1. Endoglycosidase-Mediated Incorporation of (18)O into Glycans for Relative Glycan Quantitation，Zhang, W (Zhang, Wei); Wang, H (Wang, Hong); Tang, HL (Tang, Hailin); Yang, PY *(Yang, Pengyuan). Anal Chem. 2011;83(12): 4975-81.
2. H Wang#, H Li#, W Zhang, LM Wei1, HX Yu*, and PY Yang*. Multiplex Profiling of Glycoproteins Using a Novel Bead-based Lectin Array. Proteomics. 2013; 14:78-86. 
3. HX Yu#, J Zhao#, L Lin, Y Zhang, F Zhong, YK Liu, YY Yu, HL Shen, MM Han, FC He*, PY Yang*. Proteomic study explores AGR2 as pro-metastatic protein in HCC. Molecular BioSystems. 2012; 8(10):2710-8. 
4. H Wang#, W Zhang, J Zhao, L Zhang, MQ Liu, GQ Y, J Yao, HX Yu*, and PY Yang*. N-Glycosylation Pattern of Recombinant Human CD82 (KAI1), a Tumor-Associated Membrane Protein. Journal of Proteomics.2012;75(4):1375-85. 
5. J Zhao#, HX Yu#, F Zhong, Lin L, Jun T, LL Cai, YM Chen, F Zhong, CZ Lin, FC He*, PY Yang*. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF). Journal of Proteomics.2011;75(2):588-602.
6. YY Yu#, HL Shen#, HX Yu#, F Zhong, Y Zhang,C Zhang, J Zhao, H Li, J Chen, YK Liu* and PY Yang*. Systematic proteomic analysis of human hepotacellular carcinoma cells reveals molecular pathways and networks involved in metastasis. Molecular BioSystems.2011; 7, 1908–16. 
7. Yanyan Yu, Xiuwen Pan, Ying Ding, Xiaohui Liu, Hailin Tang, Chengpin Shen, Huali Shen* and Pengyuan Yang*. An iTRAQ based quantitative proteomic strategy to explore novel secreted proteins in metastatic hepatocellular carcinoma cell lines. Analyst.2013;Advance Article, DOI: 10.1039/C3AN00517H
8. Chengpin Shen, Yanyan Yu, Hong Li, Guoquan Yan, Mingqi Liu, Huali Shen*, Pengyuan Yang*. Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network. Proteomics. 2012; 12(12):1917-27.
9. Marina Kniazeva, Huali Shen, Tetyana Euler, Chen Wang, and Min Han. Regulation of maternal phospholipid composition and IP3-dependent embryonic membrane dynamics by a specific fatty acid metabolic event in C. elegans. Genes Dev. 2012;15, 26: 554-66.
10. Yanyan Yu, Mingqi Liu, Huali Shen*, Pengyuan Yang*, et. al. Hydrazide-functionalized Magnetic Microspheres for the Selective Enrichment of Digested Tryptophan-containing Peptides in Serum. Talanta. 2011; 85(2):1001–6 
11. Ying Zhang,WanFu Ma, Cheng Zhang, ChangChun Wang,* HaoJie Lu* Magnetic mesoporoustitania composite microspheres endowed with a size-exclusive effect towards the highly specific revelation of phosphopeptidome ACS. Appl Mater & Inter. 2014;6,6290-9.
12. Ying Zhang, Min Kuang, Lijuan Zhang, Haojie Lu*, Pengyuan Yang An accessible protocol for solid-phase extraction of N-linked glycopeptides through reductive amination by amine-functionalized magnetic nanoparticles Anal Chem. 2013; 85, 5535–41. 
13. Jing Jiao, Aizhu Miao, Xinyan Zhang, Yan Cai, Yi Lu, Ying Zhang* and Haojie Lu* Realization of on-tissue protein identification by highly efficient in-situ digestion with graphene-immobilized trypsin for MALDI Imaging analysis. Analyst.2013; 138, 1645-8. 
14. Yan Cai, Ying Zhang*, Pengyuan Yang and Haojie Lu* Improved analysis of oligosaccharides for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using aminopyrazine as derivatization reagent and co-matrix. Analyst.2013;138:6270-6.
15. Ying Zhang, Huijie Wang，Haojie Lu Sequential selective enrichment of phosphopeptides and glycopeptides using amine-functionalized magnetic nanoparticles MolBiosyst，2013，9:492-500 
16. Wanfu Ma, Ying Zhang, Lulu Li, Yuting Zhang, Meng Yu, JiaGuo, Haojie Lu*,Changchun Wang* Ti4+-immobilized magnetic composite microspheres for highly selective enrichment of phosphopeptides Adv. Func. Mat., 2013, 23, 107unc.s silica Anal. Chim. Acta. 2012;753: 64-72. 
17. WanfuMa,Ying Zhang, Lulu Li, Lijun You, Peng Zhang, Yuting Zhang, Jumei Li, Meng Yu, JiaGuo, Haojie Lu*, Changchun Wang* Tailor-made magnetic Fe3O4@mTiO2 microspheres with a tunable mesoporousanatase shell for highly selective and effective enrichment of phosphopeptides ACS Nano. 2012; 6: 3179o 201.
18. Hui Wang, Weide Zhang, Qiang Zeng, Zuofeng Li, ,Kaiyan Feng, Lei Liu*, Extracting important information from Chinese Operation Notes with natural language processing methods, Journal of Biomedical Informatics.(Received 4 January 2013; accepted 13 December 2013. published online 19 February 2014). 
19. Juanjuan Xiao, Ying Wang, Zuofeng Li; Xufeng Zhang, Kaiyan Feng, Lei Liu*, Assessing the Gender Differences of Adverse Effects in HIV Infection Treatment Based on FDA AERS Database. Current Bioinformatics. 2013;5(8):583-590(8).
20. Bi-Qing Li, Hui Yu, Zheng Wang, Guohui Ding, Lei Liu*, MicroRNA mediated network and DNA Methylation in Colorectal Cancer. Protein Peptide Letter. 2013;3(20):1-12
21. Rudong Li and Lei Liu*. Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example. BMC Systems Biology. 2012;S11.
22. Bi-Qing Li, Tao Huang, Lei Liu*, Yu-Dong Cai*, Kuo-Chen Chou. Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network. PLoS One.2012;7(4):e33393
23. Zuofeng Li, Xingnan Liu, Jingran Wen, Ye Xu, Xin Zhao, Xuan Li, Lei Liu,*, and Xiaoyan Zhang*  DRUMS: A Human Disease Related Unique Gene Mutation Search Engine. HUMAN MUTATION. 2011;32:E2259-E2265 
24. Rudong Li, Yuanyuan Li, Ling-Yi Lu, Cong Ren, Yi-Xue Li, Lei Liu*. An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis. BMC Systems Biology. 2011; 5(Suppl.): S12.
25. Lele Hu, Lulu Zheng, Zhiwen Wang, Bing Li, Lei Liu*. Using Pseudo Amino Acid Composition to Predict Protease Families by Incorporating a Series of Protein Biological Features. Protein & Peptide Letters. 2011;18(6):552-558.
26. Peng Jia, Liming Xuan, Lei Liu*,Chaochun Wei*. MetaBinG: Using GPUs to accelerate metagenomic sequence classification. PLoS One. 2011;6(11):e25353. 
27. The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma, Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Yejun Tan, ZhidongTu, Yixue Li, Hongyue Dai.*, Lu Xie,* International Journal of Computational Biology and Drug Design. Inderscience.2011; 4(1), pp 5-17.
28. Cui SJ, Xu LL, Zhang T, Xu M, Yao J, Fang CY, Feng Z, Yang PY, Hu W, Liu F*. Proteomic characterization of larval and adult developmental stages in Echinococcusgranulosus reveals novel insight into host-parasite interactions. J Proteomics. 2013;12,84:158-75.
29. The Schistosomajaponicum Genome Sequencing and Functional Analysis Consortium, Liu F, Zhou Y, Wang ZQ, Lu G, Zheng H, Brindley PJ, McManus DP, Blair D, Zhang QH, Zhong Y, Wang S, Han ZG, Chen Z. The Schistosomajaponicum genome reveals features of host-parasite interplay. Nature. 2009; 460, 345-51.
30. Yan HB, Wang XF, Zhang Q, Tang ZQ, Jiang YH, Fan HZ, Sun YH, Yang PY, Liu F*. Reduced expression of the chromatin remodelling gene ARID1A enhances gastric cancer cell migration and invasion via downregulation of E-cadherin transcription. Carcinogenesis. 2014 ;35(4):867-76
31. Feng Liu, Shu-Jian Cui, Wei Hu, Zheng Feng, Zhi-Qin Wang, Ze-Guang Han. Excretory/secretory proteome of adult developmentage stage of the human blood fluke, Schistosomajaponicum. Mol Cell Proteomics. 2009;8(6): 1236-51.
32. Wang Q, Wen B, Yan G, Wei J, Xie L, Xu S, Jiang D, Wang T, Lin L, Zi J, Zhang J, Zhou R, Zhao H, Ren Z, Qu N, Lou X, Sun H, Du C, Chen C, Zhang S, Tan F, Xian Y, Gao Z, He M, Chen L, Zhao X, Xu P, Zhu Y, Yin X, Shen H, Zhang Y, Jiang J, Zhang C, Li L, Chang C, Ma J, Yan G, Yao J, Lu H, Ying W*, Zhong F*, He QY*, Liu S*. Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines. J Proteome Res. 2013; 4,12(1):151-161.
33. Zhang Y, Yan G, Zhai L, Xu S, Shen H, Yao J, Wu F, Xie L, Tang H, Yu H, Liu M, Yang P, Xu P, Zhang C, Li L, Chang C, Li N, Wu S, Zhu Y, Wang Q, Wen B, Lin L, Wang Y, Zheng G, Zhou L, Lu H*, Liu S*, He F*, Zhong F*. Proteome atlas of human chromosome 8 and its multiple 8p deficiencies in tumorigenesis of the stomach, colon, and liver. J Proteome Res. 2013;4,12(1):81-88.
34. Zhong F, Yang D, Hao Y, Lin C, Jiang Y, Ying W, Wu S, Zhu Y, Liu S, Yang P, Qian X, He F*. Regular patterns for proteome-wide distribution of protein abundance across species. PLoS One. 2012; 9,7(3):e32423.
35. Hu, L.#, Li, Z. #, Cheng, J. #, Rao, Q., Gong, W., Liu, M., Shi, YG., Zhu, J., Wang, P. and Xu, Y. * Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation. Cell.2013; 155, 1545-55.
36. Liu, W., Wen, W., Wei, Z., Yu, J., Ye, F., Liu, C.-H., Hardie, R.C., and Zhang, M. The INAD scaffold is a dynamic, redox-regulated modulator of signaling in the Drosophila eye. Cell. 2011;145, 1088-101. (Cover article)
37. Zhu, J., Wen, W., Zheng, Z., Shang, Y., Wei, Z., Xiao, Z., Pan, Z., Du, Q., Wang, W., and Zhang, M. LGN/mInsc and LGN/NuMA complex structures suggest distinct functions in asymmetric cell division for the Par3/mInsc/LGN and Gi/LGN/NuMA pathways. Mol. Cell. 2011;43, 418-31.
38. Fang, R. #, Chen, F. #, Dong, Z., Hu, D., Barbera, A. J., Clark, E. A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M. D., Zhou, Q., Li, J., Marynick, M. P., Li, X., Lu, H., Kaiser, U. B., Kingston, R. E., Xu, Y.*, and Shi, Y. G.* LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell.2013;49, 558-70.
39. Wen, W., Yu, J., Pan, L., Wei, Z., Weng, J., Wang, W., Ong, Y.S., Hoai, T.T.T., Hong, W., and Zhang, M. Lipid-induced conformational switch controls fusion activity of longin domain SNARE Ykt6. Mol. Cell. 2010;37, 383-95.
40. Gong, R. #, Li, L. #, Liu, Y. #, Wang, P., Yang, H., Wang, L., Cheng, J., Guan, K. L., and Xu, Y.* Crystal structure of the Gtr1p-Gtr2p complex reveals new insights into the amino acid-induced TORC1 activation. Genes &Development. 2011;25, 1668-73.
41. Li, Z. #, Zhao, B. #, Wang, P., Chen, F., Dong, Z., Yang, H., Guan, K. L.*, and Xu, Y.* Structural insights into the YAP and TEAD complex. Genes &Development.2010;24, 235-40.
42. Chen, F. #, Yang, H. #, Dong, Z. #, Fang, J., Wang, P., Zhu, T., Gong, W., Fang, R., Shi, Y. G., Li, Z.*, and Xu, Y.* Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell research. 2013;23, 306-9.
43. Cheng, J., Yang, Y., Fang, J., Xiao, J., Zhu, T., Chen, F., Wang, P., Li, Z., Yang, H., and Xu, Y.*Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. The Journal of biological chemistry. 2013;288, 1329-39.
44. Ma, H. #, Chen, H. #, Guo, X. #, Wang, Z., Sowa, M. E., Zheng, L., Hu, S., Zeng, P., Guo, R., Diao, J., Lan, F., Harper, J. W., Shi, Y. G., Xu, Y.*, and Shi, Y.* M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stabilit.PNAS.2012;109, 4828-33.
45. Yang, Y. #, Hu, L. #, Wang, P. #, Hou, H., Lin, Y., Liu, Y., Li, Z., Gong, R., Feng, X., Zhou, L., Zhang, W., Dong, Y., Yang, H., Lin, H., Wang, Y., Chen, C. D.*, and Xu, Y.* Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell research. 2010;20, 886-98.
46. Hu, L. #, Li, Z. #, Wang, P., Lin, Y., and Xu, Y.*Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2.Cell research. 2011;21(9):1374-8.
47. Wang, W., Weng, J., Zhang, X., Liu, M., and Zhang, M. Creating Conformational Entropy by Increasing Interdomain Mobility in Ligand Binding Regulation: A Revisit to N-Terminal Tandem PDZ Domains of PSD-95. J. Am. Chem. Soc. 2009;131,787-96.
48. Ma, W., Shang, Y., Wei, Z., Wen, W., Wang, W., and Zhang, M. Phosphorylation of DCC by ERK2 is facilitated by direct docking of the receptor P1 domain to the kinase. Structure.2010;1502-11.
49. Huo, L., Wen, W., Wang, R., Kam, C., Xia, J., Feng, W., and Zhang, M. Cdc42-dependent formation of the ZO-1/MRCKβ complex at the leading edge controls cell migration. EMBO J. 2011;30, 665-78.
50. Zhu, J., Shang, Y., Xia, C., Wang, W., Wen, W., and Zhang, M. Guanylate Kinase Domains of the MAGUK Family Scaffold Proteins as Specific Phospho-protein-binding Modules. EMBO J. 2011;30, 4986-97.
51. Jia, M., Li, J., Zhu, J., Wen, W., Zhang, M., and Wang, W. Crystal structures of the scaffolding protein LGN reveal the general mechanism by which GoLoco binding motifs inhibit the release of GDP from Gi. J. Biol. Chem. 2012; 287, 36766-76.
52. Weng, J., Fan, K. and Wang, W.* The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations. J. Biol. Chem. 2010;285, 3053-63.
53. Zhang W*, Dunkle J, Cate J. Structures of the ribosome in intermediate states of ratcheting. Science.2009;325,1014. 
54. Xu, Y. *, Yang, H. *, Joo, HY. *, Yu JH, Smith AD IV, Schneider D, Chow LT, Renfrow M, Wang H#. Ubp-M serine 552 phosphorylation by cyclin-dependent kinase 1 regulates cell cycle progression. Cell Cycle. 2013; 12(19):3219-27.