＞教授 姓　　名： 李　霞 部　　门： 生物信息学教研室 职　　称： 教授、博士生导师 学　　历： 博士研究生 职　　务： 院长、书记 办公电话： 办公地址： 分子生物学馆112室 Email： lixia(at)hrbmu.edu.cn 主要研究方向： 重大疾病的生物信息学与计算系统生物学研究 个人简介 　　李霞，教授、博士、博士生导师，“龙江学者”特聘教授、省级优秀中青年专家、省级领军人才梯队带头人、国务院特殊津贴专家、北京“百千万人才工程”入选者、五洲女子科技奖获得者、黑龙江生物医学工程学(生物信息学)一级学科重点学科带头人，创建哈尔滨医科大学生物信息学科，哈医大生物信息科学与技术学院院长、学院党总支书记。1993年任副教授，1997年破格晋升为教授，1999年12月到2001年1月受美国UNC与CWRU复杂疾病基因定位奠基人Robert Elston博士邀请，作为访问教授赴美从事复杂疾病基因定位连锁作图和基因表达谱疾病基因发现等研究工作。 　　主要学术兼职：国家863项目评审专家、国家自然科学基金评审专家、国家自然科学基金学科组评审专家、全国高等学校临床医学专业八年制卫生部规划教材《生物信息学》主编、《生物信息学理论与医学实践》主编、《医用高等数学》主编、中国细胞生物学会功能基因组信息学与系统生物学专业委员会秘书长、国际著名杂志《Nucleic Acids Research》、《Bioinformatics》、BMC系列杂志和《Journal of Drug Targeting》论文评审专家、《中国生物工程》杂志理事、《生物信息学》、《生物物理学报》、《中华现代妇产科学》杂志编委、中国信息协会常务理事、黑龙江省自然科学基金评审专家等。 　　李霞教授主要研究方向是：生物信息学与计算系统生物学；miRNA、LncRNA分子因子识别、miRNA-mRNA失调网络重建；基于RNA表达谱(mRNA/miRNA 和LncRNA等)信息学分析；复杂疾病miRNA－miRNA协同作用的分析；miRNA调控的子通路识别；人类非编码RNA的系统识别与功能分析平台建设；衰老与代谢相关疾病风险通路区域和关键节点识别的系统生物学研究；基于生物谱的复杂重大疾病的分子分型与生物标志物识别；生物信息融合分析技术；分子生物网络（SNPs虚拟网络、基因调控网络、miRNA-mRNA协同调控网、蛋白质互作网络等）重建；miRNA与复杂疾病调控机制研究；复杂疾病的风险通路（pathway）识别技术；基于新一代测序的复杂疾病风险分析；基因与蛋白质功能研究的生物芯片信息学分析技术；炎癌转化的分子机制研究；高通量药物分子靶标筛选技术；研发解析癌症分子机制的生物信息学方法与分析平台等。 　　李霞教授先后承担课题30余项，其中，国家863高科技计划项目4项，国家973项目2项，国家自然科学基金项9项（主持8项），获省部级奖、中华医学奖等9项，厅局级奖8项，在国内外重要学术刊物和学术会议上发表论文180余篇(其中SCI 140篇)，累计SCI影响因子380余点，总引次数400余次。尤其在癌症等重大疾病功能基因识别方法的研究取得重要研究成果，科学研究论文发表在国外著名生命科学杂志《Briefings in Bioinformatics》,《Nucleic Acids Research》 (12篇SCI IF：8.08),《Bioinformatics》(SCI IF:5.02), 《Scientific Reports》(SCI 5.078, Nature子刊),《BMC Bioinformatics》等上。论文“Gene mining: a novel and powerful ensemble decision approach to hunting for disease genes using microarray expression profiling.”受到了Nobel奖得主Rich Roberts博士的好评，并迅速成为英国牛津出版集团旗舰科学杂志《Nucleic Acids Research》的热点文章(Hot Papers)。主编卫生部八年制规划教材《生物信息学》、主编《计算分子生物学与基因组信息学》、《医学遗传学与遗传流行病学数据分析》等10部。 　　在研与完成科研项目30项（仅列国家级）： 　　1、国家高技术研究发展计划（863计划）： 1) 人类非编码RNA的系统识别与功能分析平台建设 (2014AA021102) 2) 面向转化医学的生物医学信息集成体系及计算平台研究 (2007AA02Z329) 3) 中药抑癌分子机理基因芯片技术平台 (2003AA2Z2051) 4) 原位合成基因芯片技术的研发 (2002AA2Z2052) 　　2、国家重点基础研究发展计划（973计划）： 1) 衰老与代谢相关疾病风险通路区域和关键节点识别的系统生物学研 (2014CB910504) 2) 复杂疾病多重分子标记识别与功能网络重建的系统生物信息融合方法研究 (2008CB517302) 　　3、国家自然科学基金项目： 1) 重大研究计划（培育项目）：心血管疾病风险循环非编码RNA（miRNA/LncRNA)识别及其协同调控风险通路功能分析 (91439117) 2) 重大研究计划（培育项目）：整合多维高通量组学数据解析炎癌转化的关键基因与功能通路 (91129710) 3) 面上项目：癌症非编码miRNA-lncRNA协同调控网络重构与功能特性研究(61473106) 4) 面上项目：复杂疾病miRNA多态风险位点识别及其生物学功能分析 (61073136) 5) 面上项目：复杂疾病关联的miRNA-mRNA功能模块识别的信息融合方法研究 (30871394) 6) 面上项目：基于生物谱的复杂疾病基因识别系统融合分析方法研究 (30571034) 7) 面上项目：人类复杂疾病基因表达谱特征基因识别技术 (30370798) 8) 面上项目：多基因复杂遗传疾病基因作图的模式识别与特征提取技术 (30170515) 9) 面上项目：人类复杂疾病基因定位的方法与优化策略 (39970397, 参加) 　　科研奖励情况： 1) 李霞等，癌风险生物标志物识别的生物信息融合系列方法研究，黑龙江省政府科学技术（自然类）二等奖（2010年）。 2) 李霞等，人类复杂疾病靶基因功能模块挖掘与基因网络重建方法研究，黑龙江省政府科学技术（自然类）二等奖（2008年）。 3) 李霞等，复杂疾病基因作图的模式识别方法研究，黑龙江省政府科学技术（自然类）二等奖（2005年）。 4) 李霞等，癌风险生物标志物及风险通路识别的生物信息融合系列方法研究，中华医学科技奖三等奖（2011年）。 5) 李霞等，癌风险miRNA及协同调控风险通路(pathway)识别方法研究，黑龙江省教育厅高校科技二等奖（2015年）。 6) 李霞等，癌风险生物标志物识别的生物信息融合系列方法研究，黑龙江省教育厅高校科技一等奖（2010年）。 7) 李霞等，人类复杂疾病靶基因功能模块挖掘与基因网络重建方法研究，黑龙江省教育厅高校科技一等奖（2008年）。 8) 李霞等，基于SNP遗传谱和表达谱的基因挖掘方法研究，黑龙江省教育厅高校科技一等奖（2006年）。 9) 李霞等，复杂疾病基因作图的模式识别方法研究，黑龙江省教育厅高校科技一等奖 （2005年）。 　　主编的著作： 1) 李霞 主编，《生物信息学》（卫生部八年制规划教材），2010 年，人民卫生出版社。 2) 李霞 主编，《生物信息学理论与医学实践》，2012年，人民卫生出版社。 3) 李霞 主编，《医用高等数学》，2013年，北京大学医学出版社。 4) 李霞 主编，《医用高等数学》，2004年，黑龙江科学技术出版社。 5) 李霞 副主编，《卫生管理运筹学》，2012年，人民卫生出版社。 6) 李霞 编委，《Systems biology in cancer research and drug discovery》，2012年。 7) 李霞 主编，《药物?受体?酶与免疫反应动力学数据分析》，2000 年，黑龙江科学技术出版社。 8) 李霞 主编，《医学遗传学与遗传流行病学数据分析》，2000 年，黑龙江科学技术出版社。 9) 李霞 主编，《计算分子生物学与基因组信息学》，1998 年，黑龙江科学技术出版社。 10) 李霞 主编，《医学信息分析方法》，2001 年，哈尔滨出版社。 　　发表科研论文180篇，其中SCI 140篇（仅列近5年代表论文）： 1. Zhi, H., S. Ning, X. Li, Y. Li, W. Wu, and X. Li, A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers. Nucleic Acids Res, 2014. 42(13): p. 8258-70. (SCI:8.808) 2. Li, C., J. Han, Q. Yao, C. Zou, Y. Xu, C. Zhang, D. Shang, L. Zhou, C. Zou, Z. Sun, J. Li, Y. Zhang, H. Yang, X. Gao, and X. Li, Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic Acids Res, 2013. 41(9): p. e101. (SCI IF: 8.808) 3. Li, Y., J. Xu, H. Chen, J. Bai, S. Li, Z. Zhao, T. Shao, T. Jiang, H. Ren, C. Kang, and X. Li, Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. Nucleic Acids Res, 2013. 41(22): p. e203. (SCI IF: 8.808) 4. Xiao, Y., J. Guan, Y. Ping, C. Xu, T. Huang, H. Zhao, H. Fan, Y. Li, Y. Lv, T. Zhao, Y. Dong, H. Ren, and X. Li, Prioritizing cancer-related key miRNA-target interactions by integrative genomics. Nucleic Acids Res, 2012. 40(16): p. 7653-65. (SCI IF: 8.278) 5. Li, X., Q. Wang, Y. Zheng, S. Lv, S. Ning, J. Sun, T. Huang, Q. Zheng, H. Ren, J. Xu, X. Wang, and Y. Li, Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. Nucleic Acids Res, 2011. 39(22): p. e153. (SCI IF: 8.026) 6. Xu, J., C.X. Li, Y.S. Li, J.Y. Lv, Y. Ma, T.T. Shao, L.D. Xu, Y.Y. Wang, L. Du, Y.P. Zhang, W. Jiang, C.Q. Li, Y. Xiao, and X. Li, MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res, 2011. 39(3): p. 825-36. (SCI IF: 8.026) 7. Zhang, Y., H. Liu, J. Lv, X. Xiao, J. Zhu, X. Liu, J. Su, X. Li, Q. Wu, F. Wang, and Y. Cui, QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res, 2011. 39(9): p. e58. (SCI IF: 8.026) 8. Zhang, Y., J. Lv, H. Liu, J. Zhu, J. Su, Q. Wu, Y. Qi, F. Wang, and X. Li, HHMD: the human histone modification database. Nucleic Acids Res, 2010. 38(Database issue): p. D149-54. (SCI IF: 7.836) 9. Su, J., Y. Zhang, J. Lv, H. Liu, X. Tang, F. Wang, Y. Qi, Y. Feng, and X. Li, CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res, 2010. 38(1): p. e6. (SCI IF: 7.836) 10. Li, Y., S. Li, J. Chen, T. Shao, C. Jiang, Y. Wang, H. Chen, J. Xu, and X. Li, Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes. Hum Mol Genet, 2014. 23(20): p. 5378-93. (SCI:6.677) 11. Wang, Q., J. Sun, M. Zhou, H. Yang, Y. Li, X. Li, S. Lv, X. Li, and Y. Li, A novel network-based method for measuring the functional relationship between gene sets. Bioinformatics, 2011. 27(11): p. 1521-8. (SCI IF: 5.468) 12. Chen, X., J. Xu, B. Huang, J. Li, X. Wu, L. Ma, X. Jia, X. Bian, F. Tan, L. Liu, S. Chen, and X. Li, A sub-pathway-based approach for identifying drug response principal network. Bioinformatics, 2011. 27(5): p. 649-54. (SCI IF: 5.468) 13. Li, X., W. Jiang, W. Li, B. Lian, S. Wang, M. Liao, X. Chen, Y. Wang, Y. Lv, S. Wang, and L. Yang, Dissection of human MiRNA regulatory influence to subpathway. Brief Bioinform, 2012. 13(2): p. 175-86. (SCI IF: 5.298) 14. Xiao, Y., Y. Ping, H. Fan, C. Xu, J. Guan, H. Zhao, Y. Li, Y. Lv, Y. Jin, L. Wang, and X. Li, Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro Oncol, 2013. 15(7): p. 818-28.(SCI IF: 5.286) 15. Xu, J., C.X. Li, J.Y. Lv, Y.S. Li, Y. Xiao, T.T. Shao, X. Huo, X. Li, Y. Zou, Q.L. Han, X. Li, L.H. Wang, and H. Ren, Prioritizing candidate disease miRNAs by topological features in the miRNA target-dysregulated network: case study of prostate cancer. Mol Cancer Ther, 2011. 10(10): p. 1857-66. (SCI IF: 5.226) 16. Dai, E., Y. Lv, F. Meng, X. Yu, Y. Zhang, S. Wang, X. Liu, D. Liu, J. Wang, X. Li, and W. Jiang, CREAM: a database for chemotherapy resistance-associated miRSNP. Cell Death Dis, 2014. 5: p. e1272. (SCI:5.177) 17. Wang, Y., L. Chen, B. Chen, X. Li, J. Kang, K. Fan, Y. Hu, J. Xu, L. Yi, J. Yang, Y. Huang, L. Cheng, Y. Li, C. Wang, K. Li, X Li, J Xu and D. Wang, Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network. Cell Death Dis, 2013. 4: p. e765. (SCI IF: 5.177) 18. Zhang, Y., H. Fan, J. Xu, Y. Xiao, Y. Xu, Y. Li, and X. Li, Network analysis reveals functional cross-links between disease and inflammation genes. Sci Rep, 2013. 3: p. 3426(SCI IF: 5.078) 19. Lv, S., Y. Li, Q. Wang, S. Ning, T. Huang, P. Wang, J. Sun, Y. Zheng, W. Liu, J. Ai, and X. Li, A novel method to quantify gene set functional association based on gene ontology. J R Soc Interface, 2012. 9(70): p. 1063-72. (SCI IF: 4.907) 20. Zhang, X., D. Wu, L. Chen, X. Li, J. Yang, D. Fan, T. Dong, M. Liu, P. Tan, J. Xu, Y. Yi, Y. Wang, H. Zou, Y. Hu, K. Fan, J. Kang, Y. Huang, Z. Miao, M. Bi, N. Jin, K. Li, X. Li, J. Xu, and D. Wang, RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. RNA, 2014. 20(7): p. 989-93. (SCI:4.622) 21. Jiang, W., Y. Zhang, F. Meng, B. Lian, X. Chen, X. Yu, E. Dai, S. Wang, X. Liu, X. Li, L. Wang, and X. Li, Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease. Bioinformatics, 2013. 29(20): p. 2596-602. (SCI IF: 4.621) 22. Liu, W., C. Li, Y. Xu, H. Yang, Q. Yao, J. Han, D. Shang, C. Zhang, F. Su, X. Li, Y. Xiao, F. Zhang, M. Dai, and X. Li, Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. Bioinformatics, 2013. 29(17): p. 2169-77. (SCI IF: 4.621) 23. Liu, X., S. Wang, F. Meng, J. Wang, Y. Zhang, E. Dai, X. Yu, X. Li, and W. Jiang, SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression. Bioinformatics, 2013. 29(3): p. 409-11(SCI IF: 4.621) 24. Dai, E., X. Yu, Y. Zhang, F. Meng, S. Wang, X. Liu, D. Liu, J. Wang, X. Li, and W. Jiang, EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications. Database (Oxford), 2014. 2014: p. bau023. (SCI:4.457) 25. Xu, Y., W. Hu, Z. Chang, H. Duanmu, S. Zhang, Z. Li, Z. Li, L. Yu, and X. Li, Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. J R Soc Interface, 2011. 8(57): p. 555-67. (SCI IF: 4.402) 26. Zhang, X., R. Zhang, Y. Jiang, P. Sun, G. Tang, X. Wang, H. Lv, and X. Li, The expanded human disease network combining protein-protein interaction information. Eur J Hum Genet, 2011. 19(7): p. 783-8. (SCI IF: 4.4) 27. Wang, Q., W. Liu, S. Ning, J. Ye, T. Huang, Y. Li, P. Wang, H. Shi, and X. Li, Community of protein complexes impacts disease association. Eur J Hum Genet, 2012. 20(11): p. 1162-7. (SCI IF: 4.319) 28. Li, Y., T. Huang, Y. Xiao, S. Ning, P. Wang, Q. Wang, X. Chen, X. Chaohan, D. Sun, X. Li, and Y. Li, Prioritising risk pathways of complex human diseases based on functional profiling. Eur J Hum Genet, 2013. 21(6): p. 666-72. (SCI IF: 4.225) 29. Ning, S., P. Wang, J. Ye, X. Li, R. Li, Z. Zhao, X. Huo, L. Wang, F. Li, and X. Li, A global map for dissecting phenotypic variants in human lincRNAs. Eur J Hum Genet, 2013. 21(10): p. 1128-33. (SCI IF: 4.225) 30. Wang, H., Q. Wang, U.J. Pape, B. Shen, J. Huang, B. Wu, and X. Li, Systematic investigation of global coordination among mRNA and protein in cellular society. BMC Genomics, 2010. 11: p. 364. (SCI IF: 4.206) 31. Li, X., C. Li, D. Shang, J. Li, J. Han, Y. Miao, Y. Wang, Q. Wang, W. Li, C. Wu, Y. Zhang, X. Li, and Q. Yao, The implications of relationships between human diseases and metabolic subpathways. PLoS One, 2011. 6(6): p. e21131. (SCI IF: 4.092) 32. Jiang, Y., R. Zhang, P. Sun, G. Tang, X. Zhang, X. Wang, X. Guo, Q. Wang, and X. Li, Identifying highly conserved and highly differentiated gene ontology categories in human populations. PLoS One, 2011. 6(11): p. e27871. (SCI IF: 4.092) 33. Chen, L., W. Li, L. Zhang, H. Wang, W. He, J. Tai, X. Li, and X. Li, Disease gene interaction pathways: a potential framework for how disease genes associate by disease-risk modules. PLoS One, 2011. 6(9): p. e24495. (SCI IF: 4.092) 34. Zhao, Z., Y. Li, H. Chen, J. Lu, P.M. Thompson, J. Chen, Z. Wang, J. Xu, C. Xu, and X. Li, PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders. BMC Med Genomics, 2014. 7(1): p. 512. (SCI:3.91) 35. Han, J., C. Li, H. Yang, Y. Xu, C. Zhang, J. Ma, X. Shi, W. Liu, D. Shang, Q. Yao, Y. Zhang, F. Su, L. Feng, and X. Li, A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways. J R Soc Interface, 2015. 12(102): p. 20140937. (SCI:3.856) 36. Liao, M., W. Jiang, X. Chen, B. Lian, W. Li, Y. Lv, Y. Wang, S. Wang, and X. Li, Systematic analysis of regulation and functions of co-expressed microRNAs in humans. Mol Biosyst, 2010. 6(10): p. 1863-72. (SCI IF: 3.825) 37. Zhou, M., J. Sun, Q.H. Wang, L.Q. Song, G. Zhao, H.Z. Wang, H.X. Yang, and X. Li, Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes. FEBS J, 2011. 278(6): p. 929-40. (SCI IF: 3.79) 38. Li, C., D. Shang, Y. Wang, J. Li, J. Han, S. Wang, Q. Yao, Y. Wang, Y. Zhang, C. Zhang, Y. Xu, W. Jiang, and X. Li, Characterizing the network of drugs and their affected metabolic subpathways. PLoS One, 2012. 7(10): p. e47326. (SCI IF: 3.730) 39. Xiao, Y., C. Xu, J. Guan, Y. Ping, H. Fan, Y. Li, H. Zhao, and X. Li, Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network. PLoS One, 2012. 7(2): p. e32201. (SCI IF: 3.730) 40. Zhang, S., C. Wu, X. Li, X. Chen, W. Jiang, B.S. Gong, J. Li, and Y.Q. Yan, From phenotype to gene: detecting disease-specific gene functional modules via a text-based human disease phenotype network construction. FEBS Lett, 2010. 584(16): p. 3635-43. (SCI IF: 3.601) 41. Wu, C., F. Zhang, X. Li, S. Zhang, J. Li, F. Su, K. Li, and Y. Yan, Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. BMC Syst Biol, 2010. 4: p. 82. (SCI IF: 3.565) 42. Wang, Z.Z., B.S. Gong, H.K. Wang, H.J. Wang, M. Zhou, Q.H. Wang, X. Chen, T. Liu, and X. Li, MicroRNA regulation constrains the organization of target genes on mammalian chromosomes. FEBS Lett, 2011. 585(12): p. 1897-904. (SCI IF: 3.538) 43. Wang, Q.H., M. Zhou, J. Sun, S.W. Ning, Y. Li, L. 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