2000-2006 北京理工大学 学士和硕士
2006-2010 德国慕尼黑-路德维希-马克西米利安大学 博士
2006-2010 德国马克斯普朗克精神病研究所 博士生
2011-2013.9 美国斯克里普斯研究所 研究助理
2013.9-至今 中国科学院生物与化学交叉研究中心 研究员、课题组长

质谱和蛋白质组实验室利用生物质谱技术来研究蛋白质在生物体系中的多种特性。其研究方向主要包括：
1.质谱蛋白质组学新技术和新方法的研究
2.神经退行性疾病和衰老过程的相关蛋白质组学研究
3.质谱蛋白质组学技术在生物学问题中的广泛应用

代表性论文及著作：

(1)      Si, C.; Cao, Y.; Zhang, Y. *, SecMS analysis of selenoproteins with selenocysteine insertion sequence and beyond, Methods in Enzymology: Selenoprotein Structure and Function 2021, ISSN 0076-6879, https://doi.org/10.1016/bs.mie.2021.10.022.

(2)      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 2021.

(3)      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.

(4)      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. Frontiers in molecular neuroscience 2021, 14, 777621.

(5)      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.

(6)      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.

(7)      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.

(8)      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.

(9)      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.

(10)   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, 2191.

(11)   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, 1054-1063.

(12)   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, 1380-1388.

(13)   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, 3830-3840.

(14)   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, 530-539.

(15)   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, 1215-1223.

(16)   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.

(17)   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.

(18)   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.

(19)   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.

(20)   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.

(21)   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.

(22)   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.

其他论文：

(23)   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. Molecular psychiatry 2021.

(24)   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 2021.

(25)   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.

(26)   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. Bioconjugate chemistry 2021, 32 (6), 1094-1104.

(27)   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.

(28)   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).

(29)   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.

(30)   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.

(31)   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.

(32)   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.

(33)   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.

(34)   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.

(35)   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, e1006623.

(36)   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.

(37)   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, 705-716.

(38)   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, E4697-4706.

(39)   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, 1836-1849.

(40)   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.

(41)   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.

(42)   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.

(43)   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.

(44)   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.

(45)   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.

(46)   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.

(47)   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.

(48)   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.