Selected Recent Publications from the Atchley Lab:

Fernandes, A. D. and W. R. Atchley. 2008. Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distance sequences. Journal of Molecular Evolution 67:51-67.

Fernandes, A. D. and W. R. Atchley. 2008. A computational framework for inferring site specific relative evolutionary rates given the phylogenetic tree. BMC Bioinformatics 24:2177-2183.

Wang, Z, C. E. Smith, and W. R. Atchley. 2007. Application of complex demodulation on bZIP and bHLH-PAS protein domains. Math. Bio. 207:204-218. [PDF reprint]

Atchley, W. R. and J. Zhao. 2006. Molecular Architecture of the DNA Binding Region and its Relationship to Classification of Basic Helix-Loop-Helix Proteins. Mol. Biol. Evol.
24:192-202. [PDF reprint ]

Fernandes, A. D. and W. R. Atchley. 2006. Gaussian Quadrature Formulae for Arbitrary Positive Measures. Evol. Bioinf. Online 2: 261-269. [PDF reprint]

Wang, Z. and W. R. Atchley. 2006. Spectral analysis of sequence variability in basic helix-loop-helix (bHLH) protein domains. Evol. Bioinf. Online 2:201.210. [PDF reprint]

Atchley, W. R., J. Zhao, A. Fernandes and T. Drueke. 2005. Solving the sequence “metric” problem: Proc. Natl. Acad. Sci. USA 102:6395-6400. [PDF Reprint]

Atchley, W. R . and A. Fernandes. 2005. Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network. Proc. Natl. Acad. Sci. USA 102:6401-6406. [PDF Reprint]

Buck, M. J. and W. R. Atchley. 2005. Networks of coevolving sites in structural and functional domains of serpin proteins. Mol. Biol. Evol. 22:1627-1634. [PDF Reprint]

Buck, M. J. and W. R. Atchley. 2003. Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 56:742-50. [PDF Reprint]

Atchley, W.R., Lokot, T., Wollenberg, K., Dress, A. and Ragg H. 2001. Phylogenetic analyses of amino acid variation in the serpin proteins. Mol Biol Evol. 18:1502-11. [PDF Reprint ]

Ragg, H., Lokot, T., Kamp, P.B., Atchley, W.R. and Dress, A. 2001. Vertebrate serpins: construction of a conflict-free phylogeny by combining exon-intron and diagnostic site analyses. Mol Biol Evol. 18:577-84. [PDF Reprint ]

Atchley, W. R., Wei, R., and P. D. Crenshaw. 2000. Cellular consequences in the brain and liver to age-specific selection for rate of development in mice. Genetics 155:1347-1357. [Abstract] [PDF Reprint]

Wollenberg, K.R. and Atchley, W.R. 2000. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. U S A 97: 3288-3291. [Abstract] [PDF Reprint]

Lowry, J.A. and Atchley, W.R. 2000. Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J. Mol. Evol. 50:103-115. [Abstract] [PDF Reprint]

Atchley, W.R., Wollenberg, K. R., Fitch, W. M., Terhalle, W., and Dress, A. W. 2000. Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis. Molecular Biology and Evolution 17:164-178. [Abstract] [PDF Reprint]

Ernst, C.A., Rhees, B. K., Maio, C. H., and Atchley, W.R. 2000. Effect of long-term selection on survival and prenatal development of transferred mouse embryos. J Reproduction and Fertility, 118: 205-210. [Abstract] [PDF Reprint]

Rhees, B.K. and W.R. Atchley. 2000. Body weight and tail length divergence in mice selected for rate of development. J.Exp. Zool. (Mol. Dev. Evol). 288:151-164. [PDF Reprint]

Rosinski, J.A. and Atchley, W.R. 1999. Molecular evolution of helix turn helix proteins. J. Mol. Evol. 49: 301-309. [Abstract] [PDF Reprint]

Morgenstern, B., and Atchley, W.R. 1999. Evolution of the bHLH family of transcription factors: Modular evolution by domain shuffling? Mol. Biol. Evol, 16: 1654-1663. [Abstract] [PDF Reprint]

Ernst, C.A., Crenshaw, P. D., and Atchley, W.R. 1999. Effect of selection for development rate on reproductive onset in female mice. Genet Res 74:55-64. [Abstract]

Rhees, B. K., Ernst, C.A., Maio, C. H., and Atchley, W.R. 1999. Uterine and postnatal maternal effects in mice selected for differential rate of early development. Genetics 153:905-917. [Abstract] [PDF Reprint]

Atchley, W.R., Terhalle, W. and Dress, A. 1998. Positional dependence, cliques and predictive motifs in the bHLH protein domain. J Mol Evol 48:501-519. [Abstract] [PDF Reprint]

Rosinski, J. and Atchley, W.R. 1998. Molecular evolution of Myb family of transcription factors. J. Mol. Evol. 46:74-83. [Abstract] [PDF Reprint]

Atchley, W.R. and Zhu, J. 1997. Developmental quantitative genetics, conditional epigenetic variability and growth in mice. Genetics 147:765-776. [Abstract] [PDF Reprint]

Atchley, W.R. and Fitch, W. M. 1997. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. USA 94:5172-5176. [Abstract] [PDF Reprint]

Atchley, W.R., Cowley, D. E. and Xu, S. 1997. Altering developmental trajectories in mice by restricted index selection. Genetics 146:629-640. [Abstract] [PDF Reprint]