Research Articles

(注:& 共同第一作者; * 共同责任作者;影响因子为近三年平均值)

◆ Liang Su, Haitao Luo, Dechao Bu, Guoguang Zhao, Kuntao Yu, Changhai Zhang, Yuanning Liu, RunSheng Chen and Yi Zhao* Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts Nucleic Acids Research 2013, (Impact Factor: 8.278) PubMed | FullText | Software Download

◆ Haitao Luo, Silong Sun, Ping Li, Dechao Bu, Haiming Cao* and Yi Zhao* Comprehensive Characterization of 10,571 Mouse Large Intergenic Noncoding RNAs from Whole Transcriptome Sequencing. PLOS ONE 2013, (Impact Factor: 4) PubMed | FullText |

◆ ZHAO GuoGuang, JIAO Fei, LIAO Qi, LUO HaiTao, LI Hui, SUN Liang, BU DeChao, YU KunTao, ZHAO Yi*, CHEN RunSheng* Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines SCIENCE CHINA Life Sciences 2013, Vol. 56 Issue (6): 503-512 , PubMed | FullText |

◆ Xingli Guo Lin Gao, Qi Liao, Hui Xiao, Xiaoke Ma, Xiaofei Yang, Haitao Luo, Guoguang Zhao, Dechao Bu, Fei Jiao, Qixiang Shao, RunSheng Chen,* and Yi Zhao* Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks Nucleic Acids Research 2012, (Impact Factor: 8.278 SCI citation: 0) PubMed | FullText

◆ Qi Liao, Changning Liu, Xiongying Yuan, Shuli Kang, Ruoyu Miao, Hui Xiao, Guoguang Zhao, Haitao Luo , Dechao Bu, Haitao Zhao, Geir Skogerb, Zhongdao Wu* Yi Zhao* Large-scale prediction of long noncoding RNA functions in a coding-noncoding gene co-expression network Nucleic Acids Research (2011; Vol. 39, No. 9) (Impact Factor: 8.278; SCI citation: 25 ) PubMed | FullText

◆ Changning Liu*, Jin Li, Yi Zhao* Exploring Hierarchical and Overlapping Modular Structure in the Yeast Protein Interaction Network BMC Genomics 2010, 11(Suppl 4):S17 (Impact Factor:4.206; SCI citation: 2 ) PubMed | FullText

◆ Zhen Yang, Fei Ren, Changning Liu, Shunmin He, Gang Sun, Qian Gao, Lei Yao, Yangde Zhang, Ruoyu Miao, Ying Cao, Yi Zhao* Yang Zhong*, Haitao Zhao* dbDEMC: a database of differentially expressed miRNAs in human cancers BMC Genomics. 2010; 11(Suppl 4): S5. (Impact Factor:4.206; SCI citation: 6 ). PubMed | FullText

◆ Yuan xiongyin, Yang Pengchen, Shunmin He, Changning Liu*, Yi Zhao* Clustered microRNAs' coordination in regulating protein-protein interaction network BMC system biology 2009 Vol 3, pp65 (Impact Factor:3.535; SCI citation: 28) PubMed | FullText

◆ Lan Chen, Lun Cai, Geir Skogerbo, Yi Zhao*, Runsheng Chen* Assessing TF regulatory relationships of divergently transcribed genes Genomics Volume 92, Issue 5, November 2008 (Impact Factor:3.327; SCI citation:1) Pubmed | Fulltext

Yi Zhao&, Shunmin He&, Changning Liu&, Geir Skogerb*, and Runsheng Chen* microRNA regulation of messenger-like non-coding RNAs- a network of mutual microRNA control. Trends in Genetics. 2008 Jul;24(7):323-7. (Impact Factor:11.364; SCI citation:14 Featured Topic by Developmental Cell) Pubmed | Fulltext

◆ Shunmin He, Hua Su, Changning Liu, Dandan He, Geir Skogerb, Yi Zhao* and Runsheng Chen* MicroRNA-encoding long non-coding RNAs BMC Genomics 2008, 9:236 (Impact Factor:3.76; SCI citation:11) Pubmed | Fulltext

◆ Shiwei Sun&, Yi Zhao&, Yishan Jiao, Yifei Yin, Lun Cai, Yong Zhang, Hongchao Lu, Runsheng Chen, Dongbo Bu* Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm. FEBS letters, 580(2006) 1891-1896 (Impact Factor:3.601; SCI citation:14) Pubmed | Fulltext

◆ Bu D&, Yi Zhao&, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Research, 2003, Vol.31,No.9 2443-2450 (Impact Factor: 8.278; SCI citation:189) Pubmed | Fulltext


◆ Dechao Bu , Kuntao Yu, Silong Sun, Chaoyong Xie, Geir Skogerb, Ruoyu Miao, Hui Xiao, Qi Liao, Haitao Luo, Guoguang Zhao, Haitao Zhao, Zhiyong Liu, Changning Liu, Runsheng Chen* and Yi Zhao* NONCODE v3.0: Integrative annotation of long noncoding RNAs Nucleic Acids Research 2012, 40(D1): D210–D215. (Impact Factor: 8.278 SCI citation:26) PubMed | FullText | Website

◆ Shunmin He, Changning Liu, Baoyan Bai, Geir Skogerbo, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao* and Runsheng Chen*. NONCODE v2.0: decoding the non-coding. Nucleic Acids Research 2008 January; 36(Database issue): D170–D172. (Impact Factor: 8.278; SCI citation:52) Pubmed | Fulltext | Website

◆ Changning Liu, Baoyan Bai, Geir Skogerbo, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao* and Runsheng Chen*. NONCODE: An integrated knowledge database of noncoding RNAs Nucleic Acids Research. Jan 2005; 33: D112 - D115. (Impact Factor: 8.278; SCI citation:76) Pubmed | Fulltext | Website

◆ Wang xiaosong, Zhao Haitao, Changning Liu, Yifei Ying, Yi Zhao* WeiFeng Chen* HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. Nucleic Acids Research. 2006, Vol. 34:D607-D612 (Impact Factor: 8.278; SCI citation:4) Pubmed | Fulltext | Website

◆ Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerb, Lan Chen, Hongchao Lu, Dongbo Bu, Yi Zhao* Runsheng Chen* NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Research, 2006, Vol. 34:D1–D3 (Impact Factor: 8.278; SCI citation:21) Pubmed | Fulltext | Website

◆ Yin yifei&, Yi Zhao&, Runsheng Chen, Haitao Zhao* antiCODE: a natural sense-antisense transcripts database. BMC Bioinformatics 2007, 8:319 (Impact Factor:3.028; SCI citation:11) Pubmed | Fulltext | Website

Web server

◆ Qi Liao, Hui Xiao, Ruoyu Miao, Guoguang Zhao, Haitao Luo, Dechao Bu, Haitao Zhao, Changning Liu*, Yi Zhao* ncFANs: a web server for functional annotation of long non-coding RNAs Nucleic Acids Research 2011, 39 (suppl 2): W118-W124. (Impact Factor: 8.278 SCI citation: 3) PubMed | FullText


◆ He shunming, Yang Zhen, Haitao Zhao*,Runsheng Chen*,Yi Zhao* The properties and functions of virus encoded microRNA, siRNA and other small noncoding RNAs Critical Reviews in Microbiology Volume 34, Issue 3 & 4 August 2008 (Impact Factor:.5.345; SCI citation: 13) PubMed | FullText


◆ Ma J, Meng Y, Kwiatkowski DJ, Chen X, Peng H, Sun Q, Zha X, Wang F, Wang Y, Jing Y, Zhang S, Chen R, Wang L, Wu E, Cai G, Malinowska-Kolodziej I, Liao Q, Liu Y, Zhao Y, Sun Q, Xu K, Dai J, Han J, Wu L, Zhao RC, Shen H, Zhang H. Mammalian target of rapamycin regulates murine and human cell differentiation through STAT3/p63/Jagged/Notch cascade. J Clin Invest. 2010 Jan;120(1):103-14. doi: 10.1172/JCI37964. Pubmed | Fulltext

◆ Qi Liao, Xiongying Yuan, Hui Xiao, Changning Liu, Zhiyue Lv, Yi Zhao*, Zhongdao Wu* Identifying Schistosoma japonicum Excretory/Secretory Proteins and Their Interactions with Host Immune System PloS one. 01/2011; 6(8):e23786. PubMed | FullText

◆ Hongchao Lu, Baochen Shi, Gaowei Wu, Yong Zhang, Xiaopeng Zhu,ZhihuaZhang, Changning Liu, Yi Zhao, Tao Wu, Runsheng Chen. Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochemical and Biophysical Research Communications 345 (2006) 302–309 Pubmed | Fulltext

◆ Donna M. Muzny, Steven E. Scherer, Rajinder Kaul, Jing Wang, Jun Yu, list contributors, et. al. (List author) The DNA sequence, annotation and analysis of human chromosome 3. (2006) Nature 440, 1194-1198 Pubmed | Fulltext

◆ Yong Zhang, Shiwei Sun, Tao Wu, Jie Wang, Changning Liu,LanChen, Xiaopeng Zhu, Yi Zhao, Runsheng Chen. Identifying Hfq-binding small RNA targets in Escherichiaco li. Biochemical and Biophysical Research Communications 343 (2006) 950–955 Pubmed | Fulltext

◆ Wei Deng, XiaoPeng zhu, Geir Skogerbo, Yi Zhao, Lun Cai, Changning Liu, Jie Wang, Baoyan Bai, Runsheng Chen. Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Research 16:20-29, 2006 Pubmed | Fulltext

◆ Zhang Z, Sun H, Zhang Y, Zhao Yi, Shi B, Sun S, Lu H, Bu D, Ling L, Chen R. Genome-wide analysis of mammalian DNA segment fusion/fission. J Theor Biol. 2006 May 21;240(2):200-8. Pubmed | Fulltext

◆ Hongchao Lu, Xiaopeng Zhu, Haifeng Li, Geir Skogerbo, Jingfen Zhang, Yong Zhang, Lun Cai, Yi Zhao, Shiwei Sun, Jingyi Xu, Dongbo Bu and Runsheng Chen. The interactome as a tree—an attempt to visualize the rotein–protein interaction network in yeast. Nucleic Acids Research. 2004 Sep 08;32(16):4804-11.Pubmed | Fulltext

◆ Hongchao Lu, Yi Zhao, Jingfen Zhang, Yuelan Wang, Wei Li, Xiaopeng Zhu, Shiwei Sun, Jingyi Xu, Lunjiang Ling, Lun Cai, Dongbo Bu, and Runsheng Chen, Date of origin of the SARS coronavirus strains, BMC Infectious Diseases 2004, 4: Pubmed | Fulltext