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2024:

· Guo, R., Liu, J., Min, X., Zeng, W., Shan, B., Zhang, M., He, Z., Zhang, Y., He, K., Yuan, J., Xu, D. *, Reduction of DHHC5-mediated beclin 1 S-palmitoylation underlies autophagy decline in aging. Nat Struct Mol Biol 2024, 31 (2):232-245.


2023:

· Li, J. #, Cao, Y. #, Yang, Y., Ma, H., Zhao, J., Zhang, Y. *, Liu, N. *, Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila. J Proteome Res 2023, 22 (9):2909-2924.

· Lou, R. #, Cao, Y. #, Li, S. #, Lang, X., Li, Y., Zhang, Y. *, Shui, W. *, Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. Nat Commun 2023, 14 (1):94.

· Yang, B., Zhang, W., Sun, L., Lu, B., Yin, C., Zhang, Y., Jiang, H. *, Creatine kinase brain-type regulates BCAR1 phosphorylation to facilitate DNA damage repair. iScience 2023, 26 (5):106684.

· Tian, S. #, Zhan, D. #, Yu, Y. #, Wang, Y., Liu, M., Tan, S., Li, Y., Song, L., Qin, Z., Li, X., Liu, Y., Li, Y., Ji, S., Wang, S., Proteomic Massive Analysis and Quality Control Consortium (Zhang, Y.), Zheng, Y. *, He, F. *, Qin, J. *, Ding, C. *, Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics. Genome biology 2023, 24 (1):202.

· 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 2023, 28 (2):931-945.

· Lyu, H., Sun, L., Guan, Z., Li, J., Yin, C., Zhang, Y., Jiang, H. *, Proximity labeling reveals OTUD3 as a DNA-binding deubiquitinase of cGAS. Cell Rep 2023, 42 (4):112309.


2022:

· Li, J. #, Cao, Y. #, Niu, K., Qiu, J., Wang, H., You, Y., Li, D., Luo, Y., Zhu, Z., Zhang, Y. *, Liu, N. *, Quantitative Acetylomics Reveals Dynamics of Protein Lysine Acetylation in Mouse Livers During Aging and Upon the Treatment of Nicotinamide Mononucleotide. Mol Cell Proteomics 2022, 21 (9), 100276.

· 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.

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