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1. Ma J, Zhang J, Wu S, Li D, Zhu Y, He F. Combination of new features improves peptide identification by Mascot in shotgun proteomics. (Proteomics, accepted)

2. Liu W, Li D, Liu Q, Zhu Y, He F. A novel parametric approach to mine gene regulatory relationship from microarray datasets. (BMC Bioinformatics, accepted) (IF 3.7817)

3. Wu X, Wu S, Li D, Zhang J, Hou L, Ma J, Liu W, Ren D*, Zhu Y*, He F*. Computational identification of rare codons of Escherichia coli based on codon pairs preference. BMC Bioinformatics. 2010 Jan 28;11(1):61 (IF 3.7817)

4. Chinese Human Liver Proteome Profiling Consortium. First insight into human liver proteome from PROTEOMESKY- LIVERHu 1.0, a publicly-available database. J Proteome Res. 2010 Jan;9(1):79-94 (IF 5.675)

5. Sun A, Jiang Y, Wang X, Liu Q, Zhong F, He Q, Guan W, Li H, Sun Y, Shi L, Yu H, Yang D, Xu Y, Song Y, Tong W, Li D, Lin C, Hao Y, Geng C, Yun D, Zhang X, Yuan X, Chen P, Zhu Y, Li Y, Liang S, Zhao X, Liu S, He F. Liverbase: a comprehensive view of human liver biology. J Proteome Res 2010, 9 (1): 50-8 (IF 5.675)

6. 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 peptide identification and its effects on quantitative proteomics. Anal Chem. 2009

7. 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. 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 (IF 5.675)

9. Liu W, Li D, Wang J, Xie H, Zhu Y, He F. Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. Mol Cell Proteomics. 2009

10. 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

11. Suresh Mathivanan, et al. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology 2008; 26(2):164-7 (IF 22.848)

12. Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X. Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy. Proteomics 2008, 8(10): 2024

13. 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

14. Li D, Li J, Ouyang S, Wang J, Wu S, Wan P, Zhu Y, Xu X, He F. Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness. Proteomics. 2006

15. Liu W, Li D, Zhang J, Zhu Y, He F. SigFlux: a novel network feature to evaluate the importance of proteins in signal transduction networks. BMC Bioinformatics. 2006

16. Wu S, Wan P, Li J, Li D, Zhu Y, He F. Multi-modality of pI distribution in whole proteome. Proteomics. 2006

17. Xue X, Wu S, Wang Z, Zhu Y, He F. Protein probabilities in shotgun proteomics: evaluating different estimation methods using a semi-random sampling model. Proteomics. 2006


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