William R. Atchley

William Neal Reynolds Distinguished Professor of Genetics, Statistics and Biomathematics

PhD, University of Kansas
Postdoctoral, University of Melbourne

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Computational biology and molecular evolution

My research focuses on integrating developmental and molecular biology with quantitative genetics to explore broad questions about the evolution of developmental processes and complex morphologies. This research is carried out at several organization levels ranging from molecular analyses to statistical studies of complex polygenically controlled phenotypes. Our research includes both theoretical as well as experimental components.

My primary research interests are on computational biology and molecular evolution. I am particularly interested in the integration of multivariate statistical procedures with information theory and applications of these procedures to analyses of biological sequences and protein structure and evolution. I am particularly interested in modeling structure and evolution in the basic helix-loop-helix family of transcriptional regulators and the serine proteinase inhibitor (serpin) proteins. Within the bHLH family, we are particularly interested in the origin and evolution of the Myc-Max-Mad network of proto-oncogenes and the bHLH-PAS proteins. Topics of current interest in computational biology include a) partitioning of covariances among amino acid sites into associations derived from phylogenetic history, structural, and functional constraints; and b) developing multivariate statistical procedures to probabilistically identify and classify proteins.

Another major project focuses on developmental quantitative genetics. We are interested in integrating developmental biology into quantitative genetics theory and methodology. This work uses the laboratory mouse to explore the changes in genetic variance-covariance structures for complex traits during ontogeny, age-specific consequences of selection, the role of uterine maternal effects in development and evolution, and the development of epigenetic models to explain the origin and evolution of heritable associations among complex traits.

Our research is generously supported by grants from the National Institutes of Health, National Science Foundation and the Alexander von Humboldt Foundation (Germany).

Selected Publications:

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

Atchley, W. R . and Fernandes, A. 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 Atchley, W.R. 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 Atchley, W.R. 2003. Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 56: 742-750. [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 ]

Kulkarni, N.H., Karavanich, C.A., Atchley, W.R. and Anholt, R.R. 2000. Characterization and differential expression of a human gene family of olfactomedin-related proteins. Genet Res. 76:41-50. [Abstract]

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. Journal of Reproduction and Fertility, 118: 205-210. [Abstract]

Rhees, B.K. and Atchley, W.R. 2000. Body weight and tail length divergence in mice selected for rate of development. J. Exp. Zool. 288:151-64. [Abstract]

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? Molecular Biology and Evolution, 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. Genetical Research 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. Journal of Molecular Evolution 48:501-519. [Abstract] [PDF Reprint]

Rosinski, J. and Atchley, W.R. 1998. Molecular evolution of Myb family of transcription factors. Journal of Molecular Evolution 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]

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]

For more information contact:

Dr. William R, Atchley
Department of Genetics
N.C. State University
Raleigh, NC 27695-7614
Tel: (919) 515-7088
E-mail: William Atchley

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