Exploring the landscape of the genome

Methods in Molecular Biology

Volumn 628, Issue , 2010, Pages 21-38

  Barnes, Michael R ^a  

^a NONE

Author keywords

Bioinformatics; Evolution; FTO; Gene; Genome; Regulation; Variation

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC DATABASE; GENOME; HUMAN;

DATABASES, GENETIC; GENOME; HUMANS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77952564321     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-367-1_2     Document Type: Review

References (27)

1. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
2. Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
3. Woollard, P. (2010) Asking complex questions of the genome without programming. Methods Mol. Biol, 39-52.
4. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature, 447, 661-678.
5. Frayling, T.M., Timpson, N.J., Weedon, M.N., Zeggini, E., Freathy, R.M., Lindgren, C.M., et al. (2007) A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science, 316, 889-894.
6. de Bakker, P.I., Yelensky, R., Pe'er, I., Gabriel, S.B., Daly, M.J. and Altshuler, D. (2005) Effciency and power in genetic association studies. Nat. Genet., 37, 1217-1223.
7. Anderson, C.A., Pettersson, F.H., Barrett, J.C., Zhuang, J.J., Ragoussis, J., Cardon, L.R. and Morris, A.P. (2008) Evaluating the effects of imputation on the power, coverage, and cost effciency of genome-wide SNP platforms. Am. J. Hum. Genet., 83, 112-119.
8. Dina, C. (2008) New insights into the genetics of body weight. Curr. Opin. Clin. Nutr. Metab. Care, 11, 378-384.
9. Sandelin, A. (2008) Prediction of regulatory elements. Methods Mol. Biol., 453, 233-244.
10. Callinan, P.A. and Feinberg, A.P. (2006) The emerging science of epigenomics. Hum. Mol. Genet., 15 Spec No 1, R95-R101.
11. Costello, J.F. and Vertino, P.M. (2002) Methylation matters: a new spin on maspin. Nat. Genet., 31, 123-124.
12. Futscher, B.W., Oshiro, M.M., Wozniak, R.J., Holtan, N., Hanigan, C.L., Duan, H. and Domann, F.E. (2002) Role for DNA methy-lation in the control of cell type specifc maspin expression. Nat. Genet., 31, 175-179.
13. Rakyan, V.K., Hildmann, T., Novik, K.L., Lewin, J., Tost, J., Cox, A.V., et al. (2004) DNA methylation profling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol., 2, e405.
14. Ozsolak, F., Song, J.S., Liu, X.S. and Fisher, D.E. (2007) High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol., 25, 244-248.
15. Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T.R. and Wadelius, C. (2008) Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res., 18, 380-392.
16. Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature, 444, 499-502.
17. Zhang, J., Feuk, L., Duggan, G.E., Khaja, R. and Scherer, S.W. (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet. Genome Res., 115, 205-214.
18. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
19. Cooper, G.M., Zerr, T., Kidd, J.M., Eichler, E.E. and Nickerson, D.A. (2008) Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat. Genet., 40, 1199-1203.
20. McCarroll, S.A. (2008) Extending genome-wide association studies to copy-number variation. Hum. Mol. Genet., 17, R135-R142.
21. Lowe, C.B., Bejerano, G. and Haussler, D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl. Acad. Sci. U.S.A., 104, 8005-8010.
22. Bejerano, G., Lowe, C.B., Ahituv, N., King, B., Siepel, A., Salama, S.R., Rubin, E.M., Kent, W.J. and Haussler, D. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441, 87-90.
23. Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet., 9, 387-402.
24. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
25. Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
26. Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
27. Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D. and Kent, W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493-D496.