主要论文：

1. Zhang J, Li J, Xie H, Zhu Y, He F. A New Strategy to Filter out False Positive Identifications of Peptides in SEQUEST Database Search Results. Proteomics, 2007; 7(22):4036-4044.

2. Zhang J, Li J, Liu X, Xie H, Zhu Y, He F. A nonparametric model for quality control of database search results in shotgun proteomics. BMC Bioinformatics. 2008;9:29.

3. Zhang J, Ma J, Dou L, Wu S, Qian X, Xie H, Zhu Y, He F. Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics. Mol Cell Proteomics. 2009;8(3):547-57.

4. Zhang J, Ma J, Dou L, Wu S, Qian X, Xie H, Zhu Y, He F. Mass Measurement Errors of Fourier-Transform Mass Spectrometry (FTMS): Distribution, Recalibration, and Application. J. Proteome Res. 2009; 8 (2), 849–859.

5. Liu K, Zhang J, Wang J, Zhao L, Peng X, Jia W, Ying W, Zhu Y, Xie H, He F, Qian X. Relationship between Sample Loading Amount and Peptides Identification and Its Effect on Quantitative Proteomics. Anal Chem. 2009;81(4):1307-14.（共同第一作者）

6. Sun A, Zhang J, Wang C, Yang D, Wei H, Zhu Y, Jiang Y, He F. Modified spectral count index (mSCI) for estimation of protein abundance by protein relative identification possibility (RIPpro): a new proteomic technological parameter. J Proteome Res. 2009;8(11):4934-42.

7. Ma J, Zhang J, Wu S, Li D, Zhu Y, He F. Improving the sensitivity of MASCOT search results validation by combining new features with Bayesian nonparametric model. Proteomics. 2010;10(23):4293-300.

8. Liu X, Zhang J, Zheng Z, Yang X, Jia W, Li L, Gong Y, Cai Y, Zhu Y, He F, Ying W, Qian X. A systematic N-terminal peptide quantitative labeling strategy for differential proteomic analysis. Proteomics Clin Appl. 2010;4(6-7):633-43.(共同第一作者)