He mainly engages in the research of proteome bioinformatics and biological big data. Now he is the chief expert of 863 key project. He developed systems for quality control of large scale proteome data and data integration. Analysis strategies were established for the liver proteome study. The availability of high confident identifications from mass spectra was improved by 20% ~ 40%. He also developed the live proteome database family. In the study of biological networks, a novel network feature to evaluate the importance of proteins in signal transduction networks was advanced. With the prediction of signal flow direction in protein interaction networks, large amount of potential signal pathways could be inferred. He led the project “Study of proteomic informatics and the development and application of supporting platform”, and won the 1st class awards for electronics information science and technology (China Institute of Electronics，KJ2012-1-07-R01), which is the only one of class 1st award from the bioinformatics field since its inauguration in 2003.
1. Chang C, Zhang J, Han M, Ma J, Zhang W, Wu S, Liu K, Xie H, He F, Zhu Y. SILVER: An efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. Bioinformatics, 2014 Feb 15; 30(4):586-7.
2. Chang C, Li L, Zhang C, Wu S, Guo K, Zi J, Chen Z, Jiang J, Ma J, Yu Q, Fan F, Qin P, Han M, Su N, Chen T, Wang K, Zhai L, Zhang T, Ying W, Xu Z, Zhang Y, Liu Y, Liu X, Zhong F, Shen H, Wang Q, Hou G, Zhao H, Li G, Liu S, Gu W, Wang G, Wang T, Zhang G, Qian X, Li N, He QY, Lin L, Yang P, Zhu Y, He F, Xu P. Systematic analysis of transcriptome, translatome and proteome provides a global view and potential strategy for C-HPP study. J Proteome Res, 2014 Jan 3; 13(1):38-49.
3. Zhang J#, Ma J#, Zhang W, Xu C, Zhu Y*, Xie H*. FTDR 2.0: A Tool To Achieve Sub-ppm Level Recalibrated Accuracy In Routine LC-MS Analysis. J Proteome Res. 2013 Sep 6;12(9):3857-64
4. Zhang Y, Yang C, Wang S, Chen T, Li M, Wang X, Li D, Wang K, Ma J, Wu S, Zhang X, Zhu Y, Wu J, He F. LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease. Liver Int. 2013, [Epub ahead of print]
5. Li N, Wu S, Zhang C, Chang C, Zhang J, Ma J, Li L, Qian X, Xu P, Zhu Y, He F. PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics. Proteomics. 2012,12(11): 1720-5.
6. Zhang Y, Wang S, Li D, Zhang J, Gu D, Zhu Y, He FC. A Systems Biology-Based Classifier for Hepatocellular Carcinoma Diagnosis. PLOS One. 2011,6(7): e22426
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 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, 8(9):2063-70
9. 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. 2009,8:547-57
10. 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