姓 名：曹志伟学 位：博士导师情况：博士生导师研究领域：生物信息学，计算生物学研究方向：中药信息学，抗体信息学，功能基因组学个人简介： 曹志伟，女，中共党员，博士，本科毕业于南开大学，硕士毕业于南京大学，博士毕业于新加坡国立大学。同济大学生命科学与技术学院教授，兼上海生物信息技术研究中心功能基因课题组组长。上海市生物信息学会理事，中国青年科协会员. 目前已承担了科研项目共15项，包括国家“973”项目2项，863 项目1 项，自然基金项目2项，传染病重大专项1项， 国际合作项目1项，以及上海市重大项目等。先后获得上海市科技启明星, 浦江人才计划，曙光学者，和教育部新世纪优秀人才资助，获得上海市新长征突击手表彰， 2008上海市自然科学二等奖，2012年上海育才奖。 在国内外学术刊物和国际会议上共发表论文100余篇，其中以第一作者或通讯作者发表在国外学术期刊56篇，论文被SCI引用1000余次。建成生物大分子模拟软件2个，中药机理特色数据库5个，已发表重要论文Pharmacological Reviews (IF>22.8), PNAS (IF>10)，Molecular Cell Proteomics (IF>9.9), Nucleic acids research (IF>7.5), Clinical Pharmacology & Therapeutics (IF>7.5)，Briefings in Bioinformatics (IF>5.5)，Drug Discovery Today (IF>7.1)，Plos one (IF>4.0)，Journal of Chemical Information and Modeling (IF>4.0)，BMC bioinformatics(IF>3.0) 等。 成员（包括研究生）：教师3名，博士后2名，博士生6名，硕士生7名。开设教学课程： 生物信息学概论，计算机辅助药物设计，基因组信息学，免疫信息学 (研究生)目前进行课题：973： 基于生物信息学的抗原抗体分子识别与系统模拟科技部新药创制：病毒性肝炎证候生物学基础研究平台的建立科技部攻关计划：人肝脏蛋白质组生物信息学研究教育部新世纪创新人才项目自然科学基金面上项目（流感病毒蛋白突变预测方面，2011-2015）上海市教委: 科研创新项目与曙光学者项目等已完成课题：973：抗体结构功能的生物信息学研究863：中药作用机理的生物信息学分析策略与相应系统构建863：人肝脏蛋白质组生物信息学研究自然基金面上： IgG抗体成熟模式的生物信息学研究主要研究方向包括中药/植药信息学，免疫信息学等: 在中药/植药信息学方面，紧扣中医药现代化特色, 率先把计算机辅助药物设计方法引入中药机理研究，先后建成了4大系列独特的数据库（中药成分及含量数据库、中药活性成分靶点数据库、中药活性成分体内代谢数据库和蛋白和疾病关系数据库），利用计算生物学模拟配对，研制了一整套的“多成分、多靶点”的中药机理预测模拟系统，国内外中药专家也对该中药机理模拟系统给予了很高的评价. 该平台已经为上海中药现代化研究中心，上海中医药大学，第二军医大学药学院，中科院药物所，上海芯片中心，曙光医院等数家中医药研发中心的几十个中药单体和多味简单复方做了计算分析，获得上海市科委及863项目资助。 在免疫信息学方面，围绕抗体抗原分子识别的关键问题，发展大量计算方法，研究抗体抗原识别规律，并建立了相应的计算平台，提供网上免费服务。其中蛋白抗原空间表位预测方法SEPPA （SEPPA1 and SEPPA2 http://lifecenter.sgst.cn/seppa/ ）的预测精度在国际同类工具中名列前茅，被收录到全球网络计算资源专刊这个方向得到了973项目和国家自然基金面上项目的持续支持。近年代表文章：1. Z.W. Cao, Y. Xue, L.Y. Han, B. Xie, H. Zhou, C.J. Zheng, H.H. Lin and Y. Z. Chen, MoViES: Molecular Vibrations Evaluation Server for Analysis of Fluctuational Dynamics of Proteins and Nucleic Acids. Nucleic Acids Research. 32,W679-W685. (2004).2. Z. W. Cao, L. Y. Han, C. J. Zheng, Z. L. Ji, X. Chen, H. H. Lin and Y. Z. Chen Computer prediction of drug resistance mutations in proteins. Drug Discovery Today 2005:10(7):521-529.3. J. F. Wang, H. Zhou, L. Y. Han, X. Chen, Y. Z. Chen, and Z.W. Cao TCM-ID: Traditional Chinese Medicine information database. Clinical Pharmacology and Therapeutics. 2005 78(1):92-93.4. C.J. Zheng, L.Y. Han, C. W. Yap, Z. L. Ji, Z. W. Cao and Y. Z. Chen. Therapeutic Targets: Progress of Their Exploration and Investigation of Their Characteristics. Pharmacological Reviews 58:259-279(2006).5. Wei W, Cao ZW, Zhu YL, Wang X, Ding G, Xu H, Jia P, Qu D, Danchin A, Li Y. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics. 2006 May 10;7:112. （Co-First Author）6. Zhao J, Yu H, Luo JH, Cao ZW, Li YX. Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics. 2006 Aug 18;7:386. (Co-corresponding author）7. Serene AK Ong, Hong Huang Lin, Yu Zong Chen, Ze Rong Li and ZhiWei Cao Efficacy of different protein descriptors in predicting protein functional families, BMC Bioinformatics 2007，8:300.8. Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, ZW Cao and Yi-Xue Li, （Co-corresponding author） Modular co-evolution of metabolic networks. BMC Bioinformatics 2007, 8:311.9. Qing-Xi Yue, Zhi-Wei Cao, Shu-Hong Guan, Lin Tao, Wan-Ying Wu, Yi-Xue Li, Xuan Liu, De-An Guo, Proteomic characterization of the cytotoxic mechanism of ganoderic acid D and computer automated estimation of the possible drug-target network, Molecular Cell Proteomics, 2008, Vol 7 No 5, 949-961Dec 31 (Co-First Author).10. Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Y.X. Li, Z.W. Cao, Ab-origin: An enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies, BMC Bioinformatics 2008, 9(Suppl 12):S20.11. 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. Nat. Rev. Drug Discov., 2009 Feb;8(2):111-28.12. Sun J, Wu D, Xu T, Wang X, Xu X, Tao L, Li YX, Cao ZW. SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W612-6. Epub 2009 May 22.13. Wu Di, Xu TianLei, Sun Jing, … Li YiXue & Cao ZhiWei, Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus Chinese Sci Bull, 2009, 54, 2171-2173. (cover paper)14. Zhao Jing; .. He Fuchu, Li Yixue & Cao Zhiwei, Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data Journal of Proteome Research,2010, 9 (4), pp 1648–1658.15. Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li and Zhiwei Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research. 2010, 1-5.16. Huang Qi, Kang Hong, Duanfeng Zhang, Sheng, Zhen, Liu Qi, Ruixin Zhu, Cao Zhiwei, Comparison of Ligand-, Target Structure-, and Protein-Ligand Interaction Fingerprint-base Virtual Screening Methods, ACTA CHIMICA SINICA,2011,69(5),515-522.17. Sheng,Zhen Huang,Qi Kang,Hong Liu,Qi Cao,Zhiwei, Zhu,Ruixin, A New Fingerprint of Chemical Compounds and Its Application to Drugs Virtual Screening，Acta Chimica Sinica, 2011,69(16),1845-1850.18. Chao Ma, Hong Kang, Qi Liu, Ruixin Zhu, Zhiwei Cao, Insight into potential toxicity mechanisms of melamine: an in silico study, Toxicology, 2011, Volume 283, Issues 2-3, 96-100.19. Ruixin Zhu, Liwei Hu, Haiyun Li, Juan Su, Zhiwei Cao, Weidong Zhang ,Novel natural inhibitors of CYP1A2 identified by in silico and in vitro screening, Int. J. Mol. Sci., 2011, 12(5), 3250-3262.20. Kailin Tang,Ruixin Zhu,Yixue Li and Zhiwei Cao, Discrimination of Approved Drugs from Experimental Drugs by Learning Methods, BMC Bioinformatics 2011, 12:157.21. Ruixin Zhu, Qi Liu, Jian Tang, Huiliang and Zhiwei Cao, Investigations on Inhibitors of Hedgehog Signal Pathway: A QSAR Study, Int. J. Mol. Sci., 12, 3018-3033, 2011.22. Gao Jun, Zhu Ruixin Liu, Qi Liu, Cao Zhiwei, Petri Net based Metabolic Network Parameters Fitting with GPU Acceleration, Chin. J. Chem., 2011, 29(9),1805-1810.23. Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu and Zhiwei Cao, Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors An In-silico Study, BMC Bioinformatics, 2011 12:294.24. Liu, Qi; Che, Dongsheng; Huang, Qi; Cao, Zhiwei; Zhu, Ruixin, Multi-target QSAR Study in the Analysis and Design of HIV-1 Inhibitors, Chin. J. Chem., 2010, 28 1587-1592.25. Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu, A New Protein-Ligand Binding Sites Prediction Method by integrating Sequence Conservation of Protein, BMC Bioinformatics, 12 Suppl 14,2011.26. Jing Sun, Tianlei Xu, Shuning Wang, Guoqing Li, Di Wu, Zhiwei Cao, Does difference exist between epitope and non-epitope residues? Analysis of the physicochemical and structural properties on conformational epitopes from B-cell protein antigens. Immune Research, Vol 7,3,2011. 1-11.28. Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu, Screening of selective histone deacetylase inhibitors by proteochemometric modeling, BMC Bioinformatics, 2012, 13:212.29. Qi Huang, Haixiao Jin, Qi Liu, Qiong Wu, Hong Kang, Zhiwei Cao, Ruixin Zhu, Proteochemometric Modeling of the Bioactivity Spectra of HIV-1 Protease Inhibitors by Introducing Protein-Ligand Interaction Fingerprint, Plos one,7(7): e41698. doi:10.1371/journal.pone.0041698,2012.30. Qi Liu, Han Zhou, Juan Cui, Zhiwei Cao and Ying Xu, Reconsideration of In-silico siRNA Design Based on Feature Selection: A Cross-platform Data Integration Perspective, Plos one, 7(5): doi:10.1371/journal.pone.0037879,2012.31. Tianlei Xu, Ruixin Zhu, Qi Liu and Zhiwei Cao, Quantitatively Integrating Molecular Structure and Bioactivity Profile Evidence into Drug-Target Relationship Analysis, BMC Bioinformatics,13:75, 2012.32. Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu and Zhiwei Cao, A virtual drug screen schema based on multi-view similarity integration and ranking aggregation, J. Chem. Inf. Model. Mar 26;52(3):834-43, 2012.33. Elaine L. Leung, Zhi-Wei Cao, Zhi-Hong Jiang, Hua Zhou, and Liang Liu, Network-based drug discovery by integrating systems biology and computational technologies, Briefings in Bioinformatics,doi: 10.1093/bib/bbs043, 2012.34. Jun Gao, Qi Liu, Hong Kang, Zhiwei Cao and Ruixin Zhu, Comparison of different ranking methods in protein-ligand binding sites prediction, Int. J. Mol. Sci., 13(7): 8752–8761, 2012.35. Linlin Yang, Kailin Tang, Ying Qi, Hao Ye, Wenlian Chen, Yongyu Zhang, Zhiwei Cao. Potential metabolic mechanism of girls’central precocious puberty: a network analysis on urine Metabonomics data. BMC System Biology,6(Suppl 3):S19, 2012.36. Ye H, Tang K, Yang L, Cao Z, Li Y. Study of drug function based on similarity of pathway fingerprint. Protein Cell. 2012 Feb;3(2):132-9. Epub 2012 Mar 17.37. Zhao J, Yang P, Li F, Tao L, Ding H, Rui Y, Cao Z*, Zhang W. Therapeutic Effects of Astragaloside IV on Myocardial Injuries: Multi-Target Identification and Network Analysis. PLoS One. 2012;7(9):e44938. doi: 10.1371/journal.pone.0044938. Epub 2012 Sep 17.38. Gao J, Huang Q, Wu D, Zhang Q, Zhang Y, Chen T, Liu Q, Zhu R, Cao Z, He Y. study on human GPCR-inhibitor interactions by proteochemometric modeling. Gene. 2013 Apr 10;518(1):124-31. doi: 10.1016/j.gene.2012.11.061. Epub 2012 Dec 14.39. Liu Q, Zhou H, Zhu R, Xu Y, Cao Z*. Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration. Brief Bioinform. 2012 Dec 29.40. Liu Q, Zhou H, Zhang K, Shi X, Fan W, Zhu R, Yu PS, Cao Z*. In silico target-specific siRNA design based on domain transfer in heterogeneous data.PLoS One. 2012;7(12):e50697. doi: 10.1371/journal.pone.0050697. Epub 2012 Dec 21.41. Yi Sun, Ruixin Zhu, Hao Ye, Jing Zhao, Yujia Chen, Qi Liu and Zhiwei Cao, Towards a bioinformatics analysis of anti-Alzheimer’s herbal medicines from a target network perspective, Briefings in Bioinformatics, May;14(3):327-43, 2013.42. Ma C, Tang K, Liu Q, Zhu R, Cao Z*. Calmodulin as a potential target by which berberine induce cell cycle arrest in human hepatoma Bel7402 cells. Chem Biol Drug Des. 2013 Feb 19. doi: 10.1111/cbdd.12124. [Epub ahead of print]43. Tian, C,; Zhu, L,; Yu, D,; Cao, Z,; Kang T.; Zhu, R., The Stereoselectivity of CYP2C19 on R- and S-isomer of Proton Pump Inhibitors. Chem Biol Drug Des. 2013 Accepted, doi: 10.1111/cbdd.12274.44. Tian, C,; Zhu, R,; Zhu, L,; Qiu, T,; Cao, Z,; Kang T., Potassium channels: structures, diseases and modulators. Chem Biol Drug Des. 2013 Oct 7. doi: 10.1111/cbdd.12237. [Epub ahead of print]44. Li G, Wu D, Wang S, Sun J, Xu D, Cao Z*. Similarity between segments in protein conformational epitopes and MHC II peptides. Int J Comput Biol Drug Des. 2013;6(1-2):107-18. doi: 10.1504/IJCBDD.2013.052205. Epub 2013 Feb 21.45. Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu, iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis, Bioinformatics, Advance Access online, 2013.46. Tao Qi, Tianyi Qiu, Qingchen Zhang, Kailin Tang, Yangyang Fan, Jingxuan Qiu, Dingfeng Wu, Wei Zhang, Yanan Chen, Jun Gao, Ruixin Zhu and Zhiwei Cao, SEPPA 2.0 - more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic Acids Research, 2014, 10.1093/nar/gku395. 47. Peng Fu, Linlin Yang, Yi Sun, Li Ye, Zhiwei Cao and Kailin Tang, Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease, BMC Bioinformatics, 2014, 15(suppl 4):S3.