Publications of Gregory A Wray    :chronological  combined  bibtex listing:

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Books

  1. Ettensohn, C.A., G. M. Wessell, and G. A. Wray (eds.), Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches (2004), Academic Press, San Diego CA .

Papers Published

  1. 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 .
  2. S.D. Bilbo, G.A. Wray, S.E. Perkins, and W. Parker, Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune disease, Medical Hypotheses, vol. 77 (2011), pp. 494-504 .
  3. G.A. Wray, CNCing is believing, Science, vol. 333 (2011), pp. 946-947 .
  4. Tung J, Akinyi MY, Matura S, Altmann J, Wray GA, and Alberts SC, Allele-specific gene expression in wild nonhuman primates, Molecular Ecology, vol. 20 (2011), pp. 725-739 .
  5. 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 .
  6. 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 .
  7. 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 .
  8. 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 .
  9. P. Szovenyi, S.A. Rensing, D. Lang, G.A. Wray, A.J. Shaw, Generation-biased gene expression in a bryophyte model systems, Molecular Biology and Evolution, vol. 28 (2011), pp. 803-812 .
  10. O. Fedrigo, L.R. Warner, A.D. Pfefferle, P. Cruz-Gordillo, C.C. Babbitt, G.A. Wray, A pipeline to determine RT-PCR control genes for evolutionary studies: application to primate gene expression across multiple tissues, PLoS One, vol. 5 (2010), pp. E12545 .
  11. 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 .
  12. T.A. Oliver, D.A. Garfield, M.K. Manier, R. Haygood, G.A. Wray, and S.R. Palumbi, Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin, Genome Biology and Evolution, vol. 2 (2010), pp. 800-814 .
  13. J. Tung, S.C. Alberts, and G.A. Wray, Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations, Trends in Genetics, vol. 26 (2010), pp. 353-362 .
  14. 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 .
  15. O. Fedrigo and G. A. Wray, Developmental evolution: how beetles evolved their shields, Current Biology, vol. 20 (2010), pp. R64-R66 .
  16. D. Garfield, G.A. Wray, The evolution of gene regulatory interactions, BioScience, vol. 60 (2010), pp. 15-23 .
  17. 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 .
  18. 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 .
  19. L.R. Warner, C.C. Babbitt, A.E. Primus, T.F. Severson, R. Haygood, G.A. Wray, The functional consequences of genetic variation on tyrosine hydroxylase (TH) expression, Brain Research, vol. 1288 (2009), pp. 1-8 .
  20. K-D. Yokoyama, U. Ohler, G.A. Wray, Spatial preferences identify known and novel cis-regulatory element candidates and functional motif-pair relationships, Nucleic Acids Research, vol. 37 (2009), pp. e92 .
  21. J. Tung, O. Fedrigo, R. Haygood, S. Mukherjee, G.A. Wray, Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation, Molecular Biology and Evolution, vol. 26 (2009), pp. 2047-2059 .
  22. D. Garfield, G.A. Wray, Comparative embryology without a microscope: using genomic approaches to understand the evolution of development, Journal of Biology, vol. 8 (2009), pp. 65-67 .
  23. J. Tung, A. Primus, A. Bouley, T.F. Severson, S. Alberts and G.A. Wray, Evolution of a malaria resistance gene in wild primates, Nature, vol. 460 (2009), pp. 388-391 (in revision.) .
  24. G.A. Wray and C.C. Babbitt, Enhancing gene regulation, Science, vol. 321 (2008), pp. 1300-1301 .
  25. J.E. Horvath, D.W. Weisrock, S.L. Embry, I. Fiorentino, J.P. Balhoff, P. Kappeler, G.A. Wray, H.F. Willard, and A.D. Yoder, Development and application of a phylogenetic toolkit: resolving the evolutionary history of Madagascar's lemurs, Genome Research, vol. 18 (2008), pp. 489-499 .
  26. Haygood, R, O Fedrigo, B Hanson, K-D Yokoyama, and GA Wray, Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution, Nature Genetics, vol. 39 (2007), pp. 1140-1144 .
  27. Babbitt, CC, R Haygood, and GA Wray, When two is better than one, Cell, vol. 19 (2007), pp. 3-4 .
  28. GA Wray, The evolutionary significance of cis-regulatory mutations, Nature Reviews Genetics, vol. 8 (2007), pp. 206-216 .
  29. Bowsher, JH, GA Wray, and E Abouheif, Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invicta, Journal of Experimental Zoology, vol. 308B (2007), pp. 769-776 .
  30. Sumrall, CD and GA Wray, Developmental control of ambulacral reduction in fossil echinoderms, Paleobiology, vol. 33 (2007), pp. 149-163 .
  31. Tishkoff, S A, F A Reed, A Ranciaro, B F Voight, C C Babbitt, J S Silverman, K Powell, H Mortensen, J B Hirbo, M Osman, M Ibrahim, S A Omar, G Lema, T B N, J Ghori, S Bumpstead, J K Pritchard, G A Wray, and P Deloukas, Convergent adaptation in humans: the genetic basis of lactase persistence in Africa, Nature Genetics, vol. 39 (2007), pp. 31-40 .
  32. G A Wray, Spot on (and off), Nature, vol. 440 (2006), pp. 1001-1002 .
  33. Rudd, M K, G A Wray, and H F Willard, The evolutionary dynamics of α-satellite, Genome Research, vol. 16 (2006), pp. 88-96 .
  34. Sumrall, C D and G A Wray, Developmental control of ambulacral reduction in fossil echinoderms, Paleobiology, vol. 33 (2006), pp. 149-163 .
  35. Romano, L and G A Wray, Endo16 is required for gastrulation in the sea urchin Lytechinus variegatus, Development, Growth, and Differentiation, vol. 48 (2006), pp. 487-497 .
  36. Sodergren, E, G M Weinstock, and The Sea Urchin Genome Sequencing Consortium, The genome of the sea urchin Stongylocentrotus purpuratus, Science, vol. 314 (2006), pp. 941-952 .
  37. G A Wray, The evolution of embryonic gene expression in sea urchins, Integrative and Comparative Biology, vol. 46 (2006), pp. 233-242 .
  38. Loisel, D A, M V Rockman, G A Wray, J Altmann, and S Alberts, Ancient polymorphism and functional variation in the primate MHC-DQA1 5’ cis-regulatory region, Proceedings of the National Academy of Sciences (USA), vol. 103 (2006), pp. 16331-16336 .
  39. Nyberg, K G, C N Ciampaglio, and G A Wray, Tracing the ancestry of the great white shark, Carcharodon carcharias, using morphometric analysis of fossil teeth, Journal of Vertebrate Paleontology, vol. 26 (2006), pp. 806-814 .
  40. Mooi, R, B.David, and G.A. Wray, Arrays in rays: terminal addition in echinoderms and its correlation with gene expression., Evolution & Development, vol. 7 (2005), pp. 542-555 .
  41. Rockman, M. V., M. W. Hahn, N. Soranzo, D. Loisel, D. B. Goldstein, and G. A. Wray, Positive selection on MMP3 regulation has shaped heart disease risk, Current Biology, vol. 14 (2004), pp. 1531-1539 .
  42. Wray, G. A., C. Kitazawa, and B. Miner, Culture of echinoderm larvae though metamorphosis, in Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches (2004), pp. 75-86, Academic Press, San Diego CA .
  43. Hahn, M.W., M.V. Rockman, N. Soranzo, D.B. Goldstein, and G.A. Wray, Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the Factor VII locus, Genetics, vol. 167 (2004), pp. 867-877 .
  44. Bely, A.E. and G.A. Wray, Molecular phylogeny of naidid worms (Annelida: Clitellata), Molecular Phylogeny and Evolution, vol. 30 (2004), pp. 50-63 .
  45. Rockman, M. V., M. W. Hahn, N. Soranzo, D. B. Goldstein, G.A. Wray, Positive selection on a human-specific transcription factor binding site regulating IL4 expression, Current Biology, vol. 130 (2003), pp. 2118-2123 .
  46. Wray, G.A., Transcriptional regulation: evolution, in Encyclopedia of the Human Genome, edited by D. Cooper (2003), Nature Publishing Group .
  47. Hahn, M.W., J. Staijch, and G.A. Wray, The effects of selection against spurious transcription factor binding sites, Molecular Biology and Evolution, vol. 20 (2003), pp. 901-906 .
  48. Knott, K.E., E.J. Balser, W.B. Jaeckle, and G.A. Wray, Identification of asteroid genera with species capable of larval cloning, Biological Bulletin, vol. 204 (2003), pp. 246-255 .
  49. G.A. Wray, Transcriptional regulation and the evolution of development, International Journal of Developmental Biology, vol. 47 (2003), pp. 675-684 .
  50. Wray, G.A., M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, and L. Romano, The evolution of transcriptional regulation in eukaryotes, Molecular Biology and Evolution, vol. 20 (2003), pp. 1377-1419 .
  51. Romano, L. and G.A. Wray, Conservation of endo16 expression in sea urchins despite divergence in both cis and trans-acting elements of transcriptional regulation, Development, vol. 130 (2003), pp. 4187-4199 .
  52. Rockman, M.V. and G.A. Wray, Abundant raw material for cis-regulatory evolution in humans, Molecular Biology and Evolution, vol. 19 (October, 2002), pp. 1991-2004 .
  53. Bely, A.E. and G.A. Wray, Getting a head in the world, Natural History, vol. 10/02 (October, 2002), pp. 30-32 .
  54. Abouheif, E.A. and G.A. Wray, Evolution of the gene network underlying wing polyphenism in ants, Science, vol. 297 (July, 2002), pp. 249-252 .
  55. Lowe, C.J., L. Issel-Tarver, and G.A. Wray, Evolution of new developmental roles for orthodenticle and distal-less in the larvae of echinoderms, Evolution & Development, vol. 4 (February, 2002), pp. 111-123 .
  56. Hahn, M.W. and G.A. Wray, The G-value paradox, Evolution & Development, vol. 4 (February, 2002), pp. 73-75 .
  57. Bely, A.E. and G.A. Wray, Evolution of regeneration and fission in an annelid: insights from engrailed- and orthodenticle-class gene expression, Development, vol. 128 (2001), pp. 2781-2791 .
  58. Stone, J.R. and G.A. Wray, Rapid appearance of new transcription factor binding sites by local point mutation, Molecular Biology and Evolution, vol. 18 (2001), pp. 1764-1770 .
  59. Wray, G.A., The evolution of embryonic patterning mechanisms in animals, Seminars in Cell and Developmental Biology, vol. 11 (2000), pp. 353-393 .
  60. Knott, K.E. and G.A. Wray, Controversy and consensus in asteroid systematics: new insights into ordinal and familial relationships, American Zoologist, vol. 40 (2000), pp. 382-392 .
  61. Wray, G.A. and C.J. Lowe, Developmental regulatory genes and echinoderm evolution, Systematic Biology, vol. 49 (2000), pp. 151-174 .
  62. Wray, G.A., Peering ahead (cautiously), Evolution and Development, vol. 2 (2000), pp. 1-2 .
  63. Cameron, RA, G Mahairas, JP Rast, TR Biondi, S Schwartzell, J Wallace, BT Livingston, GA Wray, CA Ettensohn, H Lehrach, RJ Britten, EH Davison, and L Hood, A sea urchin genome project: sequence scan, virtual map, and additional resources, Proceedings of the National Academy of Sciences (USA), vol. 97 (2000), pp. 9514-9518 .

Papers Accepted

  1. D. Garfield, R. Haygood, W. J. Nielsen, G. A. Wray, Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus, Evolution & Deveopment (2011) .
  2. M.S. Smith, G.A. Wray, R.A. Raff, Revisiting cell lineage and cell fate in light of the evolution of axis formation in Heliocidaris erythrogramma, Evolution & Development (2010) .

Papers Submitted

  1. 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 (2011) .
  2. D. A. Garfield, D. Runcie, C. C. Babbitt, R. Haygood, G.A. Wray, Evolvability and robustness in a developmental gene regulatory network (2011) .

Book Chapters

  1. G.A. Wray, Embryos and evolution: 150 years of reciprical illumination, in Evolution Since Darwin, edited by M.A. Bell, D.J. Futuyma, W.F. Eanes, J.S. Levinton (2010), pp. 215-239, Sinauer Associates .
  2. J. Tung and G.A. Wray, Evolution of traits deduced from genome comparisons, in Encyclopedia of Life Sciences, edited by Nature Publishing Group (in press) .
  3. G.A. Wray, Evolutionary synthesis in the genomic era, in Towards an Extended Evolutionary Synthesis (in press), MIT Press .
  4. G.A. Wray, Evolution and Development, in Evolution: The First Four Billion Years, edited by M. Ruse and J. Travis (in press), pp. 208-236, Belknap Press .

Book Chapter

  1. Babbitt, CC and GA Wray, Evolution of human gene expression control, in Encyclopedia of Life Sciences (2007), Nature Publishing Group (electronic resource.) .

Other

  1. G.A. Wray, Guest in radio interview on evolutionary genomics for talk show "Radio in Vivo" (February 5, 2007) (WCOM.) .
  2. Wray, G.A., Dating branches on the tree of life using DNA, Genome Biology (2001) .
  3. MW Hahn and GA Wray, the G-value paradox, Evolution and Development (2001) .
  4. Wray, G.A., Gene expression during echinoderm metamorphosis, Gamete, vol. 8 (2000), pp. S48-S49 .

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