You-Jia Hua, Zhong-Yi Tang, Kang Tu, Li Zhu1, Yi-Xue Li, Lu Xie* and Hua-Sheng Xiao*. Identification and target prediction of miRNAs specifically expressed in rat neural tissue. BMC Genomics. 2009, 10: 214 doi:10.1186/1471-2164-10-214

Hong Li, Xiaobin Xing, Guohui Ding, Qingrun Li, Chuan Wang, Lu Xie, Rong Zeng*, Yixue Li*，SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications, MCP Papers in Press. Published on April 14, 2009.

Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li*, and Hans-Juergen Thiesen*, SysZNF: the C2H2 Zinc Finger Gene database, Nucleic Acids Research. 2009 37:D267-D273.

Ruo-Yu Luo, Hai-Bin Wei, Lin Ye, Kankan Wang, Lei Liu, Yuan-Yuan Li, Yi-Xue Li* and Yang Zhong*,Photosynthetic metabolism of C3 plants shows highly cooperative regulation to maintain function under changing environmental conditions: a systems biological analysis of robustness, PNAS. 2009, vol. 106 no. 3 847-852.

Hong Li, Guohui Ding, Lu Xie* and Yixue Li*, PAnnBuilder: an R package for assembling proteomic annotation data, Bioinformatics , 2009 25(8):1094-1095.

Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li *, CHSMiner: a  GUI tool to identify chromosomal homologous segments. Algorithms Mol. Biol. 4(1):2.

Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li*，Human gene expression sensitivity according to large scale meta-analysis，BMC Bioinformatics. 2009, 10(Suppl 1):S56.

Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee and Yixue Li*, SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry, Nucleic Acids Research. 2009 37:D913-D920.