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Profile Publications(51)
ECB-PERS-4092

Publications By Gregory Wray

Results 1 - 50 of 51 results

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A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes., Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM., Genome Biol Evol. September 26, 2022;       


Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins., Davidson PL, Byrne M, Wray GA., Mol Biol Evol. September 1, 2022; 39 (9):                     


Extreme phenotypic divergence and the evolution of development., Wray GA., Curr Top Dev Biol. January 1, 2022; 146 79-112.


Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo., Massri AJ, Greenstreet L, Afanassiev A, Berrio A, Wray GA, Schiebinger G, McClay DR., Development. October 1, 2021; 148 (19):


Transcriptomic analysis of Nodal - and BMP- associated genes during development to the juvenile seastar in Parvulastra exigua (Asterinidae)., Byrne M, Koop D, Strbenac D, Cisternas P, Yang JYH, Davidson PL, Wray G., Mar Genomics. October 1, 2021; 59 100857.


Microbiome reduction and endosymbiont gain from a switch in sea urchin life history., Carrier TJ, Leigh BA, Deaker DJ, Devens HR, Wray GA, Bordenstein SR, Byrne M, Reitzel AM., Proc Natl Acad Sci U S A. April 20, 2021; 118 (16):


Methodologies for Following EMT In Vivo at Single Cell Resolution., Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR., Methods Mol Biol. January 1, 2021; 2179 303-314.


Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma., Devens HR, Davidson PL, Deaker DJ, Smith KE, Wray GA, Byrne M., Mol Ecol. December 1, 2020; 29 (23): 4618-4636.


Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses., Davidson PL, Guo H, Wang L, Berrio A, Zhang H, Chang Y, Soborowski AL, McClay DR, Fan G, Wray GA., Genome Biol Evol. July 1, 2020; 12 (7): 1080-1086.


Genetic basis for divergence in developmental gene expression in two closely related sea urchins., Wang L, Israel JW, Edgar A, Raff RA, Raff EC, Byrne M, Wray GA., Nat Ecol Evol. June 1, 2020; 4 (6): 831-840.


Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors., Byrne M, Koop D, Strbenac D, Cisternas P, Balogh R, Yang JYH, Davidson PL, Wray G., DNA Res. February 1, 2020; 27 (1):               


Embryo microinjection of the lecithotrophic sea urchin Heliocidaris erythrogramma., Edgar A, Byrne M, Wray GA., J Biol Methods. September 17, 2019; 6 (3): e119.            


A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins., Davidson PL, Thompson JW, Foster MW, Moseley MA, Byrne M, Wray GA., Evol Dev. July 1, 2019; 21 (4): 188-204.


Identifying gene expression from single cells to single genes., Oulhen N, Foster S, Wray G, Wessel G., Methods Cell Biol. January 1, 2019; 151 127-158.


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., Byrne M, Koop D, Morris VB, Chui J, Wray GA, Cisternas P., Dev Dyn. January 1, 2018; 247 (1): 239-249.


The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics., 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., Mol Phylogenet Evol. October 1, 2017; 115 161-170.


Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan., Koop D, Cisternas P, Morris VB, Strbenac D, Yang JY, Wray GA, Byrne M., BMC Dev Biol. February 13, 2017; 17 (1): 4.          


Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification., Runcie DE, Dorey N, Garfield DA, Stumpp M, Dupont S, Wray GA., Genome Biol Evol. December 1, 2016; 8 (12): 3672-3684.          


Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris., Israel JW, Martik ML, Byrne M, Raff EC, Raff RA, McClay DR, Wray GA., PLoS Biol. March 1, 2016; 14 (3): e1002391.            


EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms., Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA., BMC Bioinformatics. January 22, 2016; 17 48.      


Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma., Byrne M, Koop D, Cisternas P, Strbenac D, Yang JY, Wray GA., Mar Genomics. December 1, 2015; 24 Pt 1 41-5.


Transcriptomic analysis of the highly derived radial body plan of a sea urchin., Wygoda JA, Yang Y, Byrne M, Wray GA., Genome Biol Evol. April 1, 2014; 6 (4): 964-73.          


The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network., Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA., PLoS Biol. October 1, 2013; 11 (10): e1001696.            


Genetics of gene expression responses to temperature stress in a sea urchin gene network., Runcie DE, Garfield DA, Babbitt CC, Wygoda JA, Mukherjee S, Wray GA., Mol Ecol. September 1, 2012; 21 (18): 4547-62.


Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus., Garfield D, Haygood R, Nielsen WJ, Wray GA., Evol Dev. March 1, 2012; 14 (2): 152-67.


Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin., Oliver TA, Garfield DA, Manier MK, Haygood R, Wray GA, Palumbi SR., Genome Biol Evol. January 1, 2010; 2 800-14.                


The genome of the sea urchin Strongylocentrotus purpuratus., null null, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R., Science. November 10, 2006; 314 (5801): 941-52.


Endo16 is required for gastrulation in the sea urchin Lytechinus variegatus., Romano LA, Wray GA., Dev Growth Differ. October 1, 2006; 48 (8): 487-97.


The evolution of embryonic gene expression in sea urchins., Wray GA., Integr Comp Biol. June 1, 2006; 46 (3): 233-42.


Arrays in rays: terminal addition in echinoderms and its correlation with gene expression., Mooi R, David B, Wray GA., Evol Dev. November 1, 2005; 7 (6): 542-55.


Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites., Balhoff JP, Wray GA., Proc Natl Acad Sci U S A. June 14, 2005; 102 (24): 8591-6.


Culture of echinoderm larvae through metamorphosis., Wray GA, Kitazawa C, Miner B., Methods Cell Biol. January 1, 2004; 74 75-86.


Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation., Romano LA, Wray GA., Development. September 1, 2003; 130 (17): 4187-99.


Identification of asteroid genera with species capable of larval cloning., Knott KE, Balser EJ, Jaeckle WB, Wray GA., Biol Bull. June 1, 2003; 204 (3): 246-55.


Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae., Lowe CJ, Issel-Tarver L, Wray GA., Evol Dev. March 1, 2002; 4 (2): 111-23.


Do convergent developmental mechanisms underlie convergent phenotypes?, Wray GA., Brain Behav Evol. January 1, 2002; 59 (5-6): 327-36.


A sea urchin genome project: sequence scan, virtual map, and additional resources., 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., Proc Natl Acad Sci U S A. August 15, 2000; 97 (17): 9514-8.


Developmental regulatory genes and echinoderm evolution., Wray GA, Lowe CJ., Syst Biol. March 1, 2000; 49 (1): 28-51.


Rearing larvae of sea urchins and sea stars for developmental studies., Lowe CJ, Wray GA., Methods Mol Biol. January 1, 2000; 135 9-15.


Gene expression during echinoderm metamorphosis., Wray GA., Zygote. January 1, 2000; 8 Suppl 1 S48-9.


Promoter logic., Wray GA., Science. March 20, 1998; 279 (5358): 1871-2.


Radical alterations in the roles of homeobox genes during echinoderm evolution., Lowe CJ, Wray GA., Nature. October 16, 1997; 389 (6652): 718-21.


Archenteron precursor cells can organize secondary axial structures in the sea urchin embryo., Benink H, Wray G, Hardin J., Development. September 1, 1997; 124 (18): 3461-70.


The evolution of echinoderm development is driven by several distinct factors., Wray GA, Bely AE., Dev Suppl. January 1, 1994; 97-106.


RAPID EVOLUTION OF GASTRULATION MECHANISMS IN A SEA URCHIN WITH LECITHOTROPHIC LARVAE., Wray GA, Raff RA., Evolution. December 1, 1991; 45 (8): 1741-1750.


The dorsoventral axis is specified prior to first cleavage in the direct developing sea urchin Heliocidaris erythrogramma., Henry JJ, Wray GA, Raff RA., Development. November 1, 1990; 110 (3): 875-84.


Novel origins of lineage founder cells in the direct-developing sea urchin Heliocidaris erythrogramma., Wray GA, Raff RA., Dev Biol. September 1, 1990; 141 (1): 41-54.


The "lecithotrophic" sea urchin Heliocidaris erythrogramma lacks typical yolk platelets and yolk glycoproteins., Scott LB, Lennarz WJ, Raff RA, Wray GA., Dev Biol. March 1, 1990; 138 (1): 188-93.


Early inductive interactions are involved in restricting cell fates of mesomeres in sea urchin embryos., Henry JJ, Amemiya S, Wray GA, Raff RA., Dev Biol. November 1, 1989; 136 (1): 140-53.


Evolutionary modification of cell lineage in the direct-developing sea urchin Heliocidaris erythrogramma., Wray GA, Raff RA., Dev Biol. April 1, 1989; 132 (2): 458-70.

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