2009年

1. Ying Liu, Bo Jiang, Xuegong Zhang. Gene set analysis identifies master transcription factors in developmental courses, Genomics 2009;94:1-10 (cover story) (SCI)
2. Yunfei Pei, Xuegong Zhang. MicroRNA-regulated pathways in the differentiation of histological grades of breast cancer. Chinese Science Bulletin (In Press) (SCI)
3. Tingting Li, Jian Huang, Ying Jiang, Yan Zeng, Fuchu He, Michael Q. Zhang, Zeguang Han, Xuegong Zhang. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development, Genomics 2009;93:235-242 (SCI)
4. Shicai Fan, Xuegong Zhang. CpG island methylation pattern in different human tissues and its correlation with gene expression. BBRC 2009;383:421-425 (SCI)
5. Yunfei Pei, Ting Zhang, Victor Renault, Xuegong Zhang. An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochimica et Biophysica Sinica 2009;41(1): 1-15 (SCI)
6. 凡时财,张学工.DNA甲基化的生物信息学研究进展.生物化学与生物物理进展.2009; 36(2):143-150 (SCI)
7. Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang, Introduction: the seventh Asia Pacific Bioinformatics Conference (APBC2009), BMC Bioinformatics, 10(Suppl 1): S1, 2009  (SCI)
8. R. Mitra, S. Bandyopadhyay, U. Maulik, M. Q. Zhang, SFSSClass: an integrated approach for miRNA based tumor classification, BMC Bioinformatics, 10(Suppl 1). (SCI)
9. Li Zhu, Wanwan Tang, Guisen Li, Jicheng Lv, Jiaxiang Ding, Lei Yu, Minghui Zhao, Yanda Li, Xuegong Zhang, Yan Shen, Hong Zhang, Haiyan Wang. Interaction between variants of two glycosyltransferase genes in IgA nephropathy. Kidney International 2009;76:190-198  (SCI)
10. Wanwan Tang, Xuebing Wu, Rui Jiang, Yanda Li. Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy. PLoS Genet 2009, 5(5):e1000464. (SCI)
11. Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution human core-promoter prediction with CoreBoost_HM. Genome Research 2009;19(2):266-75. (SCI)
12. Pufeng Du, Shengjiao Cao, Yanda Li. SubChlo: Predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm. Journal of Theoretical Biology 2009;261(2):330-335 (SCI)
13. Pufeng Du, Liyan Jia, Yanda Li. CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics 2009;10:135. (SCI)
14. Pufeng Du, Yanda Li. Computational analysis of RNA editing: seeking tiny discrepancies between transcriptome and genome. Frontiers of Electrical and Electronic Engineering in China 2009;4(3): 251-258.
15. Pufeng Du, Yang Chen, Yanda Li. Computational evidence of A-to-I RNA editing in nucleus transcriptome of Arabidopsis thaliana. Frontiers of Electrical and Electronic Engineering in China 2009;4(4):349-361
16. Tao Peng, Pufeng Du, Yanda Li. PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions. Bioinformation 2009;3(8): 349-351.
17. Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 2009, Accepted (SCI)
18. Rui Jiang, Ting Chen, Fengzhu Sun. Bayesian models and Gibbs sampling strategies for local graph alignment and motif finding in stochastic networks, Communications in Systems and Information (special issue for Michael Waterman's 67th birthday), 2009, Accepted
19. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies, BMC Bioinformatics 2009;10 (Suppl 1):S65 (SCI)
20. Xuebing Wu, Qifang Liu, Rui Jiang. Align human interactome with phenome to identify causative genes and networks underlying disease families, Bioinformatics 2009;25:98-104  (SCI)
21. Li Wang, Zhidong Tu, Fengzhu Sun. A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics 2009;10:220 (SCI)
22. Shao Li. Network systems underlying traditional Chinese medicine syndrome and herb formula. Current Bioinformatics 2009;4(3):188-196 (SCI)
23. Yezhou Huang, Shao Li. Detection of characteristic sub-pathway network for angiogenesis based on the comprehensive pathway network. BMC Bioinformatics 2010;11:S32 (SCI)
24. Lisha Li, Ningbo Zhang, Shao Li. Ranking effects of candidate drugs on biological process by integrating network analysis and Gene Ontology. Chinese Science Bulletin (In Press) (SCI)
25. Shao Li, Aiping Lu, Yongyan Wang. Symptomatic comparison in efficacy on patients with benign prostatic hyperplasia treated with two therapeutic approaches. Complementary Therapies in Medicine (In Press) (SCI)
26. Tao Ma, Conge Tan, Hui Zhang, Miqu Wang, Weijun Ding, Shao Li. Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network. Molecular BioSystems (In Press) (SCI)
27. 李梢.中医证候生物分子网络标志的构想与研究.中医杂志2009;50(9):773-776
28. 李梢,张宁波,李志红,丁皓,叶永安.慢性乙型肝炎患者肝胆湿热证和肝郁脾虚证的决策树诊断模型初探.中国中西医结合杂志 2009
29. 段天璇,马长华,王文全,阎永红,魏胜利,李梢. HPLC-MS法鉴定甘草的指纹图谱.中国药师.2009;12(4): 414-417

2008年发表论文

2007年发表论文

2006年发表论文

2005年及以前发表论文

会议

•Feng J, Jiang R, Jiang T, A max-flow based approach to the identification of protein complexes (extended abstract), Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB2008), in press, Stanford, California, USA, August 26-29, 2008
•Bao Y, Liu Y, Ma T, Lin Y, Li S, Identifying phenotype-dependent modules in signaling pathway. Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB2008), in press, Stanford, California, USA, August 26-29, 2008
•Bi J and Li Y, Investigation of the mechanism of alternative promoters influencing alternative splicing. Proceedings of the 2nd International Conference on Bioinformatics and Biomedical Engineering, Shanghai, China, May 16-18, 2008
•Fan S, Zhang MQ, Zhang X, Hypothesis on the mechanism why CpG islands are resistant to DNA methylation. 2008 Keystone Symposia Conference on Molecular Basis for Chromatin Modifications and Epigenetic Phenomena, Colorado, USA, April 2-12, 2008
•Fan S, Zhang MQ, Zhang X, Histone methylation marks play important roles in predicting the methylation status of CpG islands, Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC 2008), Kyoto, Japan, Jan. 14-17, 2008
•Jiang R and Zhang X, A comparative study of statistical learning methods in the prioritization of nonsynonymous single nucleotide polymorphisms, Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC 2008), Kyoto, Japan, Jan. 14-17, 2008

2007年及以前