Gregory A Wray, Professor
Research Categories: Evolution of gene networks and developmental mechanisms
Research Description: I study the evolution of genes and genomes with the broad aim of understanding the origins of biological diversity. My approach focuses on changes in the expression of genes using both empirical and computational approaches and spans scales of biological organization from single nucleotides through gene networks to entire genomes. At the finer end of this spectrum of scale, I am focusing on understanding the functional consequences and fitness components of specific genetic variants within regulatory sequences of several genes associated with ecologically relevant traits. At the other end of the scale, I am developing molecular and analytical methods to detect changes in gene function throughout entire genomes, including statistical frameworks for detecting natural selection on regulatory elements and empirical approaches to identify functional variation in transcriptional regulation. At intermediate scales, I am investigating functional variation within a dense gene network in the context of wild populations and natural perturbations. My research leverages the advantages of several different model systems, but primarily focuses on sea urchins and primates (including humans).
- D.E. Runcie, D.A. Garfield, C.C. Babbitt, J.A. Wygoda, S. Mukherjee, and G.A. Wray, Genetics of gene expression responses to temperature stress in a sea urchin gene network, Molecular Ecology, vol. 21 (2012), pp. 4547-4562 .
- Shibata, Y., N.C. Sheffield, O. Fedrigo, C.C. Babbitt, M. Wortham, A.K. Tewari, D. London, L. Song, B-K. Lee, V.R. Iyer, S.C Parker, E.H. Margulies, G.A. Wray, T.S. Furey, and G.E. Crawford, Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection, PLoS Genetics, vol. 8 (2012), pp. e1002789 .
- D. Garfield, R. Haygood, W.J. Nielsen, and G.A. Wray, Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus, Evolution & Development, vol. 14 (2012), pp. 152-167 .
- Babbitt, C.C., J. Tung, G.A. Wray, and S.C. Alberts, Changes in gene expression associated with reproductive maturation in wild female baboons, Genome Biology and Evolution, vol. 4 no. 2 (2012), pp. 102-109 .
- A.D. Pfefferle, L.R. Warner, C.W. Wang, W.J. Nielsen, C.C. Babbitt, O. Fedrigo, and G.A. Wray, Expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution, Journal for Human Evolution, vol. 60 (2011), pp. 205-211 .
- C.C. Babbitt, L.R. Warner, O. Fedrigo, C.E. Wall, and G.A. Wray, Genomic signatures of diet-related shifts in primate evolution, Proceedings of the Royal Society of London B, vol. 278 (2011), pp. 961-969 .
- K.D. Yokoyama, J.L. Thorne, and G.A. Wray, Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution, Genome Biology and Evolution, vol. 3 (2011), pp. 66-74 .
- O. Fedrigo, A. D. Pfefferele, C. C. Babbitt, R. Haygood, C. E. Wall, G.A. Wray, Molecular evidence that a metabolic trade-off contributed to human brain size evolution, Brain, Behavior, and Evolution, vol. 78 (2011), pp. 315-326 .
- P. Cruz-Gordillo, O. Fedrigo, G.A. Wray, and C.C. Babbitt, Extensive changes in the expression of the opioid genes between humans and chimpanzees, Brain Behavior and Evolution, vol. 76 (2010), pp. 154-162 .
- C.C. Babbitt, J.S. Silverman, R. Haygood, J.M. Reininga, M.V. Rockman, and G.A. Wray, Multiple functional variants in cis modulate PDYN expression, Molecular Biology and Evolution, vol. 27 (2010), pp. 465-479 .
- C.C. Babbitt, O. Fedrigo, A.D. Pfefferle, A.P. Boyle, J.E. Horvath, T.S. Furey, G.A. Wray, Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain, Genome Biology and Evolution, vol. 2 (2010), pp. 67-69 .
- R. Haygood, C.C. Babbitt, O. Fedrigo, and G.A. Wray, Contrasts between adaptive coding and noncoding changes during human evolution, Proceedings of the National Academy of Sciences U.S.A., vol. 107 (2010), pp. 7853-7857 .