Gregory Allan Wray
Professor of Biology
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).
Summer Scholars Program in Genome Sciences and Medicine awarded by National Institutes of Health (Co-Principal Investigator). 2017 to 2022
Postdoctoral training in genomic medicine research awarded by National Institutes of Health (Mentor). 2017 to 2022
Training Program in Developmental and Stem Cell Biology awarded by National Institutes of Health (Mentor). 2001 to 2022
Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2021
NRT: Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) awarded by National Science Foundation (Co-Principal Investigator). 2015 to 2020
Genetics Training Grant awarded by National Institutes of Health (Mentor). 1979 to 2020
Organization and Function of Cellular Structure awarded by National Institutes of Health (Mentor). 1975 to 2020
Decoding schizophrenia-From GWAS to functional regulatory variants awarded by National Institutes of Health (Co Investigator). 2014 to 2019
Global Genetic Diversity Study for Malaria awarded by Naval Medical Research Center (Principal Investigator). 2018
Evolutionary Rewiring of a Developmental Gene Regulatory Network awarded by National Science Foundation (Principal Investigator). 2015 to 2018
Byrne, M, Koop, D, Morris, VB, Chui, J, Wray, GA, and Cisternas, P. "Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures." Developmental dynamics : an official publication of the American Association of Anatomists 247.1 (January 2018): 239-249. Full Text
Linchangco, GV, Foltz, DW, Reid, R, Williams, J, Nodzak, C, Kerr, AM, Miller, AK, Hunter, R, Wilson, NG, Nielsen, WJ, Mah, CL, Rouse, GW, Wray, GA, and Janies, DA. "The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics." Molecular phylogenetics and evolution 115 (October 2017): 161-170. Full Text Open Access Copy
Babbitt, CC, Haygood, R, Nielsen, WJ, and Wray, GA. "Gene expression and adaptive noncoding changes during human evolution." BMC genomics 18.1 (June 5, 2017): 435-. Full Text
Koop, D, Cisternas, P, Morris, VB, Strbenac, D, Yang, JYH, Wray, GA, and Byrne, M. "Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan." BMC developmental biology 17.1 (February 13, 2017): 4-. Full Text
Runcie, DE, Dorey, N, Garfield, DA, Stumpp, M, Dupont, S, and Wray, GA. "Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification." Genome biology and evolution 8.12 (December 2016): 3672-3684. Full Text Open Access Copy
Israel, JW, Martik, ML, Byrne, M, Raff, EC, Raff, RA, McClay, DR, and Wray, GA. "Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris." PLoS biology 14.3 (March 4, 2016): e1002391-. Full Text
Janies, DA, Witter, Z, Linchangco, GV, Foltz, DW, Miller, AK, Kerr, AM, Jay, J, Reid, RW, and Wray, GA. "EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms." BMC bioinformatics 17 (January 22, 2016): 48-. Full Text Open Access Copy
Dutta, V, Altermann, E, Olson, J, Wray, GA, Siletzky, RM, and Kathariou, S. "Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains." Genome announcements 4.4 (January 2016). Full Text
Byrne, M, Koop, D, Cisternas, P, Strbenac, D, Yang, JYH, and Wray, GA. "Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma." Marine genomics 24 Pt 1 (December 2015): 41-45. Full Text
PsychENCODE Consortium, , Akbarian, S, Liu, C, Knowles, JA, Vaccarino, FM, Farnham, PJ, Crawford, GE, Jaffe, AE, Pinto, D, Dracheva, S, Geschwind, DH, Mill, J, Nairn, AC, Abyzov, A, Pochareddy, S, Prabhakar, S, Weissman, S, Sullivan, PF, State, MW, Weng, Z, Peters, MA, White, KP, Gerstein, MB, Amiri, A, Armoskus, C, Ashley-Koch, AE, Bae, T, Beckel-Mitchener, A, Berman, BP, Coetzee, GA, Coppola, G, Francoeur, N, Fromer, M, Gao, R, Grennan, K, Herstein, J, Kavanagh, DH, Ivanov, NA, and Jiang, Y et al. "The PsychENCODE project." Nature neuroscience 18.12 (December 2015): 1707-1712. (Review) Full Text Open Access Copy
Babbitt, CC, Pfefferle, LW, Crawford, GE, and Wray, GA. "Evolution of gene expression network underlying a disease state." April 2015.
Bauernfeind, AL, Reyzer, ML, Caprioli, RM, Ely, JJ, Babbitt, CC, Wray, GA, Hof, PR, and Sherwood, CC. "Differences in energy metabolism in the brains of humans and chimpanzees: a study of protein expression." March 2015.
Babbitt, CC, and Wray, GA. "Evolution of gene expression network underlying a disease state in humans and non-human primates." March 2015.
Bauernfeind, AL, Soderblom, EJ, Turner, ME, Moseley, AM, Ely, JJ, Hof, PR, Sherwood, CC, Wray, GA, and Babbitt, CC. "Differential gene and protein expression in the human and chimpanzee brain: A comparison using high-throughput techniques." March 2014.
Wygoda, JA, Byrne, M, Mcclay, DR, and Wray, GA. "Shifts in the Expression of Developmental Regulatory Genes Involved in the Evolution of a Novel Life History Difference." 2014.
Wygoda, JA, Koop, D, Yang, J, Wray, GA, and Byrne, M. "Developmental Transcriptome of Heliociaris erythrogramma - from bilateral larva to radial juvenile." 2014.
Wray, GA, Garfield, D, and Runcie, D. "Evolution of an embryonic gene regulatory network in the sea urchin Strongylocentrotus purpuratus." 2013.
Runcie, DE, Garfield, DA, Babbitt, CC, Pfefferle, A, Nielsen, WJ, and Wray, GA. "Phenotypic plasticity and the developmental regulatory network in the purple sea urchin." 2013.
Babbitt, CC, Pfefferle, LW, Fedrigo, O, and Wray, GA. "Conservation and function of noncoding RNAs in primate evolution." April 2012.
Horvath, JE, Wu, C, Toler, M, Fedrigo, O, Pfefferle, LW, Moore, A, Ramachandran, GL, Babbitt, CC, Jernvall, J, Wray, GA, and Wall, CE. "Enamel thickness in Microcebus murinus and Macaca mulana and the evolutionary genetics of enamel matrix proteins in hominoids." 2012.