Prospects for identifying functional variation across the genome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue SUPPL. 1, 2005, Pages 6614-6621

  Macdonald, Stuart J ^a   Long, Anthony D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; GENE CONTROL; GENE MAPPING; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION DIFFERENTIATION; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

DROSOPHILA MELANOGASTER; DROSOPHILA PSEUDOOBSCURA; DROSOPHILA SIMULANS; MELANOGASTER;

EID: 18244410153     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0501990102     Document Type: Article

References (51)

1. Carlson, C. S., Eberle, M. A., Kruglyak, L. & Nickerson, D. A. (2004) Nature 429, 446-452.
2. Kruglyak, L. & Nickerson, D. A. (2001) Nat. Genet. 27, 234-236.
3. Stephens, J. C., Schneider, J. A., Tanguay, D. A., Choi, J., Acharya, T., Stanley, S. E., Jiang, R., Messer, C. J., Chew, A., Han, J.-H., et al. (2001) Science 293, 489-493.
4. Syvänen, A.-C. (2001) Nat. Rev. Genet. 2, 930-942.
5. The International HapMap Consortium (2003) Nature 426, 789-796.
6. Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. & Lander, E. S. (2001) Nat. Genet. 29, 229-232.
7. Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) Science 294, 1719-1723.
8. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) Science 296, 2225-2229.
9. Carlson, C. S., Eberle, M. A., Rieder, M. J., Smith, J. D., Kruglyak, D. & Nickerson, D. A. (2003) Nat. Genet. 33, 518-521.
10. Goldstein, D. B., Ahmadi, K. R., Weale, M. E. & Wood, N. W. (2003) Trends Genet. 19, 615-622.
11. Reich, D. E., Gabriel, S. B. & Altshuler, D. (2003) Nat. Genet. 33, 457-458.
12. Risch, N. & Merikangas, K. (1996) Science 273, 1516-1517.
13. Kruglyak, L. (1999) Nat. Genet. 22, 139-144.
14. Long, A. D. & Langley, C. H. (1999) Genome. Res. 9, 720-731.
15. Botstein, D. & Risch, N. (2003) Nat. Genet. 33, Suppl., 228-237.
16. Robin, C., Lyman, R. F., Long, A. D., Langley, C. H. & Mackay, T. F. (2002) Genetics 162, 155-164.
17. Ueda, H., Howson, J. M. M., Esposito, L., Heward, J., Snook, H., Chamberlain, G., Rainbow, D. B., Hunter, K. M. D., Smith, A. N., Di Genova, G., et al. (2003) Nature 423, 506-511.
18. Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jónsson, B., Schluter, D. & Kingsley, D. M. (2004) Nature 428, 717-723.
19. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) Science 287, 2185-2195.
20. International Human Genome Sequencing Consortium (2004) Nature 431, 931-945.
21. McDonald, J. H. & Kreitman, M. (1991) Nature 351, 652-654.
22. Nielsen, R. & Yang, Z. (1998) Genetics 148, 929-936.
23. Kreitman, M. & Hudson, R. R. (1991) Genetics 127, 565-582.
24. Norga, K. K., Gurganus, M. C., Dilda, C. L., Yamamoto, A., Lyman, R. F., Patel, P. H., Rubin, G. M., Hoskins, R. A., Mackay, T. F. & Bellen, H. J. (2003) Curr. Biol. 13, 1388-1397.
25. Kuang, B., Wu, S. C., Shin, Y., Luo, L. & Kolodziej, P. (2000) Development (Cambridge, U.K.) 127, 1517-1529.
26. Ramain, P., Khechumian, K., Seugnet, L., Arbogast, N., Ackermann, C. & Heitzler, P. (2001) Curr. Biol. 11, 1729-1738.
27. Bier, E., Vaessin, H., Younger-Shepherd, S., Jan, L. Y. & Jan, Y. N. (1992) Genes Dev. 6, 2137-2151.
28. Lage, P. Z., Shrimpton, A. D., Flavell, A. J., Mackay, T. F. C. & Brown, A. J. L. (1997) Genetics 146, 607-618.
29. Lai, C., McMahon, R., Young, C., Mackay, T. F. C. & Langley, C. H. (1998) Genetics 149, 1051-1061.
30. Tajima, F. (1989) Genetics 123, 585-595.
31. Russo, C. A. M., Takezaki, N. & Nei, M. (1995) Mol. Biol. Evol. 12, 391-404.
32. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, I., Pachter, L. & Rubin, E. M. (2003) Science 299, 1391-1394.
33. Hong, R. L., Hamaguchi, L., Busch, M. A. & Weigel, D. (2003) Plant Cell 15, 1296-1309.
34. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. (2003) Nature 423, 241-254.
35. Berman, B. P., Pfeiffer, B. D., Laverty, T. R., Salzberg, S. L., Rubin, G. M., Eisen, M. B. & Celniker, S. E. (2004) Genome Biol. 5, R61.
36. Macdonald, S. J. & Long, A. D. (2005) Mol. Biol. Evol. 22, 1-13.
37. Andolfatto, P. & Przeworski, M. (2001) Genetics 158, 657-665.
38. Kim, Y. & Stephan, W. (2002) Genetics 160, 765-777.
39. Johnson, D. S., Davidson, B., Brown, C. D., Smith, W. C. & Sidow, A. (2004) Genome Res. 14, 2448-2456.
40. Richards, S., Liu, Y., Bettencourt, B. R., Hradecky, P., Letovsky, S., Nielsen. R., Thornton, K., Hubisz, M. J., Chen, R., Meisel, R. P., et al. (2005) Genome Res. 15, 1-18.
41. Ludwig, M. Z., Bergman, C., Patel, N. H. & Kreitman, M. (2000) Nature 403, 564-567.
42. Kimura, M. (1983) The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, Cambridge, U.K.).
43. Hudson, R. R., Kreitman, M. & Aguadé, M. (1987) Genetics 116, 153-159.
44. Nurminsky, D. I., Nurminskaya, M. V., De Aguiar, D. & Hartl, D. L. (1998) Nature 396, 572-575.
45. Daborn, P. J., Yen, J. L., Bogwitz, M. R., Le Goff, G., Feil, E., Jeffers, S., Tijet, N., Perry, T., Heckel, D., Batterham, P., et al. (2002) Science 297, 2253-2256.
46. Schlenke, T. A. & Begun, D. J. (2004) Proc. Natl. Acad. Sci. USA 101, 1626-1631.
47. Wright, S. (1951) Ann. Eugen. 15, 323-354.
48. Berry, A. & Kreitman, M. (1993) Genetics 134, 869-893.
49. Stam, L. F. & Laurie, C. C. (1996) Genetics 144, 1559-1564.
50. García-Dorado, A. & González, J. A. (1996) Evolution (Lawrence, Kans.) 50, 1573-1578.
51. Mackay, T. F. (1995) Trends Genet. 11, 464-470.