CBI intro for undergrad.ppt

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1 (CBI)

2 Bioinformatics Bioinformatics is defined as the study of information content and information flow of biological systems and processes. As such, it deals with methods for storing, retrieving and analyzing biological data. It involves both the development of novel information and computational methods and the discovery of new biological insights using these methods.

3 bioinformatics

4 A Truly Interdisciplinary Field Biology Medicine Medical/Clinical informatics Chemistry Bioinformatics Computer Sciences cheminformatics Statistics mathematics physics

5 (CBI) , 973 ( ), NSFC 121-CPU IBM cluster 40 SUN X

6 Life Science Building (CBI is on 6 th floor) Seminar/training room Center for Bioinformatics Floor 121-CPU IBM cluster CBI Graduate Students Office New wet lab being set up SUN servers

7 tiling array - - RNA UC Davis RNA

8 Nucleic Acids Research ( 7.55) 3 Bioinformatics ( 6.02) 1 faculty Nucleic Acids Research

9 Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-nats) n ten species. Nucleic Acids Res Jul 18;34(12): SCI impact factor IF = Cai Z, Mao X, Li S, Wei L. Genome comparison using Gene Ontology (GO) with statistical testing, BMC Bioinformatics 2006, :374. SCI impact factor IF = Shi X, Wang X, Li Z, Zhu Q, Tang W, Ge S, Luo J. Nucleotide substitution pattern in rice paralogues: implication for negative orrelation between the synonymous substitution rate and codon usage bias. Gene Jul 19;376(2): Epub 2006 Mar 18. (IF =.694). Wu J, Mao X, Cai T, Luo J, Wei L. KOBAS server: a web-based platform for automated annotation and pathway identification. ucleic Acids Research Jul 1;34:W IF = Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Research Jul ;34:W IF = Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J, DRTF: Database of Rice Transcription factors, ioinformatics, 2006 May 15;22(10): IF = Mao, X., Cai, T., Olyarchuk, J.G., Wei, L, Automated Genome Annotation and Pathway Identification Using the KEGG Orthology KO) As a Controlled Vocabulary, Bioinformatics, 21(19): , 2005 IF = Wu, X., Walker, M.G., Luo, J., Wei, L, GBA server: EST-based digital gene expression profiling, Nucleic Acids Research, 3:W673-6, 2005 IF = Yin YB, Zhang Y, Yu P, Luo JC, Jiang Y, Li SG. Comparative study of apoptosis-related gene loci in human, mouse and rat enomes. Acta Biochim Biophys Sin (Shanghai) May;37(5):341-8 (IF = 0.505) 0. Wang X, Shi X, Hao B, Ge S, Luo J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New hytol Mar;165(3): (IF = 4.285) 1. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L, Luo, J., DATF: a Database of Arabidopsis Transcription Factors, Bioinformatics, 1(10):2568-9, 2005 IF = Wang J, He X, Ruan J, Dai M, Chen J, Zhang Y, Hu Y, Ye C, Li S, Cong L, Fang L, Liu B, Li S, Wang J, Burt DW, Wong GK, Yu J, ang H, Wang J. ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res Jan 1;33(Database ssue):d IF = Wang J, Xia Q, He X, Dai M, Ruan J, Chen J, Yu G, Yuan H, Hu Y, Li R, Feng T, Ye C, Lu C, Wang J, Li S, Wong GK, Yang H, ang J, Xiang Z, Zhou Z, Yu J. SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res Jan ;33(Database issue):d IF = Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J. SPD--a web-based secreted protein database. Nucleic Acids Res an 1;33(Database issue):d IF = 7.55

10 1. Zhang, J.M., Dean, A.M., Brunet, F. and Long, M.Y.* Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. U. S. A., 101: Wang, W., Yu, H.J. and Long, M.Y.* Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat. Genet., 36: Emerson, J.J., Kaessmann, H., Betran, E. and Long, M.Y.* Extensive gene traffic on the mammalian X chromosome. Science, 303: Long, M.*, Betran, E., Thornton, K. and Wang, W. The origin of new genes: Glimpses from the young and old. Nature Reviews Genetics, 4: Betran, E. and Long, M.* Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics, 164: Wang, W., Brunet, F.G., Nevo, E. and Long, M.* Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A., 99: Wang, W., Thornton, K., Berry, A. and Long, M.Y.* Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science, 295: Betran, E., Wang, W., Jin, L. and Long, M.Y.* Evolution of the Phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol., 19: Betran, E., Thornton, K. and Long, M.* Retroposed new genes out of the X in Drosophila. Genome Res., 12: Llopart, A., Comeron, J.M., Brunet, F.G., Lachaise, D. and Long, M.* Intronpresence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl. Acad. Sci. U. S. A., 99: Long, M.Y *. and Thornton, K. Gene duplication and evolution. Science, 293: Long,M.* Evolution of novel genes. Curr Opin Genet Dev 11: Wang, W., Zhang, J.M., Alvarez, C., Llopart, A. and Long, M.* The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol. Biol. Evol., 17: Sakharkar, M.K., Kangueane, P., Woon, T.W., Tan, T.W., Kolatkar, P.R., Long, M.Y. and de Souza, S.J. IE-Kb: intron exonknowledge base. Bioinformatics, 16: Long, M.Y.* A new function evolved from gene fusion. Genome Res., 10:

11 , 15 Yale, Harvard, U of Chicago, U Laussane, Affymetrix

13 5-10, 3-5,,

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<D2BDC1C6BDA1BFB5CDB6C8DAD7CAB8DFB7E5C2DBCCB3B2CEBBE1C3FBB5A52E786C7378> 参会人员名单 Last Name 姓名公司 Tel Fax Bai 柏煜康复之家 8610 8761 4189 8610 8761 4189 Bai 白威久禧道和股权投资管理 ( 天津 ) 有限公司 8610 6506 7108 8610 6506 7108 Bao 包景明通用技术集团投资管理有限公司 8610