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刘雷博士介绍(PI)

 

刘雷   课题组长:刘雷博士,毕业于美国康涅狄格大学(University of Connectictut)分子与细胞生物学系,曾任美国伊利诺伊大学香槟分校(University of Illinois at Urbana-Champaign)生物技术中心生物信息学实验室主任。20076月回国, 现任中心副主任。
   多年来一直致力于生物医学信息学研究(包括基础研究和转化研究):在基因组数据的拼接与注释、比较基因组学、基因芯片数据的分析与挖掘、生物网络的构建与分析、生物系统的建模与模拟、医疗数据共享整合与挖掘、临床决策支持、个性化医疗等方面做了大量工作,取得了一系列创新性成果。在转录调控网络及网络动态建模上提出了microRNA以转录因子为介导的两层调控机制;通过系统建模与模拟解析了细胞周期和生物时钟节律互相钳制的动态关系;创建了整合酶活性调控机制的代谢动力学模型;开发了基于基因本体模块的表达谱分析方法,可根据表达谱准确地找到生物功能相似的小分子及其相关的作用途径,在新药研发、药理毒理、小分子调控研究等方面具有广泛的应用前景。
   先后研发了一系列应用于医疗科研与实验的临床信息管理系统,包括:样本库信息管理系统、科研电子病例信息管理系统、实验室信息管理系统及随访和项目管理等系统,已获得多个软件著作权并在多家医院获得了良好的应用。结合基础研究中的组学数据,开发了基于基因多样性的个性化医疗临床决策支持系统,将基因、疾病、药物的信息相关联与整合;已获得多个软件著作权并申请了专利。
   近年来在《Bioinformatics》、《PLoS Computational Biology》、《Nucleic Acid Research》《Journal of Biomedical informatics》等国际上有较大影响的学术刊物及学术会议上发表论文40余篇,绝大多数的论文影响因子在3.0以上。同时还应邀参与编撰了四部专著,共同主编了《中国医疗卫生信息化进展》一书。


【课题组研究方向】生物医学信息学涉及生物信息学、图像信息学、临床信息学和公共卫生信息学。本组的主旨是研究与开发专业标准、软件技术、系统平台,从而有效地获取、存储、管理、分析,整合、共享生物医学信息和知识,提高疾病的检测、预防和治疗的水平,为政府、社会和医疗机构提供信息决策服务,并促进临床医疗和社区卫生工作。
   本组现有全职研究人员2人,实习生10多人。
   本组承担和参与了多项863、上海市科委项目,并与多家大型综合医院建立了合作关系。

【在研项目】
1. 医学知识库与临床决策支持系统研发
2. 基于重要疾病生物标志物的鉴定开发及应用
3. 面向生物医学信息大数据共享服务子平台应用及示范
4. 抗艾滋病病毒新药临床评价研究技术平台建设
5. 病毒性肝炎相关肝癌样本保藏及相关数据库共享技术平台
6. 个人健康信息智能获取技术及系统开发
7. 重要病原生物与传染病转化医学研究协同创新平台
8. 病原微生物实验室溯源和人员防护关键技术的研究


【2013年主要论文】

1.Bi-Qing Li, Hui Yu, Zhen Wang, Guo-Hui Ding and Lei Liu*, MicroRNA mediated network and DNA Methylation in Colorectal Cancer, Protein & Peptide Letters, 2013.3(20):1-12.
2.Xiao, Juanjuan; Wang, Ying; Li, Zuofeng; Zhang, Xufeng; Feng, Kaiyan; Liu, Lei*, Assessing the Gender Differences of Adverse Effects in HIV Infection Treatment Based on FDA AERS Database, Current Bioinformatics, 2013.5(8):583-590(8).
3.Hui Wang,Weide Zhangd,Qiang Zenge,Zuofeng Lie,Kaiyan Fengf,Lei Liu*, Extracting important information from Chinese Operation Notes with natural language processing methods, Journal of Biomedical Informatics(Received 4 January 2013; accepted 13 December 2013. published online 19 February 2014).

25年内发表的全部论著;

4.Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li (2009) Modeling the age distribution of gene duplications in vertebrate genome using mixture density. Genomics 93(2):146-151. (共同通讯作者)

5. Zhuo Wang, Qi Chen, Lei Liu (2009) Relationship between topology and functions in metabolic network evolution. Chinese Science Bulletin 54(5):776-782.

6.Zhuo Wang, Xinguang Zhu, Xiao Chang, Yazhu Chen, Yixue Li, Lei Liu (2009) Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network. J. Evol. Biol 22(1):71-79. (通讯作者)

7.  Ruoyu Luo, Haibin Wei, Lin Ye, Kankan Wang, Fan chen, Lijun Luo, Lei Liu, Yuanyuan Li, M.James C.Crabbe, Li Jin,  Yixue Li, Yang Zhong (2009) Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: a systems biological analysis. Proc. Natl. Acad. Sci. USA 106(3):847-852.

8.  Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li (2009) CHSMiner: a  GUI tool to identify chromosomal homologous segments. Algorithms Mol. Biol 4(1):2.

9.   Huseyin Kucuktas, Shaolin Wang, Ping Li, Chongbo He, Peng Xu, Zhenxia Sha, Hong Liu, Yanliang Jiang, Puttharat Baopraserkul, Benjaporn Somridhivej, Yaping Wang, Jason Abernathy, Ximing Guo, Lei Liu, William Muir, Zhanjiang Liu (2009) Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish. Genetics (in press).

10.  Yun Li, Pei Hao, Siyuan Zheng, Kang Tu, Haiwei Fan, Ruixin Zhu, Guohui Ding, Changzheng Dong, Chuan Wang, Xuan Li, H.-J. Thiesen, Y. Eugene Chen, Hualiang Jiang, Lei Liu, Yixue Li (2008) Gene expression module-based chemical function similarity search. Nucleic Acids Res 36(20):e137. (共同通讯作者)

11.     Kirstin Replogle, Arthur P Arnold, Gregory F Ball, Mark Band, Staffan Bensch, Eliot A Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M George, George Gong, Dennis Hasselquist, Alvaro G Hernandez, Ryan Kim, Harris A Lewin, Lei Liu, Peter V Lovell, Claudio V Mello, Sara Naurin, Sandra Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F Clayton (2008) The Songbird Neurogenomics (SoNG) Initiative: community-based tolls and strategies for study of brain gene function and evolution. Genomics 9:131.

12.   Bin Kang, Yuanyuan Li, Xiao Chang, Lei Liu, Yixue Li (2008) Modeling the effects of cell cycle m-phase transcriptional inhibition on circadian oscillation. PLoS Comput. Biol 4(3):e1000019. (共同通讯作者)

13.
Kyung Seok Kim, Susan T.Ratcliffe, B.Wade French, Lei Liu, Thomas W.Sappington (2008) Utility of EST-derived SSRs as population genetics markers in a beetle. J.Hered 99(2):112-24.

14.Fudong Yu, Yixue Li, Lei Liu, Yuanayuan Li (2008) Comparative genomics of human-like Schistosoma japonicum genes. Genomics 91(2):152-157. (共同通讯作者)

15.   Siyuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, Yixue Li (2008) MPSQ: a web tool for protein-state searching. Bioinformatics 24(20):2412-3.

16.Guohui Ding, Zhonghao Yu, Jing Zhao, Zhen Wang, Yun Li, Xiaobin Xing, Chuan Wang, Lei Liu, Yixue Li (2008) Tree of life based on genome context networks. PLoS ONE 3(10): e3357. 

17.Ray Ming , Shaobin Hou, Yun Feng, Qingyi Yu, Alexandre Dionne-Laporte, Jimmy H. Saw, Pavel Senin, Wei Wang, Benjaminv Ly, Kanako L.T.Lewis, Steven L.Salzberg, Lu Feng , Meghan R.Jones ,Rachel L. Skelton ,Jan E. Murray,Cuixia Chen,Wubin Qian, Junguo Shen, Peng Du,  Morichael Eustice, Eric Tong, Haibao Tang, Eric Lyons, Robert E.pawl , Toddp.Micheal , Kerr Wall, Danny W.Rice, Henrik Albert, Mingli Wang, Yun J. Zhu, Michael Schatz, Niranjan Nagarajan, Ricelle A. Acob, Peizhu Guan, Andrea Blas, Ching Man Wai, Christine M. Ackerman, Yan Ren, Chao Liu, Jianmei Wang, Jianping Wang, Jong-Kuk Na, Eugene V. Shakirov, Brian Haas, Jyothi Thimmapuram, David Nelson, Xiyin Wang, John E. Bowers, Andrea R. Gschwend, Arthur L. Delcher, Ratnesh Singh, Jon Y. Suzuki, Savarni Tripath, Kabi Neupane, Hairong Wei, Beth Irikura, Maya Paidi, Ning Jiang, Wenli Zhang, Gernot Presting, Aaron Windsor, Rafael Navajas-Pérez, Manuel J. Torres, F. Alex Feltus, Brad Porter, Yingjun Li, A. Max Burroughs, Ming-Cheng Luo, Lei Liu, David A. Christopher, Stephen   M. Mount, Paul H. Moore, Tak Sugimura, Jiming Jiang, Mary A. Schuler, Vikki Friedman, Thomas Mitchell-Olds, Dorothy E. Shippen, Claude W. dePamphilis, Jeffrey D. Palmer, Michael Freeling, Andrew H. Paterson, Dennis Gonsalves, Lei Wang,Maqsudul Alam. (2008) The draft genome of the transgenic tropical fruit tree papaya(Carica papaya Linnaeus). Nature 452(7190):991-6.

(3)著作书籍

18. Lei Liu (2007) Bioinformatics, Chapter 27 of “Aquaculture Genome Technologies” Ed.Zhanjiang Liu, BlackwellISBN 9780813802039.

19.Lei Liu and Ali Abbas (2006) Bioinformatics in “Encyclopedia of BiomedicalEngineering”, Ed.Metin Akay , WileyISBN 047124967X.

20.Peter Bajcsy, Lei Liu, Mark Band (2005) DNA microarray image processing in"DNA Array Image Analysis: Nuts&Bolts" Ed. Gerda Kamberova, DNA Press, ISBN9780966402759.

21.Bajcsy P., J. Han, L
ei Liu and J. Young, (2004), “Survey of Bio-Data Analysis fromData Mining Perspective,” Chapter 2 of Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T.Toivonen, and Dennis Shasha (eds.), Data Mining in Bioinformatics, Springer Verlag,ISBN 978-1-85233-671-4, pp.9-39. 

22.Lei Liu , Hans Laufer (1998) Endocrine factors regulating crustacean reproductive maturation, in New Developments in Marine Biotechnology, ed. Le Gal and Halvorson, Plenum Press, New York,  p89-91.