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Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery.

Wall CB, Ritson-Williams R, Popp BN, Gates RD.

Limnol Oceanogr. 2019 Sep;64(5):2011-2028. doi: 10.1002/lno.11166. Epub 2019 Apr 9.


Genome analysis of the rice coral Montipora capitata.

Shumaker A, Putnam HM, Qiu H, Price DC, Zelzion E, Harel A, Wagner NE, Gates RD, Yoon HS, Bhattacharya D.

Sci Rep. 2019 Feb 22;9(1):2571. doi: 10.1038/s41598-019-39274-3.


Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance.

Magel JMT, Burns JHR, Gates RD, Baum JK.

Sci Rep. 2019 Feb 21;9(1):2512. doi: 10.1038/s41598-018-37713-1.


High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata.

Barshis DJ, Birkeland C, Toonen RJ, Gates RD, Stillman JH.

J Exp Biol. 2018 Dec 10;221(Pt 24). pii: jeb188581. doi: 10.1242/jeb.188581.


Publisher Correction: Intra-colony disease progression induces fragmentation of coral fluorescent pigments.

Caldwell JM, Ushijima B, Couch CS, Gates RD.

Sci Rep. 2018 Mar 6;8(1):4267. doi: 10.1038/s41598-018-22375-w.


Coral bleaching from a single cell perspective.

Nielsen DA, Petrou K, Gates RD.

ISME J. 2018 Jun;12(6):1558-1567. doi: 10.1038/s41396-018-0080-6. Epub 2018 Feb 20.


Publisher Correction: Intra-colony disease progression induces fragmentation of coral fluorescent pigments.

Caldwell JM, Ushijima B, Couch CS, Gates RD.

Sci Rep. 2018 Jan 5;8(1):346. doi: 10.1038/s41598-017-17987-7.


Elevated pCO2 affects tissue biomass composition, but not calcification, in a reef coral under two light regimes.

Wall CB, Mason RAB, Ellis WR, Cunning R, Gates RD.

R Soc Open Sci. 2017 Nov 1;4(11):170683. doi: 10.1098/rsos.170683. eCollection 2017 Nov.


Who's there? - First morphological and DNA barcoding catalogue of the shallow Hawai'ian sponge fauna.

Núñez Pons L, Calcinai B, Gates RD.

PLoS One. 2017 Dec 21;12(12):e0189357. doi: 10.1371/journal.pone.0189357. eCollection 2017.


Corrigendum: The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

Madin JS, Anderson KD, Andreasen MH, Bridge TCL, Cairns SD, Connolly SR, Darling ES, Diaz M, Falster DS, Franklin EC, Gates RD, Harmer AMT, Hoogenboom MO, Huang D, Keith SA, Kosnik MA, Kuo CY, Lough JM, Lovelock CE, Luiz O, Martinelli J, Mizerek T, Pandolfi JM, Pochon X, Pratchett MS, Putnam HM, Roberts TE, Stat M, Wallace CC, Widman E, Baird AH.

Sci Data. 2017 Dec 5;4:170174. doi: 10.1038/sdata.2017.174.


Intra-colony disease progression induces fragmentation of coral fluorescent pigments.

Caldwell JM, Ushijima B, Couch CS, Gates RD.

Sci Rep. 2017 Nov 6;7(1):14596. doi: 10.1038/s41598-017-15084-3. Erratum in: Sci Rep. 2018 Jan 5;8(1):346. Sci Rep. 2018 Mar 6;8(1):4267.


A dynamic bioenergetic model for coral-Symbiodinium symbioses and coral bleaching as an alternate stable state.

Cunning R, Muller EB, Gates RD, Nisbet RM.

J Theor Biol. 2017 Oct 27;431:49-62. doi: 10.1016/j.jtbi.2017.08.003. Epub 2017 Aug 3.


Effects of Temperature and pCO2 on Population Regulation of Symbiodinium spp. in a Tropical Reef Coral.

Baghdasarian G, Osberg A, Mihora D, Putnam H, Gates RD, Edmunds PJ.

Biol Bull. 2017 Apr;232(2):123-139. doi: 10.1086/692718. Epub 2017 Jun 6.


Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands.

Cunning R, Gates RD, Edmunds PJ.

PeerJ. 2017 Jun 21;5:e3472. doi: 10.7717/peerj.3472. eCollection 2017.


Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals.

Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, Bhattacharya D.

Genomics. 2017 Oct;109(5-6):383-390. doi: 10.1016/j.ygeno.2017.06.003. Epub 2017 Jun 17.


The Vulnerability and Resilience of Reef-Building Corals.

Putnam HM, Barott KL, Ainsworth TD, Gates RD.

Curr Biol. 2017 Jun 5;27(11):R528-R540. doi: 10.1016/j.cub.2017.04.047. Review.


Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata.

Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D.

PeerJ. 2017 May 18;5:e3319. doi: 10.7717/peerj.3319. eCollection 2017.


Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.

Sogin EM, Putnam HM, Nelson CE, Anderson P, Gates RD.

Environ Microbiol Rep. 2017 Jun;9(3):310-315. doi: 10.1111/1758-2229.12541. Epub 2017 May 9.


Capacity shortfalls hinder the performance of marine protected areas globally.

Gill DA, Mascia MB, Ahmadia GN, Glew L, Lester SE, Barnes M, Craigie I, Darling ES, Free CM, Geldmann J, Holst S, Jensen OP, White AT, Basurto X, Coad L, Gates RD, Guannel G, Mumby PJ, Thomas H, Whitmee S, Woodley S, Fox HE.

Nature. 2017 Mar 30;543(7647):665-669. doi: 10.1038/nature21708. Epub 2017 Mar 22.


Shifting paradigms in restoration of the world's coral reefs.

van Oppen MJH, Gates RD, Blackall LL, Cantin N, Chakravarti LJ, Chan WY, Cormick C, Crean A, Damjanovic K, Epstein H, Harrison PL, Jones TA, Miller M, Pears RJ, Peplow LM, Raftos DA, Schaffelke B, Stewart K, Torda G, Wachenfeld D, Weeks AR, Putnam HM.

Glob Chang Biol. 2017 Sep;23(9):3437-3448. doi: 10.1111/gcb.13647. Epub 2017 Mar 1. Review.


Defining the Core Microbiome in Corals' Microbial Soup.

Hernandez-Agreda A, Gates RD, Ainsworth TD.

Trends Microbiol. 2017 Feb;25(2):125-140. doi: 10.1016/j.tim.2016.11.003. Epub 2016 Dec 3. Review.


Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques.

Burns JH, Alexandrov T, Ovchinnikova K, Gates RD, Takabayashi M.

Data Brief. 2016 Sep 19;9:460-462. eCollection 2016 Dec.


Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals.

Putnam HM, Davidson JM, Gates RD.

Evol Appl. 2016 Aug 2;9(9):1165-1178. eCollection 2016 Oct.


Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework.

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M.

J Invertebr Pathol. 2016 Oct;140:51-57. doi: 10.1016/j.jip.2016.08.007. Epub 2016 Aug 20.


OCEAN BIOLOGY. Corals' microbial sentinels.

Ainsworth TD, Gates RD.

Science. 2016 Jun 24;352(6293):1518-9. doi: 10.1126/science.aad9957. No abstract available.


Comparative genomics explains the evolutionary success of reef-forming corals.

Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG.

Elife. 2016 May 24;5. pii: e13288. doi: 10.7554/eLife.13288.


Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis.

Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, Falkowski PG.

Proc Biol Sci. 2016 Apr 27;283(1829). pii: 20160322. doi: 10.1098/rspb.2016.0322.


The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

Madin JS, Anderson KD, Andreasen MH, Bridge TC, Cairns SD, Connolly SR, Darling ES, Diaz M, Falster DS, Franklin EC, Gates RD, Harmer A, Hoogenboom MO, Huang D, Keith SA, Kosnik MA, Kuo CY, Lough JM, Lovelock CE, Luiz O, Martinelli J, Mizerek T, Pandolfi JM, Pochon X, Pratchett MS, Putnam HM, Roberts TE, Stat M, Wallace CC, Widman E, Baird AH.

Sci Data. 2016 Mar 29;3:160017. doi: 10.1038/sdata.2016.17. Erratum in: Sci Data. 2017 Dec 05;4:170174. Harmer, Aaron [added].


Improving the ecological relevance of toxicity tests on scleractinian corals: Influence of season, life stage, and seawater temperature.

Hédouin LS, Wolf RE, Phillips J, Gates RD.

Environ Pollut. 2016 Jun;213:240-253. doi: 10.1016/j.envpol.2016.01.086. Epub 2016 Feb 21.


Variability of Symbiodinium Communities in Waters, Sediments, and Corals of Thermally Distinct Reef Pools in American Samoa.

Cunning R, Yost DM, Guarinello ML, Putnam HM, Gates RD.

PLoS One. 2015 Dec 29;10(12):e0145099. doi: 10.1371/journal.pone.0145099. eCollection 2015.


Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs.

Burns J, Delparte D, Gates RD, Takabayashi M.

PeerJ. 2015 Jul 7;3:e1077. doi: 10.7717/peerj.1077. eCollection 2015.


Depth specialization in mesophotic corals (Leptoseris spp.) and associated algal symbionts in Hawai'i.

Pochon X, Forsman ZH, Spalding HL, Padilla-Gamiño JL, Smith CM, Gates RD.

R Soc Open Sci. 2015 Feb 4;2(2):140351. doi: 10.1098/rsos.140351. eCollection 2015 Feb.


The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts.

D Ainsworth T, Krause L, Bridge T, Torda G, Raina JB, Zakrzewski M, Gates RD, Padilla-Gamiño JL, Spalding HL, Smith C, Woolsey ES, Bourne DG, Bongaerts P, Hoegh-Guldberg O, Leggat W.

ISME J. 2015 Oct;9(10):2261-74. doi: 10.1038/ismej.2015.39. Epub 2015 Apr 17.


Building coral reef resilience through assisted evolution.

van Oppen MJ, Oliver JK, Putnam HM, Gates RD.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2307-13. doi: 10.1073/pnas.1422301112. Epub 2015 Feb 2.


Application of 1H-NMR metabolomic profiling for reef-building corals.

Sogin EM, Anderson P, Williams P, Chen CS, Gates RD.

PLoS One. 2014 Oct 29;9(10):e111274. doi: 10.1371/journal.pone.0111274. eCollection 2014.


Persistence and change in community composition of reef corals through present, past, and future climates.

Edmunds PJ, Adjeroud M, Baskett ML, Baums IB, Budd AF, Carpenter RC, Fabina NS, Fan TY, Franklin EC, Gross K, Han X, Jacobson L, Klaus JS, McClanahan TR, O'Leary JK, van Oppen MJ, Pochon X, Putnam HM, Smith TB, Stat M, Sweatman H, van Woesik R, Gates RD.

PLoS One. 2014 Oct 1;9(10):e107525. doi: 10.1371/journal.pone.0107525. eCollection 2014.


The early expansion and evolutionary dynamics of POU class genes.

Gold DA, Gates RD, Jacobs DK.

Mol Biol Evol. 2014 Dec;31(12):3136-47. doi: 10.1093/molbev/msu243. Epub 2014 Sep 25.


The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ.

PLoS Biol. 2014 Jun 24;12(6):e1001889. doi: 10.1371/journal.pbio.1001889. eCollection 2014 Jun. No abstract available.


Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution.

Pochon X, Putnam HM, Gates RD.

PeerJ. 2014 May 20;2:e394. doi: 10.7717/peerj.394. eCollection 2014.


Sedimentation and the reproductive biology of the Hawaiian reef-building coral Montipora capitata.

Padilla-Gamiño JL, Hédouin L, Waller RG, Smith D, Truong W, Gates RD.

Biol Bull. 2014 Feb;226(1):8-18.


Intracellular pH and its response to CO2-driven seawater acidification in symbiotic versus non-symbiotic coral cells.

Gibbin EM, Putnam HM, Davy SK, Gates RD.

J Exp Biol. 2014 Jun 1;217(Pt 11):1963-9. doi: 10.1242/jeb.099549. Epub 2014 Mar 13.


The founding charter of the Genomic Observatories Network.

Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Gates RD, Toonen R, Berteaux-Lecellier V, Barbier M, Barker K, Bertilsson S, Bicak M, Bietz MJ, Bobe J, Bodrossy L, Borja A, Coddington J, Fuhrman J, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Hero JM, Hoekman D, Jansson J, Jeanthon C, Kao R, Klindworth A, Knight R, Kottmann R, Koo MS, Kotoulas G, Lowe AJ, Marteinsson VT, Meyer F, Morrison N, Myrold DD, Pafilis E, Parker S, Parnell JJ, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Schonrogge K, Simon N, Valette-Silver NJ, Springer YP, Stone GN, Stones-Havas S, Sansone SA, Thibault KM, Wecker P, Wichels A, Wooley JC, Yahara T, Zingone A; GOs-COS.

Gigascience. 2014 Mar 7;3(1):2. doi: 10.1186/2047-217X-3-2.


Diversity in skeletal architecture influences biological heterogeneity and Symbiodinium habitat in corals.

Yost DM, Wang LH, Fan TY, Chen CS, Lee RW, Sogin E, Gates RD.

Zoology (Jena). 2013 Oct;116(5):262-9. doi: 10.1016/j.zool.2013.06.001. Epub 2013 Aug 3.


Symbiotic specificity, association patterns, and function determine community responses to global changes: defining critical research areas for coral-Symbiodinium symbioses.

Fabina NS, Putnam HM, Franklin EC, Stat M, Gates RD.

Glob Chang Biol. 2013 Nov;19(11):3306-16. doi: 10.1111/gcb.12320. Epub 2013 Sep 11.


The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress.

Stat M, Pochon X, Franklin EC, Bruno JF, Casey KS, Selig ER, Gates RD.

Ecol Evol. 2013 May;3(5):1317-29. doi: 10.1002/ece3.556. Epub 2013 Apr 9.


Assessing fertilization success of the coral Montipora capitata under copper exposure: does the night of spawning matter?

Hédouin L, Gates RD.

Mar Pollut Bull. 2013 Jan 15;66(1-2):221-4. doi: 10.1016/j.marpolbul.2012.11.020. Epub 2012 Dec 12.


Transmission mode predicts specificity and interaction patterns in coral-Symbiodinium networks.

Fabina NS, Putnam HM, Franklin EC, Stat M, Gates RD.

PLoS One. 2012;7(9):e44970. doi: 10.1371/journal.pone.0044970. Epub 2012 Sep 18.


Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals.

Putnam HM, Stat M, Pochon X, Gates RD.

Proc Biol Sci. 2012 Nov 7;279(1746):4352-61. Epub 2012 Aug 29.

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