y., Du, A., Gu, J., Duan, G., Wang, C., Gui, X., Ma, Z., Qian, B., Deng, X., Zhang, K., Sun, L., Tian, K., Zhang, Y., Jiang, H., Liu, C. *, Fang, Y. *, PARylation regulates stress granule dynamics, phase separation, and neurotoxicity of disease-related RNA-binding proteins. Cell Res 2019, 29(3):233-247.
2018:
· Guo, L., Yang, W., Huang, Q., Qiang, J., Hart, J. R., Wang, W., Hu, J., Zhu, Z. J., Liu, N., Zhang, Y. *, Selenocysteine-Specific Mass Spectrometry Reveals Tissue-Distinct Selenoproteomes and Candidate Selenoproteins. Cell Chem Biol 2018, 25(11), 1380-1388.
· Ma, Z., Wang, H., Cai, Y., Wang, H., Niu, K., Wu, X., Ma, H., Yang, Y., Tong, W., Liu, F., Liu, Z., Zhang, Y., Liu, R., Zhu, Z. J. *, Liu, N. *, Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila. Elife 2018, 7: e35368.
2017:
· Yang, X., Wang, Z., Guo, L., Zhu, Z. J., Zhang, Y. *, Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology. J Proteome Res 2017, 16(10), 3830-3840.
· Mu, R., Tat, J., Zamudio, R., Zhang, Y., Yates, J. R., 3rd, Kumagai, A., Dunphy, W. G., Reed, S. I. *, CKS Proteins Promote Checkpoint Recovery by Stimulating Phosphorylation of Treslin. Mol Cell Biol 2017, 37(20):e00344-17.
· Jin, H. Y., Oda, H., Chen, P., Yang, C., Zhou, X., Kang, S. G., Valentine, E., Kefauver, J. M., Liao, L., Zhang, Y., Gonzalez-Martin, A., Shepherd, J., Morgan, G. J., Mondala, T. S., Head, S. R., Kim, P. H., Xiao, N., Fu, G., Liu, W. H., Han, J., Williamson, J. R., Xiao, C. *, Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet 2017, 13(2), e1006623.
2016:
· Wang, H., Ma, Z., Niu, K., Xiao, Y., Wu, X., Pan, C., Zhao, Y., Wang, K., Zhang, Y. *, Liu, N. *, Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development 2016, 143(3), 530-539.
· Pedros, C., Zhang, Y., Hu, J. K., Choi, Y. S., Canonigo-Balancio, A. J., Yates, J. R., 3rd, Altman, A., Crotty, S., Kong, K. F. *, A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nat Immunol 2016, 17, 825-833.
2015:
· Huang, Q., Yang, L., Luo, J., Guo, L., Wang, Z., Yang, X., Jin, W., Fang, Y., Ye, J., Shan, B., Zhang, Y. *, SWATH enables precise label-free quantification on proteome scale. Proteomics 2015, 15(7), 1215-1223.
· Zhang, Y., Xu, T., Shan, B., Hart, J., Aslanian, A., Han, X., Zong, N., Li, H., Choi, H., Wang, D., Acharya, L., Du, L., Vogt, P. K., Ping, P., Yates, J. R., 3rd. *, ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects. J Proteomics 2015, 129, 25-32.
· Xia, H. G., Najafov, A., Geng, J., Galan-Acosta, L., Han, X., Guo, Y., Shan, B., Zhang, Y., Norberg, E., Zhang, T., Pan, L., Liu, J., Coloff, J. L., Ofengeim, D., Zhu, H., Wu, K., Cai, Y., Yates, J. R., 3rd, Zhu, Z. J., Yuan, J. *, Vakifahmetoglu-Norberg, H. Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death. J Cell Biol 2015, 210(5), 705-716.
· Tang, B., Wang, T., Wan, H., Han, L., Qin, X., Zhang, Y., Wang, J., Yu, C., Berton, F., Francesconi, W., Yates, J. R., 3rd, Vanderklish, P. W., Liao, L. *, Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc Natl Acad Sci U S A 2015, 112(34), E4697-4706.
· Ofengeim, D., Ito, Y., Najafov, A., Zhang, Y., Shan, B., DeWitt, J. P., Ye, J., Zhang, X., Chang, A., Vakifahmetoglu-Norberg, H., Geng, J., Py, B., Zhou, W., Amin, P., Berlink Lima, J., Qi, C., Yu, Q., Trapp, B., Yuan, J. *, Activation of necroptosis in multiple sclerosis. Cell Rep 2015, 10(11), 1836-1849.
· Hassler, J. R., Scheuner, D. L., Wang, S., Han, J., Kodali, V. K., Li, P., Nguyen, J., George, J. S., Davis, C., Wu, S. P., Bai, Y., Sartor, M., Cavalcoli, J., Malhi, H., Baudouin, G., Zhang, Y., Yates, J. R., 3rd, Itkin-Ansari, P., Volkmann, N., Kaufman, R. J. *, The IRE1alpha/XBP1s Pathway Is Essential for the Glucose Response and Protection of beta Cells. PLoS Biol 2015, 13, e1002277.
· Hart, J. R., Zhang, Y., Liao, L., Ueno, L., Du, L., Jonkers, M., Yates, J. R., 3rd, Vogt, P. K. *, The butterfly effect in cancer: a single base mutation can remodel the cell. Proc Natl Acad Sci U S A 2015, 112, 1131-1136.
2014 and before:
· Zhang, Y., Shan, B., Boyle, M., Liu, J., Liao, L., Xu, T., Yates, J. R., 3rd. *, Brain Proteome Changes Induced by Olfactory Learning in Drosophila. J Proteome Res 2014, 13, 3763-3770.
· Shan, B., Xu, C., Zhang, Y., Xu, T., Gottesfeld, J. M., Yates, J. R., 3rd. *, Quantitative proteomic analysis identifies targets and pathways of a 2-aminobenzamide HDAC inhibitor in Friedreich's ataxia patient iPSC-derived neural stem cells. J Proteome Res 2014, 13, 4558-4566.
· Kong, K. F., Fu, G., Zhang, Y., Yokosuka, T., Casas, J., Canonigo-Balancio, A. J., Becart, S., Kim, G., Yates, J. R., 3rd, Kronenberg, M., Saito, T., Gascoigne, N. R., Altman, A. *, Protein kinase C-eta controls CTLA-4-mediated regulatory T cell function. Nat Immunol 2014, 15, 465-472.
· Zhang, Y., Fonslow, B. R., Shan, B., Baek, M. C., Yates, J. R., 3rd. *, Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013, 113, 2343-2394.
· Webhofer, C. #, Zhang, Y. #, Brusis, J., Reckow, S., Landgraf, R., Maccarrone, G., Turck, C. W., Filiou, M. D. *, (1)(5)N metabolic labeling: evidence for a stable isotope effect on plasma protein levels and peptide chromatographic retention times. J Proteomics 2013, 88, 27-33.
· Ryan, S. D., Dolatabadi, N., Chan, S. F., Zhang, X., Akhtar, M. W., Parker, J., Soldner, F., Sunico, C. R., Nagar, S., Talantova, M., Lee, B., Lopez, K., Nutter, A., Shan, B., Molokanova, E., Zhang, Y., Han, X., Nakamura, T., Masliah, E., Yates, J. R., 3rd, Nakanishi, N., Andreyev, A. Y., Okamoto, S., Jaenisch, R. *, Ambasudhan, R. *, Lipton, S. A. *, Isogenic human iPSC Parkinson's model shows nitrosative stress-induced dysfunction in MEF2-PGC1alpha transcription. Cell 2013, 155, 1351-1364.
· Filiou, M. D., Webhofer, C., Gormanns, P., Zhang, Y., Reckow, S., Bisle, B., Teplytska, L., Frank, E., Kessler, M. S., Maccarrone, G., Landgraf, R., Turck, C. W. *, The (15)N isotope effect as a means for correlating phenotypic alterations and affected pathways in a trait anxiety mouse model. Proteomics 2012, 12, 2421-2427.
· Zhang, Y., Reckow, S., Webhofer, C., Boehme, M., Gormanns, P., Egge-Jacobsen, W. M., Turck, C. W. *, Proteome scale turnover analysis in live animals using stable isotope metabolic labeling. Anal Chem 2011, 83, 1665-1672.
· Zhang, Y., Filiou, M. D., Reckow, S., Gormanns, P., Maccarrone, G., Kessler, M. S., Frank, E., Hambsch, B., Holsboer, F., Landgraf, R., Turck, C. W. *, Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways. Mol Cell Proteomics 2011, 10, M111 008110.
· Filiou, M. D., Zhang, Y., Teplytska, L., Reckow, S., Gormanns, P., Maccarrone, G., Frank, E., Kessler, M. S., Hambsch, B., Nussbaumer, M., Bunck, M., Ludwig, T., Yassouridis, A., Holsboer, F., Landgraf, R., Turck, C. W. *, Proteomics and metabolomics analysis of a trait anxiety mouse model reveals divergent mitochondrial pathways. Biol Psychiatry 2011, 70, 1074-1082.
· Zhang, Y., Webhofer, C., Reckow, S., Filiou, M. D., Maccarrone, G., Turck, C. W. *, A MS data search method for improved 15N-labeled protein identification. Proteomics 2009, 9, 4265-4270.
· Haegler, K., Mueller, N. S., Maccarrone, G., Hunyadi-Gulyas, E., Webhofer, C., Filiou, M. D., Zhang, Y., Turck, C. W. *, QuantiSpec--Quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins. J Proteomics 2009, 71, 601-608.
· Frank, E., Kessler, M. S., Filiou, M. D., Zhang, Y., Maccarrone, G., Reckow, S., Bunck, M., Heumann, H., Turck, C. W., Landgraf, R., Hambsch, B. *, Stable isotope metabolic labeling with a novel N-enriched bacteria diet for improved proteomic analyses of mouse models for psychopathologies. PLoS One 2009, 4, e7821.
