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Selected Computational Genomics Publications

2007

Macarthur, D. G., Seto, J. T., Raftery, J. M., Quinlan, K. G., Huttley, G. A., Hook, J. W., Lemckert, F. A., Kee, A. J., Edwards, M. R., Berman, Y., Hardeman, E. C., Gunning, P. W., Easteal, S., Yang, N., and North, K. N.(2007) Loss of actn3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans. Nat Genet, 39(10):1261-1265.

Easton, B., Maxwell, P., Isaev, A., and Huttley, G. A. (2007) A probabilistic method to identify compensatory substitutions for pathogenic mutations. Proceedings of the 5th Asia-Pacific Bioinformatics Conference. Editors, Sankoff D., Wang L., and Chin F., vol. 5 in Advances in Bioinformatics and Computational Biology series, Imperial College Press. pages 195-204.

publication supplementary material

Faux, N., Huttley, G., Mahmood, K., Webb, G., Garcia de la Banda, M, and Whisstock, J.(2007) Rcpdb: An evolutionary classification and codon usage database for repeat-containing proteins. Genome Res.

Huttley, G. A., Wakefield, M. J., and Easteal, S. (2007) Rates of genome evolution and branching order from whole genome analysis. Molecular Biology and Evolution, pages msm094-.

Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M. Hamady, M., Lindsay, H., Liu, Z., Lozupone, C., McDonald, D., Robeson, M., Sammut, R.., Smit, S., Wakefield, M. J., Widmann, J., Wikman, S., Wilson, S., Ying H, and Huttley, G. A. (2007) PyCogent: a toolkit for making sense from sequence. Genome Biol, In press.

Mather, K. A., President, M., Eastel, S., Hollenbach, J., Klitz, W., Huttley, G and Thomson, G. (2007) Long distance linkage disequilibrium between hla microsatellites in two human populations. In H. JA, editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Congress, volume II, pages 33-36, Seattle, WA. IHWG Press.

Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S. M. J., Sharpe, T., Baker, M. L., Batzer, M. A., Benos, P. V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J. E., Fazzari, M. J., Glass, J. L., Grabherr, M., Greally, J. M., Gu, W., Hore, T. A., Huttley, G. A., Kleber, M., Jirtle, R. L., Koina, E., Lee, J. T., Mahony, S., Marra, M. A., Miller, R. D. Nicholls, R. D., Oda, M., Papenfuss, A. T., Parra, Z. E., Pollock, D. D., Ray, D. A., Schein, J. E., Speed, T. P., Thompson, K., VandeBerg, J. L., Wade, C. M., Walker, J. A., Waters, P. D., Webber, C., Weidman, J. R.., Xie, X., Zody, M. C., Graves, J. A. M., Ponting, C. P., Breen, M., Samollow, P. B., Lander, E. S and Lindblad-Toh, K. (2007) Genome of the marsupial monodelphis domestica reveals innovation in non-coding sequences. Nature, 447(7141):167-177, 2007.

2005

Wakefield, M.J., Maxwell, P., and Huttley, G.A., (2005), Vestige: maximum likelihood phylogenetic footprinting. BMC Bioinformatics 6(1):130.

2004

Butterfield, A., Vedagiri, V., Lang, E., Lawrence, C., Wakefield, M.J., Isaev,A. and Huttley,G.A.,(2004), Pyevolve: a toolkit for statistical modelling of molecular evolution. BMC Bioinformatics 5(1):1.

Huttley, G.A., (2004), Modeling the impact of dna methylation on the evolution of brca1 in mammals. Mol Biol Evol 21(9):1760–8.

Robinson, A., Huttley, G.A., Booth, H.S., and Board, P.G., (2004), Modelling and bioinformatics studies of the human kappa class glutathione transferase predict a novel third glutathione transferase family with homology to prokaryotic 2-hydroxychromene-2-carboxylate (hcca) isomerases. Biochem J 379:541–52.

2001

Adcock, G.J., Dennis, E.S., Easteal, S., Huttley, G.A., Jermiin, L.S., Peacock, W.J and Thorne, A., (2001). Mitochondrial dna sequences in ancient Australians: Implications for modern human origins. Proc Natl Acad Sci U S A 98(2):537–42.

Smith, G.A., Box, N.F., Marks, L.H., Chen, W., Smit, D.J., Wyeth, J.R., Huttley, G.A., Easteal, S. and Sturm, R.A., (2001) The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution. Gene 281(1-2):81–94.

2000

Huttley, G.A., Easteal, S., Southey, M.C., Giles, G.G., McCredie, M.R.E., Hopper, J.L. and Venter, D.J., (2000) Adaptive evolution of the tumor suppressor brca1 in humans and chimpanzees. Nature Genetics 24(4):410–413.

Huttley, G.A., Jakobsen, I.B., Wilson, S.R.. and Easteal, S., (2000) How important is dna replication for mutagenesis? Mol. Biol. Evol. 17(6):929–937.

Huttley, G.A. and Wilson, S.R., (2000) Testing for concordant equilibria between population samples. Genetics 156:2127–2135.

1999

Huttley, G.A., Smith, M.W., Carrington, M. and O’Brien, S.J., (1999) A scan for linkage disequilibrium across the human genome. Genetics 152:1711–1722.