William Atchley

McFerrin, L. G., & Atchley, W. R. (2012). A novel N-terminal domain may dictate the glucose response of Mondo proteins. PLoS One, 7(4).

McFerrin, L. G., & Atchley, W. R. (2011). Evolution of the Max and Mlx Networks in Animals. GENOME BIOLOGY AND EVOLUTION, 3, 915–937. https://doi.org/10.1093/gbe/evr082

Fronza, R., Tramonti, M., Atchley, W. R., & Nardini, C. (2011). Joint analysis of transcriptional and post-transcriptional brain tumor data: searching for emergent properties of cellular systems. BMC Bioinformatics, 12.

Atchley, W. R. (2011, May 13). Walter M. Fitch (1929-2011). SCIENCE, Vol. 332, pp. 804–804. https://doi.org/10.1126/science.1207426

Fernandes, A. D., & Atchley, W. R. (2008). Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences. JOURNAL OF MOLECULAR EVOLUTION, 67(1), 51–67. https://doi.org/10.1007/s00239-008-9124-2

Funk-Keenan, J., Haire, F., Woolard, S., & Atchley, W. R. (2008). Hepatic endopolyploidy as a cellular consequence of age-specific selection for rate of development in mice. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION, 310B(5), 385–397. https://doi.org/10.1002/jez.b.21211

Fernandes, A. D., & Atchley, W. R. (2008). Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. BIOINFORMATICS, 24(19), 2177–2183. https://doi.org/10.1093/bioinformatics/btn395

Wang, Z., Smith, C. E., & Atchley, W. R. (2007). Application of complex demodulation on bZIP and bHLH-PAS protein domains. Mathematical Biosciences, 207(2), 204–218. https://doi.org/10.1016/j.mbs.2007.01.004

Atchley, W. R., & Zhao, J. (2007). Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins. MOLECULAR BIOLOGY AND EVOLUTION, 24(1), 192–202. https://doi.org/10.1093/molbev/msl143

Buck, M. J., & Atchley, W. R. (2005). Networks of coevolving sites in structural and functional domains of serpin proteins. MOLECULAR BIOLOGY AND EVOLUTION, 22(7), 1627–1634. https://doi.org/10.1093/molbev/msi157

Atchley, W. R., & Fernandes, A. D. (2005). Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(18), 6401–6406. https://doi.org/10.1073/pnas.0408964102

Atchley, W. R., Zhao, J. P., Fernandes, A. D., & Druke, T. (2005). Solving the protein sequence metric problem. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(18), 6395–6400. https://doi.org/10.1073/pnas.0408677102

Buck, M. J., & Atchley, W. R. (2003). Phylogenetic analysis of plant basic helix-loop-helix proteins. Journal of Molecular Evolution, 56(6), 742–750. https://doi.org/10.1007/s00239-002-2449-3

Johnson, E. S., Wolff, M. F., Wernsman, E. A., Atchely, W. R., & Shew, H. D. (2002). Origin of the black shank resistance gene, Ph, in tobacco cultivar Coker 371-gold. PLANT DISEASE, 86(10), 1080–1084. https://doi.org/10.1094/PDIS.2002.86.10.1080

Atchley, W. R., Lokot, T., Wollenberg, K., Dress, A., & Ragg, H. (2001). Phylogenetic analyses of amino acid variation in the serpin proteins. MOLECULAR BIOLOGY AND EVOLUTION, 18(8), 1502–1511. https://doi.org/10.1093/oxfordjournals.molbev.a003936

Ragg, H., Lokot, T., Kamp, P. B., Atchley, W. R., & Dress, A. (2001). Vertebrate serpins: Construction of a conflict-free phylogeny by combining exon-intron and diagnostic site analyses. MOLECULAR BIOLOGY AND EVOLUTION, 18(4), 577–584. https://doi.org/10.1093/oxfordjournals.molbev.a003838

Rhees, B. K., & Atchley, W. R. (2000). Body weight and tail length divergence in mice selected for rate of development. JOURNAL OF EXPERIMENTAL ZOOLOGY, 288(2), 151–164. https://doi.org/10.1002/1097-010X(20000815)288:2<151::AID-JEZ6>3.0.CO;2-6

Atchley, W. R., Wei, R., & Crenshaw, P. (2000). Cellular consequences in the brain and liver of age-specific selection for rate of development in mice. Genetics, 155(3), 1347–1357.

Kulkarni, N. H., Karavanich, C. A., Atchley, W. R., & Anholt, R. R. H. (2000). Characterization and differential expression of a human gene family of olfactomedin-related proteins. GENETICAL RESEARCH, 76(1), 41–50. https://doi.org/10.1017/S0016672300004584

Atchley, W. R., Wollenberg, K. R., Fitch, W. M., Terhalle, W., & Dress, A. W. (2000). Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis. MOLECULAR BIOLOGY AND EVOLUTION, 17(1), 164–178. https://doi.org/10.1093/oxfordjournals.molbev.a026229

Miller, R. A., Chrisp, C., & Atchley, W. (2000). Differential longevity in mouse stocks selected for early life growth trajectory. JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES, 55(9), B455–B461. https://doi.org/10.1093/gerona/55.9.b455

Ernst, C. A., Rhees, B. K., Miao, C. H., & Atchley, W. R. (2000). Effect of long-term selection for early postnatal growth rate on survival and prenatal development of transferred mouse embryos. Journal of Reproduction & Fertility, 118(1), 205–210.

Lowry, J. A., & Atchley, W. R. (2000). Molecular evolution of the GATA family of transcription factors: Conservation within the DNA-binding domain. JOURNAL OF MOLECULAR EVOLUTION, 50(2), 103–115. https://doi.org/10.1007/s002399910012

Wollenberg, K. R., & Atchley, W. R. (2000). Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 97(7), 3288–3291. https://doi.org/10.1073/pnas.070154797

Ernst, C. A., Crenshaw, P. D., & Atchley, W. R. (1999). Effect of selection for development rate on reproductive onset in female mice. GENETICAL RESEARCH, 74(1), 55–64. https://doi.org/10.1017/S001667239900381X

Morgenstern, B., & Atchley, W. R. (1999). Evolution of bHLH transcription factors: Modular evolution by domain shuffling? MOLECULAR BIOLOGY AND EVOLUTION, 16(12), 1654–1663. https://doi.org/10.1093/oxfordjournals.molbev.a026079

Rosinski, J. A., & Atchley, W. R. (1999). Molecular evolution of helix-turn-helix proteins. JOURNAL OF MOLECULAR EVOLUTION, 49(3), 301–309. https://doi.org/10.1007/PL00006552

Atchley, W. R., Terhalle, W., & Dress, A. (1999). Positional dependence, cliques, and predictive motifs in the bHLH protein domain. JOURNAL OF MOLECULAR EVOLUTION, 48(5), 501–516. https://doi.org/10.1007/PL00006494

Rhees, B. K., Ernst, C. A., Miao, C. H., & Atchley, W. R. (1999). Uterine and postnatal maternal effects in mice selected for differential rate of early development. Genetics, 153(2), 905–917.

Rosinski, J. A., & Atchley, W. R. (1998). Molecular evolution of the Myb family of transcription factors: Evidence for polyphyletic origin. JOURNAL OF MOLECULAR EVOLUTION, 46(1), 74–83. https://doi.org/10.1007/PL00006285

Atchley, W. R., & Fitch, W. M. (1997). A natural classification of the basic helix-loop-helix class of transcription factors. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 94(10), 5172–5176. https://doi.org/10.1073/pnas.94.10.5172

Atchley, W. R., Xu, S., & Cowley, D. E. (1997). Altering developmental trajectories in mice by restricted index selection. Genetics, 146(2), 629–640.

Atchley, W. R., & Zhu, J. (1997). Developmental quantitative genetics, conditional epigenetic variability and growth in mice. Genetics, 147(2), 765–776.

ATCHLEY, W. R., XU, S. Z., & VOGL, C. (1994). DEVELOPMENTAL QUANTITATIVE GENETIC MODELS OF EVOLUTIONARY CHANGE. DEVELOPMENTAL GENETICS, 15(1), 92–103. https://doi.org/10.1002/dvg.1020150110

Atchley, W. R., & Fitch, W. (1993). Genetic affinities of inbred mouse strains of uncertain origin. Molecular Biology and Evolution, 10(6), 1150.

ATCHLEY, W. R., LOGSDON, T., COWLEY, D. E., & EISEN, E. J. (1991). UTERINE EFFECTS, EPIGENETICS, AND POSTNATAL SKELETAL DEVELOPMENT IN THE MOUSE. EVOLUTION, 45(4), 891–909. https://doi.org/10.2307/2409697

ATCHLEY, W. R., & NEWMAN, S. (1989). A QUANTITATIVE-GENETICS PERSPECTIVE ON MAMMALIAN DEVELOPMENT. AMERICAN NATURALIST, 134(3), 486–512. https://doi.org/10.1086/284993