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 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。2007年6月回国, 现任中心副主任。
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。本研究 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，和共享生物医学信 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。生物医学信息学组致力于开发相关的软件平台，以促进临床医疗和社区卫生工作。另外，我们还进行了临床实践指南的数字化的方法论研究，设计和实现以患者为中心的HIS系统，开发特殊领域的知识获取工具，开发医学数据共享标准等工作。本课题组现有研究人员六人， 全职人员四人，兼职人员两人，还有实习生十多人。本课题组承担和参与了三项863项目，两项上海市科委项目，与多家上海地区的大型综合与专科医院建立了合作关系。
现有项目包括：
--基于临床医疗信息共享平台的医疗决策支持系统
--组织样本库的管理系统
--基于生物标志物和基因多态性的个性化医疗支持系统
--医院内信息系统的连接与整合（LIS-HIS-PACS）
--结直肠癌早期诊断，治疗的信息共享平台。
(1) 5篇代表性论著；
1. 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)
2. 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)
3.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)
4. 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)
5. Zhou Wang, Xinguang Zhu, Yazhu Chen, Yuan-Yuan Li, Jing Hou, Yixue Li, Lei Liu (2006) Exploring photosynthesis evolution by comparative analysis of metabolic network between chloroplast and photosynthetic bacteria. BMC Genomics 7:100. (通讯作者)
（2）近5年内发表的全部论著；
6.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)
7. Zhuo Wang, Qi Chen, Lei Liu (2009) Relationship between topology and functions in metabolic network evolution. Chinese Science Bulletin 54(5):776-782.
8.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)
9. 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.
10. 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.
11. 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).
12. 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)
13. 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.
14. 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)
15.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.
16.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)
17. 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.
18.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. 19.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.
20. Ping Li, Eric Peatman, Shaolin Wang, Jinian Feng, Chongbo He, Puttharat Baoprasertkul, Peng Xu, Huseyin Kucuktas, Samiran Nandi, Benjaporn Somridhivej, Jeery Serapion, Micah Simmons, Cemal Turan, Lei Liu, William Muir, Rex Dunham, Yolanda Brady, John Grizzle, Zhangjiang Liu (2007) Towards the ictalurid catfish transcriptome: generation and analysis of catfish ESTs. BMC Genomics 8:177. 21.Peng Xu, Shaolin Wang, Lei Liu, Jim Thorsen, Huseyin Kucuktas, Zhanjiang Liu (2007) A BAC-based physical map of the channel catfish genome. Genomics 90: 1-8.
22.James V. Anderson, David P. Horvath, Wun S. Chao, Michael E, Foley, Alvaro G. Hernandez, Jyothi Thimmapuram, Lei Liu, George L.Gong, Mark Band, Ryan Kim, Mark A. Mikel. (2007) Characterization of an EST database for the perennial weed leafy spurge: An important resource for weed biology research. Weed Science 55 (3): 193-203.
23. S. J. Coleman, George L. Gong, D. P. Gaile, B. P. Chowdhary, E. Bailey, Lei Liu.,J. N. MacLeod. (2007) Evaluation of Compass as a comparative mapping tool for ESTs using horse radiation hybrid maps. Animal Genetics 38 (3): 294-302.
24.Peng Xu, Shaolin Wang, Lei Liu, Peatman, E, Somridhivej. B, Thimmapuram. J, George Gong, Zhanjiang Liu. (2006) Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species. Animal Genetics 37 (4):321-326. 25.Annette Leon-Rossell, Lei Liu, Yan Yang, Danielle Studer, Kia-Joo Puan, Craig T.
Morita, Patrick Hall, Eric Oldfield (2006) Isoprenoid Biosynthesis as a Drug Target: Bisphosphonate Inhibition of Escherichia coli K12 Growth and Synergistic Effects of Fosmidomycin. J. Med. Chem 49 (25): 7331 -7341. 26.Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei- Zhong He and Yi-Xue Li (2006) In silicodiscovery of human natural antisense transcripts. BMC Bioinformatics 7:18. 27.Zhou Wang, Xinguang Zhu, Yazhu Chen, Yuan-Yuan Li, Jing Hou, Yixue Li, Lei Liu (2006) Exploring photosynthesis evolution by comparative analysis of metabolic network between chloroplast and photosynthetic bacteria. BMC Genomics 7:100. (通讯作者) 28.Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yi-Xue Li, Lei Liu (2006) Comparison of Modularization Methods in Application to Different Biological Networks. Lecture Note in Computer Science, Springer 4316: 185-195. (通讯作者) 29.Zhuo Fang, Jiong Yang, Yixue Li, Qingming Luo, Lei Liu (2006) Knowledge guided analysis of microarray data. J. Biomed. Info. 39(4)： 401-411. (通讯作者) 30.Zhuo Fang, Lei Liu, Jiong Yang, Qingming Luo, Yixue Li (2006) Graph-structure Clustering Methods Biochimica et Biophysica Sinica 38(6): 379–384. 31.Huixia Wang, Xuming He, Mark band, Carole Wilson, Lei Liu (2005) A study of inter-lab and inter- -lab and inter-platform agreement of DNA microarray data. BMC Genomics 6:71. (通讯作者) 32.Vimal Selvaraj, David Bunick, Carrol Finnigan-Bunick, Rodney W. Johnson, HuixiaWang, Lei Liu, Paul S. Cooke (2005) Gene Expression Profiling of 17β-Estradiol and Genistein Effects on Mouse Thymus. Taxicological Sciences 87 (1): 97-112. 33.Lei Liu, Jiong Yang, Anthony Tung (2005) Data mining techniques for microarray datasets. Proceedings of 21st International Conference on data engineering (ICDE2005) p1149. 34.Norikatsu Mizumoto, Francis Hui, Dale Edelbaum, M Ryan Weil, Jonathan D Wren, David Shalhevet, Hiroyuki Matsue, Lei Liu, Harold R Garner, Akira Takashima (2005) Differential activation profiles of multiple transcription factors during dendritic cell maturation. J. Invest. Dermatology 124 (4): 718-724. 35. Robin E.Everts, Mark R.Band, Z.Lewis Liu, Charu G.Kumar, Lei Liu, Juan J.Loor, Rosane Oliveira, Harris A.Lewin.(2005)A 7872 cDNA microarray and its use in bovine functional genomics. Vet. Immun. & Immunopat 105 (3-4): 235-245. 36.Jyothi Thimmapuram, Hui Duan, Lei Liu, Mary A. Schuler (2005) Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome. RNA 11:128 – 138. 37.Lei Liu, George Gong, Yong Liu, Shreedhar Natarajan, Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, Jonathan E. Beever (2004) Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics 20, 148-154. (通讯作者)
38.Charu G. Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A. Lewin Lei Liu (2004) ESTIMA, a Tool for EST Management in a Multi-Project Environment. BMC Bioinformatics 5:176. (通讯作者) 39.Selvaraj V, Bunick D, Johnson RW, Lei Liu, Cooke PS (2004) Gene expression profiling of 17 beta-estradiol and genistein effects on mouse thymus. Biol. Reprod 173-173 351 Sp. Iss.
40.Lila O. Vodkin, Anupama Khanna, Robin Shealy, Steven J Clough, Delkin O. Gonzalez, Reena Philip, Gracia Zabala, Francoise Thibaud-Nissen, Mark Sidarous, Martina V.Stromvik, Elizabeth Shoop, Christina Schmidt, Ernest Retzel, John Erpelding, Randy C,Shoemaker, Alicia M. Rodriguez-Huete, Joseph C. Polacco, Virginia Coryell, Paul Keim, George Gong, Lei Liu, Jose Pardinas and Peter Schweitzer (2004) Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAsrepresenting an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5:73.
41.Juli Wade, Camilla Peabody, Paul Coussens, Robert J. Tempelman, David F. Clayton, Lei Liu, Arthur P. Arnold, Robert Agate (2004) A cDNA microarray from the telencephalon of juvenile male and female zebra finches, J. Neurosci. Meth 138:199-206.
42. Hui Fang, Chengxiang Zhai, Lei Liu, Jiong Yang (2004) Subspace clustering formicroarray data analysis: multiple criteria and significance assessment. Proceedings of the 2004 IEEE computational systems bioinformatics conference (CSB2004) p582-583. 43. Annelie Everts-van der Wind, Srinivas R. Kata, Mark R. Band, Mark Rebeiz, Denis M.Larkin, Robin E. Everts, Cheryl A. Green, Lei Liu, Shreedhar Natarajan, Tom Goldammer, Jun Heon Lee, Stephanie McKay, James E. Womack and Harris A. Lewin (2004) A 1,463 Gene Cattle-Human Comparative Map with Anchor Points Defined by Human Genome Sequence Coordinates. Genome Research 14:1424 - 1437.
（3）其余论著
44. Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, Peter A. Schweitzer, Sharon Bachman, Cheryl Green, Chris L. Wright, Edhilvia J. Campos, Leslie D. Benson, Jennifer Edwards, Lei Liu, Kazutoyo Osoegawa, James E. Womack, Pieter J. de Jong, and Harris, A. Lewin (2003) A cattle-human comparative map built with cattle BAC-ends and human genome sequence, Genome Research 13:1966-1973.
45.Zangerl B, Pillardy J, Miller B, Sun Q, Johnson J, Schweitzer P, Hernandez AG, Lei Liu, Acland GM, Aguirre GD (2003) Development of a normalized canine retinal cDNA library for microarray analysis and characterization of 10,000 ESTs, Investigative Ophthalmology & Visual Science 44: U387-U387 2256 Suppl. 46. Xin A. Zhang, William S. Lane, Stephanie Charrin, Eric Rubinstein, Lei Liu (2003) EW12/PGRL associates with the metastasis suppressor KAI1/CD82 and inhibits the migratio of prostate cancer cells. Cancer Research 63:2665-2674. 47. Kevin Miyashiro, Andrea Beckel-Mitchener, T. Patrick Purk, Kevin Becker, Tanya Barret, Lei Liu, Salvatore Carbonetto, Ivan Jeanne Weiler, William Greenough, James Eberwine (2003) RNA Cargoes Associating With FMRP Reveal Deficits in Cellular Functioning in Fmr1 Null Mice. Neuron 37: 417-431. 48. Charles Whitfield, Jose Pardines, Mark Band, Lei Liu, Charu Kumar, Gene Robinson, (2002), EST microarray from Honey Bee Brain, Genome Research 12(4):555-566. 49. Lorraine Olendzenski, Lei Liu, Olga Zhaxybayeva, Ryan Murphey, Dong-Guk Shin, J. Peter Gogarten (2000) Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by Molecular and Computer-Based Approaches. J. Mole. Evol 51:587-599
50 Rotllant G, Takac P, Lei Liu, Scott GL, Laufer H (2000) Role of ecdysteroids and methyl farnesoate in morphogenesis and terminal moult in polymorphic males of the spider crab Libinia emarginata Acquaculture 190 (1-2): 103-118.51 Lei Liu, Hans Laufer, Peter Gogarten, Minhua Wang (1997) Molecular cloning of a mandibular organ inhibiting hormone from the spider crab Libinia emarginata, Invertebrate Neuroscience 3:199-204 51. Lei Liu, Hans Laufer, Peter Gogarten, Minhua Wang (1997) Molecular cloning of a mandibular organ inhibiting hormone from the spider crab Libinia emarginata, Invertebrate Neuroscience 3:199-204. 52. Lei Liu, Hans Laufer, Yajun Wang, and Timothy Hayes (1997) A Neurohormone Regulating Both Methyl Farnesoate Synthesis and Glucose Metabolism in a Crustacean. Biochem. Biophy. Res. Communi 237: 694. 53. Lei Liu, Hans Laufer (1996) Isolation and characterization of sinus gland neuropeptide with both mandibular organ inhibiting and hyperglycemic effects from the eyestalks of the spider crab Libinia emarginata, The Archive of Insect Biochemistry and Physiology 32, p376 - 386. （4）著作书籍 54. Lei Liu (2007) Bioinformatics, Chapter 27 of “Aquaculture Genome Technologies” Ed.Zhanjiang Liu, Blackwell，ISBN 9780813802039. 55.Lei Liu and Ali Abbas (2006) Bioinformatics in “Encyclopedia of BiomedicalEngineering”, Ed.Metin Akay , Wiley，ISBN 047124967X. 56.Peter Bajcsy, Lei Liu, Mark Band (2005) DNA microarray image processing in"DNA Array Image Analysis: Nuts&Bolts" Ed. Gerda Kamberova, DNA Press, ISBN9780966402759.
57.Bajcsy P., J. Han, Lei 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.
58.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.
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