Publications of Gregory A. Wray

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. Frederik Nijhout, H; Wray, GA; Kremen, C; Teragawa, CK, Ontogeny, phylogeny and evolution of form: An algorithmic approach, Systematic Zoology, vol. 35 no. 4 (January, 1986), pp. 445-457, Oxford University Press (OUP), ISSN 0039-7989
  2. Nijhout, HF; Wray, GA, Homologies in the colour patterns of the genus Charaxes (Lepidoptera: Nymphalidae), Biological Journal of the Linnean Society, vol. 28 no. 4 (January, 1986), pp. 387-410, Oxford University Press (OUP), ISSN 0024-4066
  3. WRAY, GA; MCCLAY, DR, THE EMBRYONIC MESENCHYME IN A PRIMITIVE SEA-URCHIN, EUCIDARIS-TRIBULOIDES, JOURNAL OF CELL BIOLOGY, vol. 103 no. 5 (November, 1986), pp. A371-A371, ROCKEFELLER UNIV PRESS, ISSN 0021-9525
  4. NIJHOUT, HF; WRAY, GA, Homologies in the colour patterns of the genus Heliconius (Lepidoptera: Nymphalidae), Biological Journal of the Linnean Society, vol. 33 no. 4 (January, 1988), pp. 345-365, Oxford University Press (OUP), ISSN 0024-4066
  5. Wray, GA; McClay, DR, The origin of spicule-forming cells in a 'primitive' sea urchin (Eucidaris tribuloides) which appears to lack primary mesenchyme cells., Development (Cambridge, England), vol. 103 no. 2 (June, 1988), pp. 305-315, ISSN 0950-1991
  6. WRAY, GA; MCCLAY, DR, MOLECULAR HETEROCHRONIES AND HETEROTOPIES IN EARLY ECHINOID DEVELOPMENT, EVOLUTION, vol. 43 no. 4 (1989), pp. 803-813, JSTOR, ISSN 0014-3820
  7. Raff, RA; Wray, GA, Heterochrony: Developmental mechanisms and evolutionary results, Journal of Evolutionary Biology, vol. 2 no. 6 (January, 1989), pp. 409-434, WILEY, ISSN 1010-061X
  8. Wray, GA; Raff, RA, Evolutionary modification of cell lineage in the direct-developing sea urchin Heliocidaris erythrogramma., Developmental biology, vol. 132 no. 2 (April, 1989), pp. 458-470, ISSN 0012-1606
  9. Henry, JJ; Amemiya, S; Wray, GA; Raff, RA, Early inductive interactions are involved in restricting cell fates of mesomeres in sea urchin embryos., Developmental biology, vol. 136 no. 1 (November, 1989), pp. 140-153, ISSN 0012-1606
  10. NIJHOUT, HF; WRAY, GA; GILBERT, LE, An analysis of the phenotypic effects of certain colour pattern genes in Heliconius (Lepidoptera: Nymphalidae), Biological Journal of the Linnean Society, vol. 40 no. 4 (January, 1990), pp. 357-372, Oxford University Press (OUP), ISSN 0024-4066
  11. Raff, RA; Parr, BA; Parks, AL; Wray, GA, Heterochrony and other mechanisms of radical evolutionary change in early development, Evolutionary innovations (January, 1990), pp. 71-98
  12. Scott, LB; Lennarz, WJ; Raff, RA; Wray, GA, The "lecithotrophic" sea urchin Heliocidaris erythrogramma lacks typical yolk platelets and yolk glycoproteins., Developmental biology, vol. 138 no. 1 (March, 1990), pp. 188-193, ISSN 0012-1606
  13. Wray, GA; Raff, RA, Novel origins of lineage founder cells in the direct-developing sea urchin Heliocidaris erythrogramma., Developmental biology, vol. 141 no. 1 (September, 1990), pp. 41-54, ISSN 0012-1606
  14. Henry, JJ; Wray, GA; Raff, RA, The dorsoventral axis is specified prior to first cleavage in the direct developing sea urchin Heliocidaris erythrogramma., Development (Cambridge, England), vol. 110 no. 3 (November, 1990), pp. 875-884, ISSN 0950-1991
  15. Hernry, JJ; Wray, GA; Raff, RA, Mechanism of an alternate type of echinoderm blastula formation: The wrinkled blastula of the sea urchin Heliocidaris erythrogramma, Development Growth and Differentiation, vol. 33 no. 4 (1991), pp. 317-328, ISSN 0012-1592
  16. Wray, GA; Raff, RA, The evolution of developmental strategy in marine invertebrates, Trends in Ecology and Evolution, vol. 6 no. 2 (January, 1991), pp. 45-50, Elsevier BV
  17. Henry, JJ; Wray, GA; Raff, RA, Mechanism of an Alternate Type of Echinoderm Blastula Formation: The Wrinkled Blastula of the Sea Urchin Heliocidaris erythrogramma direct development/echinoderm development/morphogenesis/sea urchin embryos/wrinkled blastula, Development, Growth & Differentiation, vol. 33 no. 4 (January, 1991), pp. 317-328, WILEY
  18. Wray, GA, Rates of evolution in developmental processes, American Zoologist, vol. 32 no. 1 (1992), pp. 123-134
  19. Wray, GA, The evolution of larval morphology during the post-Paleozoic radiation of echinoids, Paleobiology, vol. 18 no. 3 (January, 1992), pp. 258-287, Cambridge University Press (CUP)
  20. Wray, GA, Rates of evolution in developmental processes, Integrative and Comparative Biology, vol. 32 no. 1 (December, 1992), pp. 123-134, Oxford University Press (OUP), ISSN 1540-7063
  21. Wray, GA, Developmental evolution: new paradigms and paradoxes., Developmental genetics, vol. 15 no. 1 (January, 1994), pp. 1-6
  22. Wray, GA; Bely, AE, The evolution of echinoderm development is driven by several distinct factors., Development (Cambridge, England). Supplement, vol. 120 no. SUPPL. (January, 1994), pp. 97-106
  23. Wray, GA; Bely, AE, The evolution of echinoderm development is driven by several distinct factors, Development, vol. 120 no. SUPPL. (January, 1994), pp. 97-106
  24. Wray, GA, The evolution of cell lineage in echinoderms, Integrative and Comparative Biology, vol. 34 no. 3 (December, 1994), pp. 353-363, Oxford University Press (OUP), ISSN 1540-7063
  25. Smith, AB; Littlewood, DTJ; Wray, GA, Comparing patterns of evolution: larval and adult life history stages and ribosomal RNA of post-Palaeozoic echinoids, Philosophical Transactions - Royal Society of London, B, vol. 349 no. 1327 (January, 1995), pp. 11-18, The Royal Society
  26. Craig, SF; Slobodkin, LB; Wray, G, The 'paradox' of polyembryony, Trends in Ecology & Evolution, vol. 10 no. 9 (January, 1995), pp. 371-372, Elsevier BV, ISSN 0169-5347
  27. Wray, GA, Punctuated evolution of embryos, Science, vol. 267 no. 5201 (February, 1995), pp. 1115-1116, American Association for the Advancement of Science (AAAS)
  28. Wray, GA; Levinton, JS; Shapiro, LH, Molecular evidence for deep Precambrian divergences among metazoan phyla, Science, vol. 274 no. 5287 (January, 1996), pp. 568-581, American Association for the Advancement of Science (AAAS)
  29. Wray, GA, Parallel evolution of nonfeeding larvae in echinoids, Systematic Biology, vol. 45 no. 3 (January, 1996), pp. 308-322, Oxford University Press (OUP)
  30. Craig, SF; Slobodkin, LB; Wray, GA; Biermann, CH, The 'paradox' of polyembryony: A review of the cases and a hypothesis for its evolution, Evolutionary Ecology, vol. 11 no. 2 (January, 1997), pp. 127-143, Springer Nature
  31. Panganiban, G; Irvine, SM; Lowe, C; Roehl, H; Corley, LS; Sherbon, B; Grenier, JK; Fallon, JF; Kimble, J; Walker, M; Wray, GA; Swalla, BJ; Martindale, MQ; Carroll, SB, The origin and evolution of animal appendages., Proceedings of the National Academy of Sciences of the United States of America, vol. 94 no. 10 (May, 1997), pp. 5162-5166, ISSN 0027-8424
  32. Benink, H; Wray, G; Hardin, J, Archenteron precursor cells can organize secondary axial structures in the sea urchin embryo., Development (Cambridge, England), vol. 124 no. 18 (September, 1997), pp. 3461-3470, ISSN 0950-1991
  33. Lowe, CJ; Wray, GA, Radical alterations in the roles of homeobox genes during echinoderm evolution., Nature, vol. 389 no. 6652 (October, 1997), pp. 718-721, ISSN 0028-0836
  34. Abouheif, E; Akam, M; Dickinson, WJ; Holland, PW; Meyer, A; Patel, NH; Raff, RA; Roth, VL; Wray, GA, Homology and developmental genes., Trends in genetics : TIG, vol. 13 no. 11 (November, 1997), pp. 432-433, ISSN 0168-9525
  35. Passini, MA; Kurtzman, AL; Canger, AK; Asch, WS; Wray, GA; Raymond, PA; Schechter, N, Cloning of zebrafish vsx1: expression of a paired-like homeobox gene during CNS development., Developmental genetics, vol. 23 no. 2 (January, 1998), pp. 128-141, WILEY, ISSN 0192-253X
  36. Wray, GA, Promoter logic., Science (New York, N.Y.), vol. 279 no. 5358 (March, 1998), pp. 1871-1872, ISSN 0036-8075
  37. Lowe, CJ; Wray, GA, Erratum: Radical alterations in the roles of homeobox genes during echinoderm evolution (Nature (1997) 389 (718-721)), Nature, vol. 392 no. 6671 (March, 1998), pp. 105, Springer Nature
  38. Wray, GA; Abouheif, E, When is homology not homology?, Current opinion in genetics & development, vol. 8 no. 6 (December, 1998), pp. 675-680, ISSN 0959-437X
  39. Abouheif, E; Wray, GA, The evolutionary and developmental genetic basis of wing polymorphism in ants., AMERICAN ZOOLOGIST, vol. 39 no. 5 (January, 1999), pp. 12A-12A, SOC INTEGRATIVE COMPARATIVE BIOLOGY, ISSN 0003-1569
  40. Bely, AE; Wray, GA, Expression of homeobox genes during regeneration and asexual reproduction in an annelid., AMERICAN ZOOLOGIST, vol. 39 no. 5 (January, 1999), pp. 12A-12A, SOC INTEGRATIVE COMPARATIVE BIOLOGY, ISSN 0003-1569
  41. Wray, GA, Evolutionary dissociations between homologous genes and homologous structures., in Homology, edited by B. Hall, Novartis Foundation symposium, vol. 222 (January, 1999), pp. 189-203, Chichester (Novartis Foundation Symposium 222): Wiley
  42. Raff, RA; Arthur, W; Carroll, SB; Coates, MI; Wray, G, Chronicling the birth of a discipline., Evolution & development, vol. 1 no. 1 (July, 1999), pp. 1-2
  43. Wray, GA, Peering ahead (cautiously), Evolution and Development, vol. 2 no. 3 (2000), pp. 1-2
  44. Wray, GA; Lowe, CJ, Developmental regulatory genes and echinoderm evolution, Systematic Biology, vol. 49 no. 1 (2000), pp. 151-174, ISSN 1063-5157
  45. Wray, GA, The evolution of embryonic patterning mechanisms in animals, Seminars in Cell and Developmental Biology, vol. 11 no. 6 (2000), pp. 353-393, ISSN 1084-9521
  46. Wray, GA, The evolution of sea urchin development, in Regulatory Processes in Development, edited by Olsson, L; Jacobson, CO, REGULATORY PROCESSES IN DEVELOPMENT, vol. 76 (January, 2000), pp. 49-60, PORTLAND PRESS LTD, ISBN 1-85578-136-0
  47. Wray, GA, Gene expression during echinoderm metamorphosis., Zygote (Cambridge, England), vol. 8 Suppl 1 (January, 2000), pp. S48-S49, ISSN 0967-1994
  48. Lowe, CJ; Wray, GA, Rearing larvae of sea urchins and sea stars for developmental studies., in Methods in Molecular Biology, Vol. 135: Developmental Biology Protocols, edited by R. Tuan & C. Lo, Methods in molecular biology (Clifton, N.J.), vol. 135 (January, 2000), pp. 9-15, Totowa NJ: Humana Press
  49. Emily, K; Wray, GA, Controversy and consensus in asteroid systernatics: New insights to ordinal and familial relationships, American Zoologist, vol. 40 no. 3 (January, 2000), pp. 382-392, Society for Integrative and Comparative Biology, ISSN 0003-1569
  50. Wray, GA; Lowe, CJ, Developmental regulatory genes and echinoderm evolution., Systematic biology, vol. 49 no. 1 (March, 2000), pp. 28-51, ISSN 1063-5157
  51. Wray, GA, Peering ahead (cautiously)., Evolution & development, vol. 2 no. 3 (May, 2000), pp. 125-126
  52. Cameron, RA; Mahairas, G; Rast, JP; Martinez, P; Biondi, TR; Swartzell, S; Wallace, JC; Poustka, AJ; Livingston, BT; Wray, GA; Ettensohn, CA; Lehrach, H; Britten, RJ; Davidson, EH; Hood, L, A sea urchin genome project: sequence scan, virtual map, and additional resources., Proceedings of the National Academy of Sciences of the United States of America, vol. 97 no. 17 (August, 2000), pp. 9514-9518
  53. Pizer, M; Wray, GA, The evolution and development of left-right asymmetry in echinoderms., AMERICAN ZOOLOGIST, vol. 40 no. 6 (December, 2000), pp. 1173-1173, AMER SOC ZOOLOGISTS, ISSN 0003-1569
  54. Wray, GA, The evolution of embryonic patterning mechanisms in animals., Seminars in cell & developmental biology, vol. 11 no. 6 (December, 2000), pp. 385-393, ISSN 1084-9521
  55. Stone, JR; Wray, GA, Rapid appearance of new transcription factor binding sites by local point mutation, Molecular Biology and Evolution, vol. 18 no. 9 (2001), pp. 1764-1770, ISSN 0737-4038
  56. Wray, GA, A world apart - The larval lifestyle may seem alien to us terrestrial bipeds, but it comes quite naturally to most creatures - especially inhabitants of the world's oceans., NATURAL HISTORY, vol. 110 no. 2 (March, 2001), pp. 52-+, AMER MUSEUM NAT HISTORY, ISSN 0028-0712
  57. Wray, GA, Resolving the Hox Paradox, Science, vol. 292 no. 5525 (June, 2001), pp. 2256-2257, American Association for the Advancement of Science (AAAS), ISSN 0036-8075
  58. Bely, AE; Wray, GA, Evolution of regeneration and fission in annelids: insights from engrailed- and orthodenticle-class gene expression., Development (Cambridge, England), vol. 128 no. 14 (July, 2001), pp. 2781-2791
  59. Stone, JR; Wray, GA, Rapid evolution of cis-regulatory sequences via local point mutations., Molecular biology and evolution, vol. 18 no. 9 (September, 2001), pp. 1764-1770, ISSN 0737-4038
  60. Wray, GA, Dating branches on the tree of life using DNA., Genome biology, vol. 3 no. 1 (January, 2002), pp. REVIEWS0001
  61. Wray, GA, Do convergent developmental mechanisms underlie convergent phenotypes?, Brain, behavior and evolution, vol. 59 no. 5-6 (January, 2002), pp. 327-336, ISSN 0006-8977
  62. Lowe, CJ; Issel Tarver, L; Wray, GA, Evolution of new developmental roles for orthodenticle and distal-less in the larvae of echinoderms, Evolution & Development, vol. 4 (February, 2002), pp. 111-123
  63. Lowe, CJ; Issel-Tarver, L; Wray, GA, Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae., Evolution & development, vol. 4 no. 2 (March, 2002), pp. 111-123, ISSN 1520-541X
  64. Hahn, MW; Wray, GA, The g-value paradox., Evolution & development, vol. 4 no. 2 (March, 2002), pp. 73-75, ISSN 1520-541X
  65. Abouheif, E; Wray, GA, Evolution of the gene network underlying wing polyphenism in ants., Science (New York, N.Y.), vol. 297 no. 5579 (July, 2002), pp. 249-252
  66. Wray, GA, Evolution of a well-characterized embryonic promoter: the Endo16 cis-regulatory system of sea urchins., DEVELOPMENTAL BIOLOGY, vol. 247 no. 2 (July, 2002), pp. 519-519, ACADEMIC PRESS INC ELSEVIER SCIENCE, ISSN 0012-1606
  67. Bely, AE; Wray, GA, Getting a head in the world, Natural History, vol. 10/02 (October, 2002), pp. 30-32
  68. Rockman, MV; Wray, GA, Abundant raw material for cis-regulatory evolution in humans., Molecular biology and evolution, vol. 19 no. 11 (November, 2002), pp. 1991-2004, ISSN 0737-4038
  69. Wray, GA; Strathmann, RR, Stasis, change, and functional constraint in the evolution of animal body plans, whatever they may be, Vie et Milieu, vol. 52 no. 4 (December, 2002), pp. 189-199
  70. Wray, G.A., Transcriptional regulation: evolution, in Encyclopedia of the Human Genome, edited by D. Cooper (2003), Nature Publishing Group
  71. Wray, GA, Transcriptional regulation and the evolution of development., The International journal of developmental biology, vol. 47 no. 7-8 (January, 2003), pp. 675-684, ISSN 0214-6282
  72. Knott, KE; Balser, EJ; Jaeckle, WB; Wray, GA, Identification of asteroid genera with species capable of larval cloning., The Biological bulletin, vol. 204 no. 3 (June, 2003), pp. 246-255
  73. Hahn, MW; Stajich, JE; Wray, GA, The effects of selection against spurious transcription factor binding sites., Molecular biology and evolution, vol. 20 no. 6 (June, 2003), pp. 901-906, ISSN 0737-4038
  74. Romano, LA; Wray, GA, Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation., Development (Cambridge, England), vol. 130 no. 17 (September, 2003), pp. 4187-4199, ISSN 0950-1991
  75. Wray, GA; Hahn, MW; Abouheif, E; Balhoff, JP; Pizer, M; Rockman, MV; Romano, LA, The evolution of transcriptional regulation in eukaryotes., Molecular biology and evolution, vol. 20 no. 9 (September, 2003), pp. 1377-1419, ISSN 0737-4038
  76. Rockman, MV; Hahn, MW; Soranzo, N; Goldstein, DB; Wray, GA, Positive selection on a human-specific transcription factor binding site regulating IL4 expression., Current biology : CB, vol. 13 no. 23 (December, 2003), pp. 2118-2123, ISSN 0960-9822
  77. Bely, AE; Wray, GA, Molecular phylogeny of naidid worms (Annelida: Clitellata), Molecular Phylogeny and Evolution, vol. 30 (2004), pp. 50-63
  78. 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
  79. Levinton, J; Dubb, L; Wray, GA, Simulations of evolutionary radiations and their application to understanding the probability of a Cambrian explosion, Journal of Paleontology, vol. 78 no. 1 (January, 2004), pp. 31-38, Cambridge University Press (CUP)
  80. Bely, AE; Wray, GA, Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase I., Molecular phylogenetics and evolution, vol. 30 no. 1 (January, 2004), pp. 50-63, ISSN 1055-7903
  81. Ettensohn, CA; Wessel, GM; Wray, GA, The invertebrate deuterostomes: an introduction to their phylogeny, reproduction, development, and genomics., Methods in cell biology, vol. 74 (January, 2004), pp. 1-13, ISSN 0091-679X
  82. Wray, GA; Kitazawa, C; Miner, B, Culture of echinoderm larvae through metamorphosis., Methods in cell biology, vol. 74 (January, 2004), pp. 75-86, ISSN 0091-679X
  83. Hahn, MW; Rockman, MV; Soranzo, N; Goldstein, DB; Wray, GA, Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans., Genetics, vol. 167 no. 2 (June, 2004), pp. 867-877, ISSN 0016-6731
  84. Rockman, MV; Hahn, MW; Soranzo, N; Loisel, DA; Goldstein, DB; Wray, GA, Positive selection on MMP3 regulation has shaped heart disease risk., Current biology : CB, vol. 14 no. 17 (September, 2004), pp. 1531-1539, ISSN 0960-9822
  85. Wray, GA, Evolutionary mechanisms that operate on embryonic gene expression in purple sea urchin Strongylocentrotus purpuratus, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 44 no. 6 (December, 2004), pp. 668-668, OXFORD UNIV PRESS INC, ISSN 1540-7063
  86. Balhoff, JP; Wray, GA, Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites., Proceedings of the National Academy of Sciences of the United States of America, vol. 102 no. 24 (June, 2005), pp. 8591-8596, ISSN 0027-8424
  87. Mooi, R; David, B; Wray, GA, Arrays in rays: terminal addition in echinoderms and its correlation with gene expression., Evolution & development, vol. 7 no. 6 (November, 2005), pp. 542-555, ISSN 1520-541X
  88. Rockman, MV; Hahn, MW; Soranzo, N; Zimprich, F; Goldstein, DB; Wray, GA, Ancient and recent positive selection transformed opioid cis-regulation in humans., PLoS biology, vol. 3 no. 12 (December, 2005), pp. e387, ISSN 1545-7885
  89. Sodergren, ; E, ; Weinstock, GM; Consortium, TSUGS, The genome of the sea urchin Stongylocentrotus purpuratus, Science, vol. 314 no. 5801 (2006), pp. 941-952
  90. Sumrall, CD; Wray, GA, Developmental control of ambulacral reduction in fossil echinoderms, Paleobiology, vol. 33 (2006), pp. 149-163
  91. Wray, GA, Spot on (and off), Nature, vol. 440 no. 7087 (2006), pp. 1001-1002, ISSN 0028-0836
  92. Rudd, MK; Wray, GA; Willard, HF, The evolutionary dynamics of alpha-satellite., Genome research, vol. 16 no. 1 (January, 2006), pp. 88-96, ISSN 1088-9051
  93. Wray, GA, Evolution: spot on (and off)., Nature, vol. 440 no. 7087 (April, 2006), pp. 1001-1002, ISSN 0028-0836
  94. Wray, GA, The evolution of embryonic gene expression in sea urchins., Integrative and comparative biology, vol. 46 no. 3 (June, 2006), pp. 233-242, ISSN 1540-7063
  95. Loisel, DA; Rockman, MV; Wray, GA; Altmann, J; Alberts, SC, Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region., Proceedings of the National Academy of Sciences of the United States of America, vol. 103 no. 44 (October, 2006), pp. 16331-16336, ISSN 0027-8424
  96. Romano, LA; Wray, GA, Endo16 is required for gastrulation in the sea urchin Lytechinus variegatus., Development, growth & differentiation, vol. 48 no. 8 (October, 2006), pp. 487-497, ISSN 0012-1592
  97. Babbitt, CC; Wray, GA, Functional analysis of cis-regulatory evolution in humans and other primates, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 46 (December, 2006), pp. E6-E6, OXFORD UNIV PRESS INC, ISSN 1540-7063
  98. Nyberg, KG; Ciampaglio, CN; Wray, GA, Tracing the ancestry of the great white shark, Carcharodon carcharias, using morphometric analyses of fossil teeth, Journal of Vertebrate Paleontology, vol. 26 no. 4 (December, 2006), pp. 806-814, Informa UK Limited, ISSN 0272-4634
  99. Babbitt, ; CC, ; Haygood, R; Wray, GA, When two is better than one, Cell, vol. 19 no. 2 (2007), pp. 3-4, ISSN 0092-8674
  100. Haygood, ; R, ; Fedrigo, O; Hanson, B; Yokoyama, K-D; Wray, GA, Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution, Nature Genetics, vol. 39 no. 9 (2007), pp. 1140-1144, ISSN 1061-4036
  101. Tishkoff, ; A, S; Reed, FA; Ranciaro, A; Voight, BF; Babbitt, CC; Silverman, JS; Powell, K; Mortensen, H; Hirbo, JB; Osman, M; Ibrahim, M; Omar, SA; Lema, G; N, TB; Ghori, J; Bumpstead, S; Pritchard, JK; Wray, GA; Deloukas, P, Convergent adaptation in humans: the genetic basis of lactase persistence in Africa, Nature Genetics, vol. 39 no. 1 (2007), pp. 31-40, ISSN 1061-4036
  102. Tishkoff, SA; Reed, FA; Ranciaro, A; Voight, BF; Babbitt, CC; Silverman, JS; Powell, K; Mortensen, HM; Hirbo, JB; Osman, M; Ibrahim, M; Omar, SA; Lema, G; Nyambo, TB; Ghori, J; Bumpstead, S; Pritchard, JK; Wray, GA; Deloukas, P, Convergent adaptation of human lactase persistence in Africa and Europe., Nature genetics, vol. 39 no. 1 (January, 2007), pp. 31-40, ISSN 1061-4036
  103. Wray, GA, The evolutionary significance of cis-regulatory mutations., Nature reviews. Genetics, vol. 8 no. 3 (March, 2007), pp. 206-216, ISSN 1471-0056
  104. Babbitt, CC; Haygood, R; Wray, GA, When two is better than one., Cell, vol. 131 no. 2 (October, 2007), pp. 225-227, ISSN 0092-8674
  105. Sumrall, CD; Wray, GA, Ontogeny in the fossil record: Diversification of body plans and the evolution of "aberrant" symmetry in Paleozoic echinoderms, Paleobiology, vol. 33 no. 1 (December, 2007), pp. 149-163, Cambridge University Press (CUP), ISSN 0094-8373
  106. Bowsher, JH; Wray, GA; Abouheif, E, 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. Part B, Molecular and developmental evolution, vol. 308 no. 6 (December, 2007), pp. 769-776, ISSN 1552-5007
  107. Wray, GA, Developmental Genes and the Evolution of Morphology, in Palaeobiology II (December, 2007), pp. 147-152, ISBN 9780632051496
  108. Wray, GA; Babbitt, CC, Enhancing gene regulation, Science, vol. 321 no. 5894 (2008), pp. 1300-1301
  109. Mitchell-Olds, T; Feder, M; Wray, G, Evolutionary and ecological functional genomics., Heredity, vol. 100 no. 2 (February, 2008), pp. 101-102
  110. Horvath, JE; Weisrock, DW; Embry, SL; Fiorentino, I; Balhoff, JP; Kappeler, P; Wray, GA; Willard, HF; Yoder, AD, Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs., Genome research, vol. 18 no. 3 (March, 2008), pp. 489-499, ISSN 1088-9051
  111. Wray, GA; Babbitt, CC, Genetics. Enhancing gene regulation., Science (New York, N.Y.), vol. 321 no. 5894 (September, 2008), pp. 1300-1301
  112. Haygood, R; Fedrigo, O; Wray, GA, Reply to "Rapidly evolving human promoter regions", Nature Genetics, vol. 40 no. 11 (November, 2008), pp. 1263-1264, Springer Nature, ISSN 1061-4036
  113. Yokoyama, KD; Ohler, U; Wray, GA, Spatial preferences identify known and novel cis-regulatory element candidates and functional motif-pair relationships, Nucleic Acids Research, vol. 37 no. 13 (2009), pp. e92
  114. Warner, LR; Babbitt, CC; Primus, AE; Severson, TF; Haygood, R; Wray, GA, The functional consequences of genetic variation on tyrosine hydroxylase (TH) expression, Brain Research, vol. 1288 (2009), pp. 1-8
  115. Garfield, DA; Wray, GA, Comparative embryology without a microscope: using genomic approaches to understand the evolution of development., Journal of biology, vol. 8 no. 7 (January, 2009), pp. 65
  116. Tung, J; Primus, A; Bouley, AJ; Severson, TF; Alberts, SC; Wray, GA, Evolution of a malaria resistance gene in wild primates., Nature, vol. 460 no. 7253 (July, 2009), pp. 388-391 (in revision.)
  117. Yokoyama, KD; Ohler, U; Wray, GA, Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships., Nucleic Acids Res, vol. 37 no. 13 (July, 2009), pp. e92
  118. Tung, J; Fédrigo, O; Haygood, R; Mukherjee, S; Wray, GA, Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation., Molecular biology and evolution, vol. 26 no. 9 (September, 2009), pp. 2047-2059
  119. Fedrigo, O; Warner, LR; Pfefferle, AD; Babbitt, CC; Cruz-Gordillo, P; Wray, GA, A pipeline to determine RT-QPCR control genes for evolutionary studies: Application to primate gene expression across multiple tissues, PLoS ONE, vol. 5 no. 9 (2010), pp. 1-7, ISSN 1932-6203
  120. Fedrigo, O; Warner, LR; Pfefferle, AD; Cruz Gordillo, P; Babbitt, CC; Wray, GA, A pipeline to determine RT-PCR control genes for evolutionary studies: application to primate gene expression across multiple tissues, PLoS One, vol. 5 no. 9 (2010), pp. E12545
  121. Tung, J; Alberts, SC; Wray, GA, Evolution of functional genetic variation at immune loci in wild baboons., AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY (January, 2010), pp. 231-231, WILEY-LISS, ISSN 0002-9483
  122. Oliver, TA; Garfield, DA; Manier, MK; Haygood, R; Wray, GA; Palumbi, SR, Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin., Genome biology and evolution, vol. 2 (January, 2010), pp. 800-814, ISSN 1759-6653
  123. Cruz-Gordillo, P; Fedrigo, O; Wray, GA; Babbitt, CC, Extensive changes in the expression of the opioid genes between humans and chimpanzees., Brain, behavior and evolution, vol. 76 no. 2 (January, 2010), pp. 154-162
  124. Babbitt, CC; Fedrigo, O; Pfefferle, AD; Boyle, AP; Horvath, JE; Furey, TS; Wray, GA, Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain., Genome biology and evolution, vol. 2 (January, 2010), pp. 67-79
  125. Garfield, DA; Wray, GA, The evolution of gene regulatory interactions, BioScience, vol. 60 no. 1 (January, 2010), pp. 15-23, Oxford University Press (OUP), ISSN 0006-3568
  126. Fédrigo, O; Wray, GA, Developmental evolution: how beetles evolved their shields., Current biology : CB, vol. 20 no. 2 (January, 2010), pp. R64-R66
  127. Babbitt, CC; Silverman, JS; Haygood, R; Reininga, JM; Rockman, MV; Wray, GA, Multiple Functional Variants in cis Modulate PDYN Expression., Molecular biology and evolution, vol. 27 no. 2 (February, 2010), pp. 465-479
  128. Haygood, R; Babbitt, CC; Fedrigo, O; Wray, GA, Contrasts between adaptive coding and noncoding changes during human evolution., Proceedings of the National Academy of Sciences of the United States of America, vol. 107 no. 17 (April, 2010), pp. 7853-7857
  129. Tung, J; Alberts, SC; Wray, GA, Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations., Trends in genetics : TIG, vol. 26 no. 8 (August, 2010), pp. 353-362, ISSN 0168-9525
  130. Babbitt, CC; Warner, LR; Fedrigo, O; Wall, CE; Wray, GA, Genomic signatures of diet-related shifts in primate evolution, Proceedings of the Royal Society of London B, vol. 278 (2011), pp. 961-969
  131. Fedrigo, O; Pfefferele, AD; Babbitt, CC; Haygood, R; Wall, CE; Wray, GA, Molecular evidence that a metabolic trade-off contributed to human brain size evolution, Brain, Behavior, and Evolution, vol. 78 (2011), pp. 315-326
  132. Yokoyama, KD; Thorne, JL; Wray, GA, Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution, Genome Biology and Evolution, vol. 3 (2011), pp. 66-74
  133. Pfefferle, AD; Warner, LR; Wang, CW; Nielsen, WJ; Babbitt, CC; Fedrigo, O; Wray, GA, Expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution, Journal for Human Evolution, vol. 60 (2011), pp. 205-211
  134. 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
  135. Fedrigo, O; Pfefferle, AD; Babbitt, CC; Haygood, R; Wall, CE; Wray, GA, A potential role for glucose transporters in the evolution of human brain size., Brain, behavior and evolution, vol. 78 no. 4 (January, 2011), pp. 315-326
  136. Szövényi, P; Rensing, SA; Lang, D; Wray, GA; Shaw, AJ, Generation-biased gene expression in a bryophyte model system., Molecular biology and evolution, vol. 28 no. 1 (January, 2011), pp. 803-812
  137. Pfefferle, AD; Warner, LR; Wang, CW; Nielsen, WJ; Babbitt, CC; Fedrigo, O; Wray, GA, Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution., Journal of human evolution, vol. 60 no. 2 (February, 2011), pp. 205-212
  138. Tung, J; Akinyi, MY; Mutura, S; Altmann, J; Wray, GA; Alberts, SC, Allele-specific gene expression in a wild nonhuman primate population., Molecular ecology, vol. 20 no. 4 (February, 2011), pp. 725-739
  139. Babbitt, CC; Warner, LR; Fedrigo, O; Wall, CE; Wray, GA, Genomic signatures of diet-related shifts during human origins., Proceedings. Biological sciences, vol. 278 no. 1708 (April, 2011), pp. 961-969
  140. Wray, GA, Evolution. CNCing is believing., Science (New York, N.Y.), vol. 333 no. 6045 (August, 2011), pp. 946-947
  141. Bilbo, SD; Wray, GA; Perkins, SE; Parker, W, Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases., Med Hypotheses, vol. 77 no. 4 (October, 2011), pp. 494-504
  142. Smith, MS; Wray, GA; Raff, RA, Revisiting cell lineage and cell fate in light of the evolution of axis formation in Heliocidaris erythrogramma, Evolution & Development (2012)
  143. Horvath, JE; Wu, C; Toler, M; Fedrigo, O; Pfefferle, LW; Moore, A; Ramachandran, GL; Babbitt, CC; Jernvall, J; Wray, GA; Wall, CE, Enamel thickness in Microcebus murinus and Macaca mulana and the evolutionary genetics of enamel matrix proteins in hominoids., AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, vol. 147 (January, 2012), pp. 168-168, WILEY-BLACKWELL, ISSN 0002-9483
  144. Babbitt, CC; Tung, J; Wray, GA; Alberts, SC, Changes in gene expression associated with reproductive maturation in wild female baboons., Genome biology and evolution, vol. 4 no. 2 (January, 2012), pp. 102-109, ISSN 1759-6653
  145. Garfield, D; Haygood, R; Nielsen, WJ; Wray, GA, Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus., Evolution & development, vol. 14 no. 2 (March, 2012), pp. 152-167
  146. Babbitt, CC; Pfefferle, LW; Fedrigo, O; Wray, GA, Conservation and function of noncoding RNAs in primate evolution, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 52 (April, 2012), pp. E8-E8, OXFORD UNIV PRESS INC, ISSN 1540-7063
  147. Shibata, Y; Sheffield, NC; Fedrigo, O; Babbitt, CC; Wortham, M; Tewari, AK; London, D; Song, L; Lee, B-K; Iyer, VR; Parker, SCJ; Margulies, EH; Wray, GA; Furey, TS; Crawford, GE, Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection., PLoS Genet, vol. 8 no. 6 (June, 2012), pp. e1002789
  148. Runcie, DE; Garfield, DA; Babbitt, CC; Wygoda, JA; Mukherjee, S; Wray, GA, Genetics of gene expression responses to temperature stress in a sea urchin gene network., Molecular ecology, vol. 21 no. 18 (September, 2012), pp. 4547-4562
  149. L.W. Pfefferle and G.A. Wray, Insights from a chimpanzee adipose stromal cells population: opportunities for adult stem cells to expand primate functional genomics, Genome Biology and Evolution, vol. 5 (2013), pp. 1995-2005
  150. Runcie, DE; Garfield, DA; Babbitt, CC; Pfefferle, A; Nielsen, WJ; Wray, GA, Phenotypic plasticity and the developmental regulatory network in the purple sea urchin, edited by Johnson, C, ECHINODERMS IN A CHANGING WORLD (January, 2013), pp. 300-301, CRC PRESS-TAYLOR & FRANCIS GROUP, ISBN 978-1-138-00010-0
  151. Wray, GA; Garfield, D; Runcie, D, Evolution of an embryonic gene regulatory network in the sea urchin Strongylocentrotus purpuratus, edited by Johnson, C, ECHINODERMS IN A CHANGING WORLD (January, 2013), pp. 276-276, CRC PRESS-TAYLOR & FRANCIS GROUP, ISBN 978-1-138-00010-0
  152. Wray, GA, Genomics and the evolution of phenotypic traits, Annual Review of Ecology, Evolution, and Systematics, vol. 44 no. 1 (January, 2013), pp. 51-72, ANNUAL REVIEWS, ISSN 1543-592X
  153. Pfefferle, LW; Wray, GA, Insights from a chimpanzee adipose stromal cell population: opportunities for adult stem cells to expand primate functional genomics., Genome biology and evolution, vol. 5 no. 10 (January, 2013), pp. 1995-2005
  154. Runcie, DE; Wiedmann, RT; Archie, EA; Altmann, J; Wray, GA; Alberts, SC; Tung, J, Social environment influences the relationship between genotype and gene expression in wild baboons., Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol. 368 no. 1618 (May, 2013), pp. 20120345
  155. Garfield, DA; Runcie, DE; Babbitt, CC; Haygood, R; Nielsen, WJ; Wray, GA, The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network., PLoS biology, vol. 11 no. 10 (October, 2013), pp. e1001696
  156. Ganapathy, G; Howard, JT; Ward, JM; Li, J; Li, B; Li, Y; Xiong, Y; Zhang, Y; Zhou, S; Schwartz, DC; Schatz, M; Aboukhalil, R; Fedrigo, O; Bukovnik, L; Wang, T; Wray, G; Rasolonjatovo, I; Winer, R; Knight, JR; Koren, S; Warren, WC; Zhang, G; Phillippy, AM; Jarvis, ED, High-coverage sequencing and annotated assemblies of the budgerigar genome., Gigascience, vol. 3 (2014), pp. 11
  157. Wygoda, JA; Byrne, M; Mcclay, DR; Wray, GA, Shifts in the Expression of Developmental Regulatory Genes Involved in the Evolution of a Novel Life History Difference, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 54 (January, 2014), pp. E230-E230, OXFORD UNIV PRESS INC
  158. Wygoda, JA; Koop, D; Yang, J; Wray, GA; Byrne, M, Developmental Transcriptome of Heliociaris erythrogramma - from bilateral larva to radial juvenile, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 54 (January, 2014), pp. E372-E372, OXFORD UNIV PRESS INC
  159. Bauernfeind, AL; Soderblom, EJ; Turner, ME; Moseley, AM; Ely, JJ; Hof, PR; Sherwood, CC; Wray, GA; Babbitt, CC, Differential gene and protein expression in the human and chimpanzee brain: A comparison using high-throughput techniques, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, vol. 153 (March, 2014), pp. 73-73, WILEY-BLACKWELL, ISSN 0002-9483
  160. Wygoda, JA; Yang, Y; Byrne, M; Wray, GA, Transcriptomic analysis of the highly derived radial body plan of a sea urchin., Genome biology and evolution, vol. 6 no. 4 (April, 2014), pp. 964-973
  161. Liu, S; Lorenzen, ED; Fumagalli, M; Li, B; Harris, K; Xiong, Z; Zhou, L; Korneliussen, TS; Somel, M; Babbitt, C; Wray, G; Li, J; He, W; Wang, Z; Fu, W; Xiang, X; Morgan, CC; Doherty, A; O'Connell, MJ; McInerney, JO; Born, EW; Dalén, L; Dietz, R; Orlando, L; Sonne, C; Zhang, G; Nielsen, R; Willerslev, E; Wang, J, Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears., Cell, vol. 157 no. 4 (May, 2014), pp. 785-794, ISSN 0092-8674
  162. Horvath, JE; Ramachandran, GL; Fedrigo, O; Nielsen, WJ; Babbitt, CC; St Clair, EM; Pfefferle, LW; Jernvall, J; Wray, GA; Wall, CE, Genetic comparisons yield insight into the evolution of enamel thickness during human evolution., Journal of human evolution, vol. 73 (August, 2014), pp. 75-87, ISSN 0047-2484
  163. Laland, K; Uller, T; Feldman, M; Sterelny, K; Müller, GB; Moczek, A; Jablonka, E; Odling-Smee, J; Wray, GA; Hoekstra, HE; Futuyma, DJ; Lenski, RE; Mackay, TFC; Schluter, D; Strassmann, JE, Does evolutionary theory need a rethink?, Nature, vol. 514 no. 7521 (October, 2014), pp. 161-164, NATURE PUBLISHING GROUP, ISSN 0028-0836
  164. Bauernfeind, AL; Reyzer, ML; Caprioli, RM; Ely, JJ; Babbitt, CC; Wray, GA; Hof, PR; Sherwood, CC, Differences in energy metabolism in the brains of humans and chimpanzees: a study of protein expression, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, vol. 156 (March, 2015), pp. 80-80, WILEY-BLACKWELL
  165. Babbitt, CC; Wray, GA, Evolution of gene expression network underlying a disease state in humans and non-human primates, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, vol. 156 (March, 2015), pp. 74-74, WILEY-BLACKWELL
  166. Boyd, JL; Skove, SL; Rouanet, JP; Pilaz, L-J; Bepler, T; Gordân, R; Wray, GA; Silver, DL, Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex., Curr Biol, vol. 25 no. 6 (March, 2015), pp. 772-779, ISSN 0960-9822
  167. Babbitt, CC; Pfefferle, LW; Crawford, GE; Wray, GA, Evolution of gene expression network underlying a disease state, INTEGRATIVE AND COMPARATIVE BIOLOGY, vol. 55 (April, 2015), pp. E7-E7, OXFORD UNIV PRESS INC
  168. Muntané, G; Horvath, JE; Hof, PR; Ely, JJ; Hopkins, WD; Raghanti, MA; Lewandowski, AH; Wray, GA; Sherwood, CC, Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission., Cerebral cortex (New York, N.Y. : 1991), vol. 25 no. 6 (June, 2015), pp. 1596-1607, ISSN 1047-3211
  169. Bauernfeind, AL; Soderblom, EJ; Turner, ME; Moseley, MA; Ely, JJ; Hof, PR; Sherwood, CC; Wray, GA; Babbitt, CC, Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees., Genome Biol Evol, vol. 7 no. 8 (July, 2015), pp. 2276-2288
  170. Bauernfeind, AL; Reyzer, ML; Caprioli, RM; Ely, JJ; Babbitt, CC; Wray, GA; Hof, PR; Sherwood, CC, High spatial resolution proteomic comparison of the brain in humans and chimpanzees., The Journal of comparative neurology, vol. 523 no. 14 (October, 2015), pp. 2043-2061, ISSN 0021-9967
  171. Byrne, M; Koop, D; Cisternas, P; Strbenac, D; Yang, JYH; Wray, GA, Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma., Marine genomics, vol. 24 Pt 1 (December, 2015), pp. 41-45, ISSN 1874-7787
  172. 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; Jiang, Y; Kitchen, RR; Kozlenkov, A; Kundakovic, M; Li, M; Li, Z; Liu, S; Mangravite, LM; Mattei, E; Markenscoff-Papadimitriou, E; Navarro, FCP; North, N; Omberg, L; Panchision, D; Parikshak, N; Poschmann, J; Price, AJ; Purcaro, M; Reddy, TE; Roussos, P; Schreiner, S; Scuderi, S; Sebra, R; Shibata, M; Shieh, AW; Skarica, M; Sun, W; Swarup, V; Thomas, A; Tsuji, J; van Bakel, H; Wang, D; Wang, Y; Wang, K; Werling, DM; Willsey, AJ; Witt, H; Won, H; Wong, CCY; Wray, GA; Wu, EY; Xu, X; Yao, L; Senthil, G; Lehner, T; Sklar, P; Sestan, N, The PsychENCODE project., Nat Neurosci, vol. 18 no. 12 (December, 2015), pp. 1707-1712
  173. Wray, GA, Molecular clocks and the early evolution of metazoan nervous systems., Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol. 370 no. 1684 (December, 2015), pp. 20150046
  174. Janies, DA; Witter, Z; Linchangco, GV; Foltz, DW; Miller, AK; Kerr, AM; Jay, J; Reid, RW; Wray, GA, EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms., BMC bioinformatics, vol. 17 (January, 2016), pp. 48
  175. Schierwater, B; Holland, PWH; Miller, DJ; Stadler, PF; Wiegmann, BM; Wörheide, G; Wray, GA; DeSalle, R, Never ending analysis of a century old evolutionary debate: "Unringing" the urmetazoon bell, Frontiers in Ecology and Evolution, vol. 4 no. FEB (February, 2016)
  176. Israel, JW; Martik, ML; Byrne, M; Raff, EC; Raff, RA; McClay, DR; 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, vol. 14 no. 3 (March, 2016), pp. e1002391
  177. Dutta, V; Altermann, E; Olson, J; Wray, GA; Siletzky, RM; Kathariou, S, Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains., Genome announcements, vol. 4 no. 4 (August, 2016), pp. e00833-e00816
  178. Runcie, DE; Dorey, N; Garfield, DA; Stumpp, M; Dupont, S; Wray, GA, Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification., Genome biology and evolution, vol. 8 no. 12 (December, 2016), pp. 3672-3684
  179. Koop, D; Cisternas, P; Morris, VB; Strbenac, D; Yang, JYH; Wray, GA; 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, vol. 17 no. 1 (February, 2017), pp. 4
  180. Babbitt, CC; Haygood, R; Nielsen, WJ; Wray, GA, Gene expression and adaptive noncoding changes during human evolution., BMC genomics, vol. 18 no. 1 (June, 2017), pp. 435
  181. 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; Janies, DA, The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics., Molecular phylogenetics and evolution, vol. 115 (October, 2017), pp. 161-170
  182. Byrne, M; Koop, D; Morris, VB; Chui, J; Wray, GA; 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, vol. 247 no. 1 (January, 2018), pp. 239-249
  183. Singh, A; Pinto, L; Martin, C; Rutherford, N; Ragunathan, A; Upadhyay, U; Kapoor, P; McRae, M; Siddiqui, A; Cantelmi, D; Heyland, A; Wray, G; Stone, JR, Rudiment resorption as a response to starvation during larval development in the sea urchin Strongylocentrotus droebachiensis, Canadian Journal of Zoology, vol. 96 no. 10 (January, 2018), pp. 1178-1185
  184. Pizzollo, J; Nielsen, WJ; Shibata, Y; Safi, A; Crawford, GE; Wray, GA; Babbitt, CC, Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee., Genome Biol Evol, vol. 10 no. 3 (March, 2018), pp. 826-839
  185. Bryois, J; Garrett, ME; Song, L; Safi, A; Giusti-Rodriguez, P; Johnson, GD; Shieh, AW; Buil, A; Fullard, JF; Roussos, P; Sklar, P; Akbarian, S; Haroutunian, V; Stockmeier, CA; Wray, GA; White, KP; Liu, C; Reddy, TE; Ashley-Koch, A; Sullivan, PF; Crawford, GE, Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia., Nat Commun, vol. 9 no. 1 (August, 2018), pp. 3121
  186. Eisthen, HL; Halanych, KM; Kelley, DB; White, SA; Phelps, SM; 66 additional authors, , New NSF policy will stifle innovation., Science (New York, N.Y.), vol. 362 no. 6412 (October, 2018), pp. 297-298, AMER ASSOC ADVANCEMENT SCIENCE
  187. Li, M; Santpere, G; Imamura Kawasawa, Y; Evgrafov, OV; Gulden, FO; Pochareddy, S; Sunkin, SM; Li, Z; Shin, Y; Zhu, Y; Sousa, AMM; Werling, DM; Kitchen, RR; Kang, HJ; Pletikos, M; Choi, J; Muchnik, S; Xu, X; Wang, D; Lorente-Galdos, B; Liu, S; Giusti-Rodríguez, P; Won, H; de Leeuw, CA; Pardiñas, AF; BrainSpan Consortium, ; PsychENCODE Consortium, ; PsychENCODE Developmental Subgroup, ; Hu, M; Jin, F; Li, Y; Owen, MJ; O'Donovan, MC; Walters, JTR; Posthuma, D; Reimers, MA; Levitt, P; Weinberger, DR; Hyde, TM; Kleinman, JE; Geschwind, DH; Hawrylycz, MJ; State, MW; Sanders, SJ; Sullivan, PF; Gerstein, MB; Lein, ES; Knowles, JA; Sestan, N, Integrative functional genomic analysis of human brain development and neuropsychiatric risks., Science, vol. 362 no. 6420 (December, 2018), pp. eaat7615
  188. Edgar, A; Byrne, M; McClay, D; Wray, G, Evolution of abbreviated development inHeliocidaris erythrogrammadramatically re-wired the highly conserved sea urchin developmental gene regulatory network to decouple signaling center function from ultimate fate (2019)
  189. Swain-Lenz, D; Berrio, A; Safi, A; Crawford, G; Wray, G, Comparative analyses of chromatin landscape in white adipose tissue suggest humans may have less beigeing potential than other primates (2019)
  190. Oulhen, N; Foster, S; Wray, G; Wessel, G, Identifying gene expression from single cells to single genes., Methods in cell biology, vol. 151 (January, 2019), pp. 127-158, Elsevier
  191. Edgar, A; Byrne, M; Wray, GA, Embryo microinjection of the lecithotrophic sea urchin Heliocidaris erythrogramma., Journal of biological methods, vol. 6 no. 3 (January, 2019), pp. e119
  192. Wray, GA; Haag, ES, Rudolf A. Raff (1941-2019)., Nature ecology & evolution, vol. 3 no. 4 (April, 2019), pp. 518-519
  193. Davidson, PL; Thompson, JW; Foster, MW; Moseley, MA; Byrne, M; Wray, GA, A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins., Evol Dev, vol. 21 no. 4 (July, 2019), pp. 188-204
  194. Swain-Lenz, D; Berrio, A; Safi, A; Crawford, GE; Wray, GA, Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates., Genome Biol Evol, vol. 11 no. 7 (July, 2019), pp. 1997-2008
  195. Edsall, LE; Berrio, A; Majoros, WH; Swain-Lenz, D; Morrow, S; Shibata, Y; Safi, A; Wray, GA; Crawford, GE; Allen, AS, Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach., Genome Biol Evol, vol. 11 no. 10 (October, 2019), pp. 3035-3053
  196. Berrio, A; Gartner, V; Wray, G, Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function (2020)
  197. Berrio, A; Gartner, V; Wray, GA, Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function., PeerJ, vol. 8 (January, 2020), pp. e10234
  198. Byrne, M; Koop, D; Strbenac, D; Cisternas, P; Balogh, R; Yang, JYH; Davidson, PL; Wray, G, Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors., DNA research : an international journal for rapid publication of reports on genes and genomes, vol. 27 no. 1 (February, 2020), pp. dsaa007
  199. Muley, VY; López-Victorio, CJ; Ayala-Sumuano, JT; González-Gallardo, A; González-Santos, L; Lozano-Flores, C; Wray, G; Hernández-Rosales, M; Varela-Echavarría, A, Conserved and divergent expression dynamics during early patterning of the telencephalon in mouse and chick embryos., Progress in neurobiology, vol. 186 (March, 2020), pp. 101735
  200. Berrio, A; Haygood, R; Wray, GA, Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral., BMC genomics, vol. 21 no. 1 (May, 2020), pp. 359
  201. Wang, L; Israel, JW; Edgar, A; Raff, RA; Raff, EC; Byrne, M; Wray, GA, Genetic basis for divergence in developmental gene expression in two closely related sea urchins., Nature ecology & evolution, vol. 4 no. 6 (June, 2020), pp. 831-840
  202. Davidson, PL; Guo, H; Wang, L; Berrio, A; Zhang, H; Chang, Y; Soborowski, AL; McClay, DR; Fan, G; Wray, GA, Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses., Genome biology and evolution, vol. 12 no. 7 (July, 2020), pp. 1080-1086
  203. Devens, HR; Davidson, PL; Deaker, DJ; Smith, KE; Wray, GA; Byrne, M, Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma., Molecular ecology, vol. 29 no. 23 (December, 2020), pp. 4618-4636
  204. Massri, AJ; Schiebinger, GR; Berrio, A; Wang, L; Wray, GA; McClay, DR, Methodologies for Following EMT In Vivo at Single Cell Resolution., Methods in molecular biology (Clifton, N.J.), vol. 2179 (January, 2021), pp. 303-314
  205. Song, H; Guo, X; Sun, L; Wang, Q; Han, F; Wang, H; Wray, GA; Davidson, P; Wang, Q; Hu, Z; Zhou, C; Yu, Z; Yang, M; Feng, J; Shi, P; Zhou, Y; Zhang, L; Zhang, T, The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia., BMC biology, vol. 19 no. 1 (January, 2021), pp. 15
  206. Markunas, AM; Manivannan, PKR; Ezekian, JE; Agarwal, A; Eisner, W; Alsina, K; Allen, HD; Wray, GA; Kim, JJ; Wehrens, XHT; Landstrom, AP, TBX5-encoded T-box transcription factor 5 variant T223M is associated with long QT syndrome and pediatric sudden cardiac death., Am J Med Genet A, vol. 185 no. 3 (March, 2021), pp. 923-929
  207. Benito-Kwiecinski, S; Giandomenico, SL; Sutcliffe, M; Riis, ES; Freire-Pritchett, P; Kelava, I; Wunderlich, S; Martin, U; Wray, GA; McDole, K; Lancaster, MA, An early cell shape transition drives evolutionary expansion of the human forebrain., Cell, vol. 184 no. 8 (April, 2021), pp. 2084-2102.e19
  208. Carrier, TJ; Leigh, BA; Deaker, DJ; Devens, HR; Wray, GA; Bordenstein, SR; Byrne, M; Reitzel, AM, Microbiome reduction and endosymbiont gain from a switch in sea urchin life history., Proceedings of the National Academy of Sciences of the United States of America, vol. 118 no. 16 (April, 2021), pp. e2022023118
  209. Hu, B; Won, H; Mah, W; Park, RB; Kassim, B; Spiess, K; Kozlenkov, A; Crowley, CA; Pochareddy, S; PsychENCODE Consortium, ; Li, Y; Dracheva, S; Sestan, N; Akbarian, S; Geschwind, DH, Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders., Nat Commun, vol. 12 no. 1 (June, 2021), pp. 3968
  210. Brazeau, NF; Mitchell, CL; Morgan, AP; Deutsch-Feldman, M; Watson, OJ; Thwai, KL; Gelabert, P; van Dorp, L; Keeler, CY; Waltmann, A; Emch, M; Gartner, V; Redelings, B; Wray, GA; Mwandagalirwa, MK; Tshefu, AK; Likwela, JL; Edwards, JK; Verity, R; Parr, JB; Meshnick, SR; Juliano, JJ, The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo., Nature communications, vol. 12 no. 1 (July, 2021), pp. 4169
  211. Byrne, M; Koop, D; Strbenac, D; Cisternas, P; Yang, JYH; Davidson, PL; Wray, G, Transcriptomic analysis of Nodal - and BMP- associated genes during development to the juvenile seastar in Parvulastra exigua (Asterinidae)., Marine genomics, vol. 59 (October, 2021), pp. 100857
  212. Massri, AJ; Greenstreet, L; Afanassiev, A; Berrio, A; Wray, GA; Schiebinger, G; McClay, DR, Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo., Development (Cambridge, England), vol. 148 no. 19 (October, 2021), pp. dev198614
  213. Gartner, V; Redelings, B; Gaither, C; Parr, J; Kalonji, A; Phanzu, F; Brazeau, N; Juliano, J; Wray, G, Genomic insights intoPlasmodium vivaxpopulation structure and diversity in central Africa, in bioRxiv (2022)
  214. Wray, GA, Extreme phenotypic divergence and the evolution of development., in Current Topics in Developmental Biology, vol. 146 (January, 2022), pp. 79-112
  215. Davidson, PL; Byrne, M; Wray, GA, Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins., Molecular biology and evolution, vol. 39 no. 9 (September, 2022), pp. msac172
  216. Ketchum, RN; Davidson, PL; Smith, EG; Wray, GA; Burt, JA; Ryan, JF; Reitzel, AM, A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes., edited by O’Neill, R, Genome biology and evolution, vol. 14 no. 10 (October, 2022), pp. evac144, Oxford University Press (OUP)
  217. Davidson, PL; Guo, H; Swart, JS; Massri, AJ; Edgar, A; Wang, L; Berrio, A; Devens, HR; Koop, D; Cisternas, P; Zhang, H; Zhang, Y; Byrne, M; Fan, G; Wray, GA, Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins., Nature ecology & evolution, vol. 6 no. 12 (December, 2022), pp. 1907-1920
  218. Devens, HR; Davidson, PL; Byrne, M; Wray, GA, Hybrid epigenomes reveal extensive local genetic changes to chromatin accessibility contribute to divergence in embryonic gene expression between species., bioRxiv (January, 2023)
  219. Xing, L; Wang, L; Roos, F; Lee, M; Wray, GA, CRISPR/Cas9-Mediated Disruption of Endo16 Cis-Regulatory Elements in Sea Urchin Embryos, Fishes, vol. 8 no. 2 (February, 2023)
  220. Davidson, PL; Lessios, HA; Wray, GA; McMillan, WO; Prada, C, Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea., Genome biology and evolution, vol. 15 no. 6 (June, 2023), pp. evad093
  221. Massri, AJ; McDonald, B; Wray, GA; McClay, DR, Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks., EvoDevo, vol. 14 no. 1 (June, 2023), pp. 10
  222. Devens, HR; Davidson, PL; Byrne, M; Wray, GA, Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species., Molecular biology and evolution, vol. 40 no. 11 (November, 2023), pp. msad222
  223. Gartner, V; Redelings, BD; Gaither, C; Parr, JB; Kalonji, A; Phanzu, F; Brazeau, NF; Juliano, JJ; Wray, GA, Genomic insights into Plasmodium vivax population structure and diversity in central Africa., Malaria journal, vol. 23 no. 1 (January, 2024), pp. 27

Papers Accepted

  1. J. Muntane, J.E. Horvath, P. Hof, J. Ely, W.D. Hopkins, M.A. Raghanti, A.H. Lewandowski, G.A. Wray, and C. Sherwood, Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission, Cerebral Cortex (2013)

Papers Submitted

  1. L. Pinto, A. Ragunathan, P. Kapoor, M. McRae, D. Cantelmi, A. Heyland, G.A. Wray, and J. Stone, Rudiment resorption observed serendipitously during sea urchin development (2012)

Book Chapters

  1. G.A. Wray, Evolutionary synthesis in the genomic era, in Towards an Extended Evolutionary Synthesis (2009), MIT Press
  2. G.A. Wray, Evolution and Development, in Evolution: The First Four Billion Years, edited by M. Ruse and J. Travis (2009), pp. 208-236, Belknap Press
  3. J. Tung and G.A. Wray, Evolution of traits deduced from genome comparisons, in Encyclopedia of Life Sciences, edited by Nature Publishing Group (2009)
  4. 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, ISBN 978-0878934133

Other

  1. MW Hahn and GA Wray, the G-value paradox, Evolution and Development (2001)
  2. G.A. Wray, Guest in radio interview on evolutionary genomics for talk show "Radio in Vivo" (February 5, 2007) (WCOM.)

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.)