1、Ruoyu Luo, Haibin Wei, Lin Ye, Kankan Wang, Fan Chen, Lijun Luo, Lei Liu, Yuanyuan Li, M. James C. Crabbe, Li Jin, Yixue Li and Yang Zhong. Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments:A systems biological analysis.  Proceedings of the National Academy of Sciences. 2009 January 20, 106(3):847-852

2、J. Jia，F. Zhu, X.H. Ma, Z.W. Cao, Y.X. Li and Y.Z. Chen，Mechanisms of drug combinations from interaction and network perspectives. Nature Rev. Drug Discov, 2009 Feb, 8:111

3、Yang, X., Xie, L., Li, Y., Wei, C. More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body, PLoS ONE, 2009 June，4(6): e6074.

4、Hao P, Zheng S, Ping J, Tu K, Gieger C, Wang-Sattler R, Zhong Y, Li Y. Human gene expression sensitivity according to large scale meta-analysis. BMC Bioinformatics, 2009,10(Suppl 1):S56

5、Hao P, Yu Y, Zhang X, Tu K, Fan H, Zhong Y. The contribution of cis-regulatory elements to head-to-head gene pairs’ co-expression pattern. Sci China C Life Sci., 2009 Jan,52(1):74-79

6、Hong Sun,Geir Skogerbø, Xiaohui Zheng, Wei Liu* and Yixue Li*. Genomic regions with distinct genomic distance conservation in vertebrate genomes. BMC Genomics, 2009, 10:133

7、Hui Yu, Fu-Dong Yu, Guo-Qing Zhang, Xiang Shen, Yun-Qin Chen, Yuan-Yuan Li* and Yi-Xue Li*. DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database, Vol. 2009, Article ID bap006, doi:10.1093/database/bap006

8、Kang Tu, Hui Yu, You-Jia Hua, Yuan-Yuan Li, Lei Liu, Lu Xie，Yi-Xue Li. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Research, 2009, 37(18): 5969-5980

9、YouJia Hua, ZhongYi Tang, Kang Tu, Li Zhu, YiXue Li, Lu Xie*, Hua-Sheng Xiao*. Identification and target prediction of miRNAs specifically expressed in rat neural tissue. BMC Genomics, 2009, 10:214.

10、Hong Li, Xiaobin Xing, Guohui Ding, Qingrun Li, Chuan Wang, Lu Xie, Rong Zeng, Yixue Li. SysPTM: a Systematic Resource for Proteomic Research of Post-translational Modifications. Molecular and Cellular Proteomics, 2009 Aug;8(8):1839-1849

11、Songling Li, Hong Li, Mingfa Li, Yu Shyr, Lu Xie, Yixue Li. Improved Prediction of Lysine Acetylation by Support Vector Machines. Protein and Peptide Letters, 2009, 16(8): 977-983

12、Hong Li, Guohui Ding, Lu Xie, Yixue Li. PAnnBuilder: An R Package for Assembling Proteomic Annotation Data. Bioinformatics, 2009 Apr 15;25(8):1094-1095

13、 Guangyong Zheng, Hong Li, Chuan Wang, Quanhu Sheng, Haiwei Fan, Shaoyou Yang, Boshu Liu,Jianliang Dai, Rong Zeng, Lu Xie. A Platform to Standardize, Store, and Visualize Proteomics Experimental Data. Acta Biochimica et Biophysica Sinica, 2009 Apr, 41(4):273-279

14、咎启杰，任竹梅，李后魂，李罡，王勇军，王莉，钟扬*. 用mtDNA COII基因序列确定我国北部湾红树植物白骨壤虫灾虫源. 自然科学进展, 2009年2月,19卷2期:1380-1385