Courtney T., Lenz B, Gates RD et al. Coral reef disturbances and the ecological booms and busts of coral calcification capacity. Product from the USGS Powell Workshop. Global Change Biology. 

Drury, C. February 2020. Resilience in Reef-Building Corals: The ecological and evolutionary importance of the host response to thermal stress. Molecular Ecology

Huffmyer AS, Matsuda SB, Eggers AR, Lemus JD and RD Gates. February 2020. Evaluation of laser scanning confocal microscopy as a method for characterizing reef-building coral tissue thickness and Symbiodiniaceae fluorescence. Journal of Experimental Biology 223, jeb220335

Kitchen, R, Piscetta, M, Lenz, E, Rocha de Souza, M, Schar, D and C Wall. 2019. Symbiont transmission and reproductive mode influence responses of three Hawaiian coral larvae to elevated temperatures and nutrients. Coral Reefs

Claar DC, KL Tietjen, KD Cox, RD Gates, JK Baum (2020) Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef. Scientific Reports 10 (1), 1-13

Wall CB, M Kaluhiokalani, BN Popp, MJ Donahue, RD Gates (2020) Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient. The ISME Journal, 14, pages 945–958

Shumaker, A, Putnam, HM, Qiu, H, Price, DC, Zelzion, E, Harel, A, Wagner, N, Gates, RD, Yoon, HS and D Bhattacharya (2020) Genome analysis of the rice coral Montipora capitata. Scientific Reports 9 (1), 1-16


Magel JMT,  JHR Burns, RD Gates, JK Baum (2019) Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance. Scientific Reports 9 (1), 1-12

Price NN, S Muko, L Legendre, R Steneck, MJH van Oppen, R Albright et al. (2019) Global biogeography of coral recruitment: tropical decline and subtropical increase. Marine Ecology Progress Series 621, 1-17

Wal CBl, R Ritson‐Williams, BN Popp, RD Gates(2019) Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery. Limnology and Oceanography 64 (5), 2011-2028

Padilla‐Gamiño JL, MS Roth, LJ Rodrigues, CJ Bradley, RR Bidigare et al. (2019) Ecophysiology of mesophotic reef‐building corals in Hawai ‘i is influenced by symbiont–host associations, photoacclimatization, trophic plasticity, and adaptation. Limnology and Oceanography 64 (5), 1980-1995

Ainsworth TD, CL Hurd, RD Gates, PW Boyd (2019) How do we overcome abrupt degradation of marine ecosystems and meet the challenge of heatwaves and climate extremes? Global Change Biology 26: 343-354

Menezes S, Canfield K, Matsuda S, Moore A, Austin A, Dewsbury B, Feliú-Mójer, Mcduffie K, Moore K, Reich C and H Smith. 2019. Science communication demands a critical approach based in inclusion, equity, and intersectionality. Frontiers in Communication, section Science and Environmental Communication. Journal of Experimental Biology, Methods & Techniques.


Barshis DJ, C Birkeland, RJ Toonen, RD Gates, JH Stillman (2018) High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata. Journal of Experimental Biology 221 (24): jeb188581.  ​

Forsman ZH, Maurin P, Parry M, Chung A, Sartor C, Hixon MA, Hughes K, Rodgers K, Knapp ISS, Gulko DA, Franklin EC, Del Rio Torres L, Chan NT, Wolke CS, Gates RD, Toonen RJ (2018) The First Hawai‘i Workshop For Coral Restoration & Nurseries. Marine Policy 96:133-135.

Innis T, R Cunning, R Ritson-Williams, CB Wall, RD Gates (2018)  Coral color and depth drive symbiosis ecology of Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i. Coral Reefs 37 (2): 423-430.

Gattuso JP et al. (2018) Ocean solutions to address climate change and its effects on marine ecosystems. Frontiers in Marine Science 5: 337.

Hawthorne LB, Kennedy EV, Berger M, Chen CA, Cinner JE, Darling ES, Eakin CM, Gates RD, Heron SF, Knowlton N, Obura DO, Palumbi SR, Possingham HP, Puotinen M, Runting RK, Skirving WJ, Spalding M, Wilson KA, Wood S, Veron JE, Hoegh-Guldberg O. (2018) Risk‐sensitive planning for conserving coral reefs under rapid climate change. Conservation Letters 2018:e12587.

Wall CB, CA Ricci, GE Foulds, LD Mydlarz, RD Gates, HM Putnam (2018) The effects of environmental history and thermal stress on coral physiology and immunity. Marine Biology 165(3): 56

Putnam HM, R Ritson-Williams, JA Cruz, JM Davidson, & RD Gates (2018) Nurtured by nature: Considering the role of environmental and parental legacies in coral ecological performance. bioRxiv, 317453.

Guest JR, PJ Edmunds, RD Gates, IB Kuffner, AJ Andersson, BB Barnes, I Chollett, R Elahi, K Gross, EA Lenz, S Mitarai, PJ Mumby, HR Nelson, BA Parker, HM Putnam, CS Rogers, LT Toth (2018) A framework for identifying and characterizing coral reef “oases” against a backdrop of degradation J. Appl. Ecol.

Gibbin EM, T Krueger, HM Putnam, KL Barott, J Bodin, RD Gates, A Meibom (2018) Short-term thermal acclimation modifies the metabolic condition of the coral holobiont. Frontiers in Marine Science 5: 10.

Neilson BJ, Wall CB, Mancini FT, Gewecke CA (2018). Herbivore biocontrol and manual removal successfully reduce invasive macroalgae on coral reefs. PeerJ 6: e5332

Nielsen DA, K Petrou, RD Gates (2018) Coral bleaching from a single cell perspective. ISME Journal 12:1558-1567.


Núñez Pons L, B Calcinai, RD Gates (2017) Who’s there? – First morphological and DNA barcoding catalogue of the shallow Hawai’ian sponge fauna. PLoS ONE 12(12): e0189357.
Caldwell JM, B Ushijima, CS Couch, RD Gates (2017) Intra-colony disease progression induces fragmentation of coral fluorescent pigments. Scientific Reports 8(1):346
Wall, CB, RAB Mason, WR Ellis, R Cunning, RD Gates (2017) Elevated pCO2 affects tissue biomass composition, but not calcification, in a reef coral under two light regimes. Royal Society Open Science 4:170683

Qiu H, E Zelzion, HM Putnam, RD Gates, NE Wagner, DK Adams, D Bhattacharya (2017) Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals. Genomics

Putnam HM, Barott KL, Ainsworth TD, Gates RD (2017) The vulnerability and resilience of reef-building corals. Current Biology 27(11):PR528-R540

​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. (2017) Capacity shortfalls hinder the performance of marine protected areas globally. Nature 543(7647):665-669

Baghdasarian G, Osberg A, Mihora D, Putnam HM, Gates RD, Edmunds PJ (2017) Effects of Temperature and p CO2 on Population Regulation of Symbiodinium spp. in a Tropical Reef Coral. The Biological Bulletin 232(2):123-139.
Putnam HM, DK Adams, E Zelzion, NE Wagner, H Qiu, T Mass, PG Falkowski, RD Gates, D Bhattacharya (2017) Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ 5:e3319

Cunning R, RD Gates, PJ Edmunds (2017) Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands. PeerJ e2925v1

Sogin EM, HM Putnam, CE Nelson, P Anderson, RD Gates (2017) Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea, and Symbiodinium communities. Environmental Microbiology Reports 9:310-315

van Oppen MJH, RD Gates, LL Blackall, N Cantin, LJ Chakravarti, WY Chan, C Cormick, A Crean, K Damjanovic, H Epstein, PL Harrison, TA Jones, M Miller, RJ Pears, LM Peplow, DA Raftos, B Schaffelke, K Steward, G Torda, D Wachenfeld, AR Weeks, HM Putnam (2017) Shifting paradigms in restoration of the world's coral reefs. Global Change Biology 23:3437-3448.

Claar DC, NS Fabina, HM Putnam, R Cunning, E Sogin, JK Baum, RD Gates (2017) "Embracing complexity in coral-algal symbioses". Chapter 15 in: Algal and Cyanobacteria Symbioses. Ed. Grube M, Seckbach J, Muggia L. World Scientific Publishing Europe Limited. Pages  467-492. Book.

Cunning R, EB Muller, RD Gates, RM Nisbet (2017) A dynamic bioenergetic model for coral-symbiodinium symbioses and coral bleaching as an alternate stable state. J Theor Biol 431:49-62.


Hernandez-Agreda A, Gates RD, Ainsworth TD (2016) Defining the core microbiome in corals' microbial soup. Trends in Microbiology 25:125-140. .

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M (2016) Investigating the spatial distribution of Growth Anomalies affecting Montipora capitata corals in a 3-dimensional framework. Journal of Invertebrate Pathology 140:51-56.

Putnam HM, Davidson JM, Gates RD (2016) Ocean acidification influences host DNA methylation and phenotypic plasticity in environmentally susceptible corals. Evolutionary Applications .

Ainsworth TD, Gates RD (2016) Corals' microbial sentinels. Science 352:1518-1519
Caldwell, J.M., Burns, J.H.R., Couch, C., Ross, M., Runyon, C., Takabayashi, M., Vargas-Ángel, B., Walsh, W., Walton, M., White, D. and Williams, G. (2016) Hawaiʻi Coral Disease database (HICORDIS): species-specific coral health data from across the Hawaiian archipelago. Data in Brief, 8, pp.1054-1058.

Cunning R, Ritson-Williams R, Gates RD (2016) Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA. Mar Ecol Prog Ser 551:131-139.

Bhattacharaya D, S Agrawal, M Aranda, S Baumgarten, M Belcaid, JL Drake, D Erwin, S Foret, RD Gates, DF Gruber, B Kamel, MP Lesser, O Levy, YJ Liew, M MacManes, T Mass, M Medina, S Mehr, W Meyer, DC Price, HM Putnam, H Qiu, C Shinzato, E Shoguchi, J Stokes, S Tambutte, D Thernov, CR Voolstra, N Wagner, CW Walker, APM Weber, V Weis, E Zelzion, D Zoccola, PG Falkowski (2016) Comparative genomics explains the evolutionary success of reef-forming corals. eLife 2016;5:e13288.

Burns JHR, Delparte D, Kapono L, Belt M, Gates RD, Takabayashi M (2016) Assessing the impact of acute disturbances on the structure and composition of a coral community using innovative 3D reconstruction techniques. Methods in Oceanography 15-16: 49-59.

Madin, JS, KD Anderson, MH  Andreasen, TCL Bridge, SD Cairns, SR Connolly, ES Darling, M Diaz, DS Falster, EC Franklin, RD Gates, AMT Harmer, MO Hoogenboom, D Huang, SA Keith, MA Kosnik, CY Kuo, JM Lough, CE Lovelock, O Luiz, J Martinelli, T Mizerek, JM Pandolfi, X Pochon, MS Pratchett, HM Putnam, TE Roberts, M Stat, CC Wallace, E Widman, AH Baird (2016) The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Scientific Data 3: 160017.

​Hédouin LS, Wolf RE, Jeff Phillips J, Gates RD (2016) Improving the ecological relevance of toxicity tests on scleractinian corals: Influence of season, life stage, and seawater temperature. Environmental Pollution 213: 240-253.

Sogin EM, Putnam HM, Anderson PE, RD Gates (2016) Metabolomic signatures of increases in temperature and ocean acidification from the reef-building coral, Pocillopora damicornis. Metabolomics 12: 1-12.  https://10.1007/s11306-016-0987-8

Davis N, D Field, D Gavaghan, SJ Holbrook, S Planes, M Troyer, M Bonsall, J Claudet, G Roderick, RJ Schmitt, LA Zettler, V Berteaux, HC Bossin, C Cabasse, A Collin, J Deck, T Dell, J Dunne, R Gates, M Harfoot, JL Hench, M Hopuare, P Kirch, G Kotoulas, A Kosenkov, A Kusenko, JJ Leichter, H Lenihan, A Magoulas, N Martinez, C Meyer, B Stoll, B Swalla, DM Tartakovsky, HT Murphy, S Turyshev, F Valdvinos, R Williams, S Wood, IDEA Consortium (2016) Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium. GigaScience 5:1.


Cunning R, Yost DM, Guarinello ML, Putnam HM, Gates RD (2015) Variability of Symbiodinium communities in waters, sediments, and corals of thermally distinct reef pools in American Samoa. PLoS ONE 10(12):e0145099.

Putnam, H. M. and Gates, R. D.  (2015) Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions. Journal of Experimental Biology 218 (15):2365-2372.
Burns, J. H. R., Delparte, D., Gates, R. D. and Takabayashi, M. (2015) Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077.

Stat M., Yost, D. M. and Gates R. D. (2015) Geographic structure and host-specificity shape the community composition of symbiotic dinoflagellates in corals from the Northwestern Hawaiian Islands. Coral Reefs 34 (4):1075-1086.
Burns, J. H. R., Delparte, D., Gates, R. D. and Takabayashi, M. (2015) Utilizing underwater three-dimensional modeling to enhance ecological and biological studies of coral reefs. Proceeding of the International Society for Photogrammetry and Remote Sensing 40 (5): 61-66.
Ainsworth, T. D., Bridge, T., Torda, G., Raina, J. B., Gates, R. D., Zakrzewski, M., Padilla-Gamiño, J. P L., Spalding, H. L., Smith, C., Woosley, E. S., Krause, L., Bourne, D. G. , Bongaerts, P., Hoegh-Guldberg, O., Leggat, W. (2015) The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. The ISME Journal 9:2261-2274.
van Oppen, M. J. H., Oliver, J. K., Putnam, H. M. and Gates, R. D. (2015)  Building coral reef resilience through assisted evolution. Invited perspective. Proceedings of the National Academy of Sciences . Volume cover photograph.
Pochon, X., Forsman,Z.H., Spalding, H.L., Padilla-Gamiño, J.L., Smith, C.M., and Gates, R.D. (2015) Depth specialization in mesophotic corals (Leptoseris spp.) and associated algal symbionts in Hawai'i. Royal Society Open Science 2:140351. . Volume cover photograph.
Edmunds, P. J., Steneck, R., Albright, R., Carpenter, R. C., Chui Pui, A., Fan, T. Y., Harii, S., Kitano, H., Kurihara, H., Legendre, L., Mitarai, S., Muko, S., Nozawa, T., Padilla-Gamino, J. L., Price, N. N., Sakai, K., Suzuki, G., van Oppen, M. J. H., Yarid, A. and Gates, R. D. (2015)  Geographic variation in long-term trajectories of change in coral recruitment: a global to-local perspective. Marine and Freshwater Research 66(7)
Roth, M. S., Padilla-Gamiño, J. L., Pochon, X., Bidigare, R. R., Gates, R. D., Smith, C. M., Spalding, H. L. (2015) Fluorescent protein expression in mesophotic reef-building corals. Marine Ecology Progress Series 521: 63-79.
Gibbin, E. M., Putnam, H. M., Gates, R. D., Nitschke, M. R. and Davy, S. K. (2015) Species-specific differences in thermal tolerance may define susceptibility to intracellular acidosis in reef corals. Marine Biology 162: 717-723. 10.1007/s00227-015-2617-9


Sogin EM, Anderson P, Williams P, Chen C-S, Gates RD (2014) Application of 1H-NMR Metabolomic Profiling for Reef-Building Corals. PLoS ONE 9(10): e111274.
Edmunds PJ, Burgess S, Putnam HM, Baskett ML, Bramanti L, Fabina NS, Han X, Lesser MP, Madin JS, Wall CB, Yost DM, and Gates RD. (2014) Evaluating the causal basis of ecological success within the Scleractinia: An integral projection model approach. Marine Biology 161:2719-2734.
Edmunds PJ, Adjeroud M, Baskett M, Baum J, Baums I., Budd A, Carpenter RC, Fabina N, Fan T-Y, Franklin E, Gross K, Han S, Jacobson L, McClanahan T, O’Leary J, van Oppen, MJH, Pochon X, Putnam HM, Smith TB, Stat M, Sweatman H, van Woesik R, and Gates RD. Persistence and change in community composition of reef corals through present, past, and future climates. PLoS ONE 9(10): e107525.

Gold DA, Gates RD, and Jacobs DK (2014) The early expansion and evolutionary dynamics of POU class genes. Molecular Biology and Evolution 31:3136-3147.

Pochon X, Gates RD, Vik D and Edmunds PJ (2014) Molecular characterization of symbiotic algae (Symbiodinium spp.) in soritid foraminifera (Sorites orbiculus) and a scleractinian coral (Orbicella annularis) from St John, US Virgin Islands. Marine Biology 161:2307-2318.
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 B, 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 AGB, 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. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 12(6):e1001889.
Edmunds PJ, Pochon X, Levitan DR, Yost DM, Belcaid M, Putnam HM, Gates RD (2014) Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands. MEPS 506:129-144.
Pochon X, Putnam HM, Gates RD. (2014) Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution. PeerJ 2:e394
Gibbin EM, Putnam HM, Davy SK and Gates RD (2014). Intracellular pH and its response to CO2-driven seawater acidification in symbiotic versus non-symbiotic coral cells. Journal of Experimental Biology
Padilla-Gamiño JL, Hédouin L, Waller RG, Smith D, Truong W and Gates RD (2014). Sedimentation and the reproductive biology of the Hawaiian reef building coral Montipora capitata.  Biological Bulletin 226:8-18
Davies N, Field D, Amaral-Zettler L, Clark M, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch P, Leong J, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Berteaux-Lecellier V, Gates RD, Toonen R, Bertilsson S, Bicak M, Bietz MJ, Bodrossy L, Borja A, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Jeanthon C,Klindworth A, Koo MS, Kotoulas G, Marteinsson VT, Morrison N, Myrold DD, Pafilis E, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Simon N, Valette-Silver NJ, Wichels A, Wooley JC and Zingone A (2014). The founding charter of the Genomic Observatories Network. GigaScience 2014 3:2


Briggs RA, Padilla-Gamiño JL, Bidigare R. Gates RD, and Ruttenberg KC (2013).  Impact of coral spawning on the biogeochemistry of a Hawaiian reef. Estuarine Coastal and Shelf Science 134:57-68.
Yost, DM, Wang LH, Fan TY, Chen CS, Lee RW, Sogin E and Gates RD (2013). Diversity in skeletal architecture influences biological heterogeneity and Symbiodinium habitat in corals. Zoology 116(5): 262-269.
Fabina NS, Putnam HM, Franklin EC, Stat M and Gates RD (2013) Symbiotic specificity, association patterns, and function determine community responses to global changes: Defining critical research areas for coral Symbiodinium symbioses. Global Change Biology 19(11): 3301-3316.
Putnam HM, Mayfield AB, Fan TY, Chen CS, and Gates RD (2013) The physiological and molecular responses of larvae from the reef-building coral Pocillopora damicornis exposed to near-future increases in temperature and pCO2. Marine Biology 160: 2157-2173.
Lesser, MP,  Stat M and Gates RD (2013) The endosymbiotic dinoflagellates (Symbiodinium sp.) of corals are parasites and mutualists. Coral Reefs 32: 603-611.
Stat M, Pochon X, Franklin EC, Bruno JF, Casey KS, Selig ER and Gates RD (2013) The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and history of ocean thermal stress. Ecology and Evolution 3(5):1317-1329.
Farrar CE, Forsman ZH, Gates RD, Leong JAC and Toonen RJ (2013) Observing the coral symbiome using laser scanning confocal microscopy. Science 339 (6119): 518. [ LINK ] [ VIDEO ]
Padilla-Gamiño JL, Bidigare RR, Barshis DJ, Alamaru A, Hedouin L, Hernandez-Pech X, Kandel F, Leon Soon S, Roth MS, Rodrigues LJ, Grottoli AG,   Portocarrero C, Wagenhauser SA, Buttler F and Gates RD (2013) Are all eggs created equal? A case study from the Hawaiian reef-building coral Montipora capitata. Coral Reefs 32(1): 137-152.
Hedouin L and Gates RD (2013) Assessing fertilization success of the coral Montipora capitata under copper exposure: Does the night of spawning matter? Marine Pollution Bulletin 66: 221–224.


Edmunds, PJ, Putnam HM and Gates RD (2012). Photophysiological consequences of vertical stratification of Symbiodinium in tissue of the coral Porites lutea. Biological Bulletin 223(2): 226-235.
Fabina NS, Putnam HM, Franklin EC, Stat M, Gates RD (2012) Transmission mode predicts specificity and interaction patterns in coral-Symbiodinium networks. PLoS ONE 7(9): e44970
Padilla-Gamiño JL, Hanson KM, Stat M and Gates RD (2012) Phenotypic plasticity of the coral Porites rus: acclimatization responses to a turbid environment. Journal of Experimental Marine Biology and Ecology 434–435: 71–80.
Putnam HM, Stat M, Pochon X and Gates RD (2012) Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals. Proceedings of the Royal Society B 279 (1746):4352-4361.
Stat M, Baker AC, Bourne DG, Forsman Z, Huggett MJ, Pochon X, Skillings D, Toonen RJ, van Oppen MJH and Gates RD (2012) Molecular delineation of species in the coral holobiont. Advances in Marine Biology 63: 1-65.
Padilla-Gamiño JL, Pochon X, Bird C, Concepcion GT and Gates RD (2012) From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS ONE 7(6) :e38440.
Padilla-Gamiño JL and Gates, RD (2012) Spawning dynamics in the Hawaiian reef building coral Montipora capitata. Marine Ecology Progress Series 449: 145-160.
Franklin EC, Stat M, Pochon X, Putnam HM and Gates RD (2012) GeoSymbio: A hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses. Molecular Ecology Resources 12(2): 369-373.
Takabayashi M, Adams LM, Pochon X and Gates RD (2012) Genetic diversity of free-Living Symbiodinium in surface water and sediment of Hawaii and Florida. Coral Reefs 31(1):157-167.
Krueger T and Gates RD (2012) Cultivating endosymbionts - host environmental mimics support the survival of Symbiodinium C15 ex hospite. Journal of Experimental Marine Biology and Ecology 413: 169-176.
Pochon X, Putnam HM, Burki F and Gates RD (2012) Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus Symbiodinium.  PLoS ONE 7(1): e29816.


Franklin EC, Stat M, Pochon X, Putnam HM and Gates RD (2011) Rapid Development of a hybrid web application for synthesis science of Symbiodinium with Google Apps. in Jones, M. (ed.), Proceedings of the Environmental Information Management Conference 2011 Santa Barbara, CA.
Gates, RD and Ainsworth, TD (2011). The nature and taxonomic composition of coral symbiomes as drivers of performance limits in scleractinian corals.  Journal of Experimental Marine Biology and Ecology 408: 94-101.
Hedouin L, Metian M and Gates RD (2011) Contamination of a Hawaiian coral reef ecosystem (Honolua Bay, Maui) by metals and a metalloid: An ecotoxicological and ecological study. Marine Environmental Research 71: 149-161.
Stat M, Bird CE, Pochon X, Chasqui L, Chauka LJ, Concepcion GT, Logan D, Takabayashi M, Toonen RJ, and Gates RD (2011) Variation in Symbiodinium ITS2 sequence assemblages among coral colonies. Plos One 6: e15854.
Wagner D, Pochon X, Irwin L, Toonen RJ, Gates RD (2011) Azooxanthellate? Most Hawaiian black corals contain Symbiodinium. Proceedings of the Royal Society of London B 278:1323-1329.
Padilla-Gamiño JL, Weatherby TM, Waller RG and Gates RD (2011) Formation and structural organization of the egg-sperm bundle of the scleractinian coral Montipora capitata. Coral Reefs 30(2): 371-380.
Stat M, and Gates RD (2011) Clade D Symbiodinium in scleractinian corals: a “nugget” of hope, a selfish opportunist, an ominous sign, or all of the above? Journal of Marine Biology: 730715.
Salerno JL, Reineman DR, Gates RD and Rappé MS (2011) The effect of a sub-lethal temperature elevation on the structure of bacterial communities associated with the coral Porites compressa. Journal of Marine Biology, 969173.
English K, Pochon X, Gates RD, and Poisson G (2011) MEST (Multiple EST Screening Tool): A web application for automation of BLAST queries of EST libraries.  Technical Report, Information & Computer Sciences, University of Hawaii. [ LINK ]


Mayfield AB, Hsiao YY, Fan TY, Chen CS and Gates RD (2010) Evaluating the temporal stability of stress-activated protein kinase and cytoskeleton gene expression in the Pacific reef corals Pocillopora damicornis and Seriatopora hystrix. Journal of Experimental Marine Biology and Ecology 395:215-222.
Hofmann GE, Barry JP, Edmunds PJ, Gates RD, Hutchins DA, Klinger T and Sewell MA (2010). The Effect of ocean acidification on polar, tropical and temperate marine calcifying organisms: An organism to ecosystem perspective. Annual Reviews of Ecology, Evolution and Systematics. Annual Review Ecology Evolution and Systematics 41: 127-147.
Lesser MP, Slattery M, Stat M, Ojimi M, Gates RD, and Grottoli A (2010) Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics. Ecology: 91(4): 990-1003.
Ainsworth TD, Vega Thurber R, and Gates RD (2010) The future of coral reefs - a microbial perspective. Trends in Ecology and Evolution 25(4): 233-240.
Pochon X and Gates RD (2010) A new Symbiodinium clade (Dinophyceae) from Soritid foraminifera in Hawai’i. Molecular Phylogenetics and Evolution 56:492-497.
Barshis DJ, Stillman JH, Gates RD, Toonen RJ, Smith LW, and Birkeland C (2010) Protein expression and genetic structure of the coral Porites lobata in an environmentally extreme Samoan back reef: does host genotype limit phenotypic plasticity? Molecular Ecology 19(8): 1705-1720.
Palmer CV and Gates RD (2010) Skeletal eroding band in Hawaiian corals. Coral Reefs 29(2): 469-469.    
Green DH, Edmunds PJ, Pochon X, and Gates RD (2010) The effects of substratum type on the growth, mortality, and photophysiology of juvenile corals in St. John, US Virgin Islands. Journal of Experimental Marine Biology and Ecology 384(1-2): 18-29.
Pochon X, Stat M, Takabayashi M, Logan D, Chasqui L, Jones L, and Gates RD (2010) Comparison of endosymbiotic and free-living Symbiodinium (Dinophyceae) diversity in a Hawaiian reef environment. Journal of Phycology 46: 53-65.
Yancey PH, Heppenstall M, Ly S, Raymond M, Andrell RM, Gates RD, Carter VL, and Hagedorn M (2010) Betaines and dimethylsulfoniopropionate (DMSP) as major osmolytes in Cnidaria with endosymbiotic dinoflagellates. Physiological and Biochemica Zoology 83: 167-173.


Hédouin L, Reichelt-Brushett AJ, and Gates RD (2009) Assessment of metals and a metalloid in sediments from Hawaiian coral reef ecosystems. Marine Pollution Bulletin 58: 1739-1765.
Chan YL, Pochon X, Fisher M, Wagner D, Concepcion GT, Kahng S, Toonen RJ, and Gates RD (2009) Host genotypes and endosymbiotic dinoflagellate diversity in the coral Leptoseris sampled between 60-100 meter depths. BMC Ecology 9:21.
Stat M, Pochon X, Cowie ROM, and Gates RD (2009) Specificity in communities of Symbiodinium in corals from Johnston Atoll. Marine Ecology Progress Series 386: 83-96.
Fitt WK, Gates RD, Hoegh-Guldberg O, Bythell J, Jatkar A, Grottoli AG, Gomez M, Fisher P, LaJeunesse T, Pantos O, Iglesias-Prieto R, Franklin DJ,
Rodrigues LJ, Torregiani JM, van Woesik R, and Lesser MP (2009) Response of two species of Indo-Pacific corals, Porites cylindrica and Stylophora pistillata, to thermal stress: The host does matter in determining the tolerance of corals to bleaching. Journal of Experimental Marine Biology and Ecology 373 (2): 102-110.
Olson ND, Ainsworth TD, Gates RD, and Takabayashi M (2009)  Diazotrophic bacteria associated with Hawaiian Montipora corals: Diversity and abundance in correlation with symbiotic dinoflagellates. Journal of Experimental Marine Biology and Ecology 371(2): 140-146.
Palmer CV, Roth MS, and Gates RD (2009) Red fluorescent protein responsible for pigmentation in trematode infected Porites compressa tissues. Biological Bulletin 216: 68-74.
Mayfield AB, Hirst MB, and Gates RD (2009) Gene expression normalization in a dual-compartment system: A real-time quantitative polymerase chain reaction protocol for symbiotic anthozoans. Molecular Ecology Resources 9(2): 462- 470.
van Oppen MJH, Leong JA and Gates RD (2009) Coral-virus interactions: a double-edged sword? Symbiosis 47: 1-8.


Stat M, Morris E, and Gates RD (2008) Functional diversity in coral-dinoflagellate symbiosis. Proceedings of the National Academy of Science 105(27): 9256-9261.
Manning MM and Gates RD (2008) Diversity in populations of free-living Symbiodinium from a Caribbean and Pacific reef. Limnology and Oceanography 53(5): 1853-1861.
Edmunds PJ and Gates RD (2008) Acclimatization in tropical reefs corals. Marine Ecological Progress Series 361: 307-310.
Stat M and Gates RD (2008) Vectored introductions of marine endosymbiotic dinoflagellates into Hawaii. Biological Invasions 10(4) : 576-583.


Leggat W, Ainsworth TA, Bythell JC, Dove S, Gates RD, Hoegh-Guldberg O, Iglesias-Prieto R, Yellowlees D (2007) The hologenome theory disregards the coral holobiont. Communication arising from Rosenberg et al (2007). Nature Reviews Microbiology 5:826
Hoegh-Guldberg O, Muller-Parker G, Cook CB, Gates RD, Gladfelter E, Trench RK, and Weis V (2007) Len Muscatine (1932-2007) and his contributions to the understanding of algal-invertebrate endosymbiosis. Coral Reefs 26(4):731-739.
Lesser MP, Bythell JC, Gates RD, Johnstone RW, Hoegh Guldberg O (2007) Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological Data. Journal of Experimental Marine Biology and Ecology 346: 36–44.
Apprill AM, Bidigare RR, and Gates RD (2007) Visibly healthy corals exhibit variable pigment concentrations and symbiont phenotypes. Coral Reefs 26: 387-397.
Mayfield AB and Gates RD (2007) Osmoregulation and osmotic stress in coral dinoflagellate symbiosis: Role in coral bleaching. Comparative Biochemistry and Physiology 147 (1): 1-10.
Biel KY, Gates RD, and Muscatine L (2007) Effects of free amino acids on the photosynthetic carbon metabolism of symbiotic dinoflagellates. Russian Journal Of Plant Physiology 54 (2): 171-183.
Apprill AM and Gates RD (2007) Recognizing diversity in coral symbiotic dinoflagellate communities. Molecular Ecology (16): 1127-1134.


van Oppen MJH and Gates RD (2006) Conservation genetics and the resilience of reef-building corals. Invited Review. Molecular Ecology 15 (13): 3863-3883.
Ridgway T and Gates RD (2006) Why are there so few genetic markers available for coral population analyses? Symbiosis 41: 1-7. [ LINK ]
Gleason DF, Edmunds PJ, and Gates RD (2006) Ultraviolet radiation effects on the behavior and recruitment of larvae from the reef coral Porites astreoides. Marine Biology 148: 503–512.


Edmunds PJ, Gates RD, Leggat W, and Hoegh-Guldberg O. 2005. The effect of temperature on the size and population density of dinoflagellates in larvae from the reef coral Porites astreoides. Invertebrate Biology 124 (3): 185-193.


Bebenek IG, Gates RD, Morris J, Hartenstein V, Jacobs DK (2004) Sine oculis in the basal metazoa. Development, Genes and Evolution 214 (7): 342-351.
Edmunds PJ, and Gates RD (2004) Size-dependent differences in the photophysiology of the reef coral Porites astreoides. Biological Bulletin 206: 61-64.


Edmunds PJ, and Gates RD (2003) Has coral bleaching delayed our understanding of fundamental aspects of coral-dinoflagellate symbioses? BioScience 53(10): 976-980.[0976:HCBDOU]2.0.CO;2
Jacobs DJ and Gates RD (2003) Developmental genes and the reconstruction of metazoan evolution – Implications of evolutionary loss, limits on inference of ancestry and Type 2 errors. Integrative and Comparative Biology 43: 11-18.
Lee SE, Gates RD, and Jacobs DK (2003) Gene fishing: the use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa. Journal of Molecular Evolution 56: 509-516.
Edmunds PJ, Gates RD, and Gleason DF (2003) Tissue composition of Montastraea franksi during and eleven months after a natural bleaching event. Coral Reefs 22: 54-62.


Gates RD, Hadrys T, Arenas-Mena C, and Jacobs DK (2002) Determining spatial and temporal patterns of developmental gene expression in vertebrates and invertebrates using in situ hybridization techniques. In: Methods and Tools in Biosciences and Medicine: Techniques in Molecular Evolution and Systematics (Eds. DeSalle, R., Giribet, G. and Wheeler, W.). Birkhauser Pp. 365-399.
Edmunds PJ and Gates RD (2002) Normalizing physiological data for scleractinian corals. Coral Reefs 21 (2): 193-197.
Nallur RB, Gates RD, Ladurner P, Jacobs DK and Hartenstein V (2002) Neurogenesis in the primitive bilaterian Neochildea I. Normal development and isolation of genes controlling neural fate. Development, Genes and Evolution 212 (2): 55-69.


Lee SE, Gates RD, and Jacobs DK (2001) The isolation of a Distal-less gene fragment from two molluscs. Development, Genes and Evolution 211: 506-508.
Edmunds PJ, Gates RD, and Gleason DF (2001) The biology of planulae freshly released from the reef coral Porites astreoides and their response to temperature disturbances. Marine Biology 139: 981-989.


Jacobs DK, Wray CG, Wedeen CJ, Kostriken R, DeSalle R, Staton JL., Gates RD, and Lindberg DL (2000) Molluscan engrailed expression, serial organization, and shell evolution. Evolution and Development 2(6): 340-347.


Gates RD and Edmunds PJ (1999) The physiological mechanisms of acclimatization in tropical reef corals. American Zoologist 39(1): 30-43.
Gates RD, Bil KY and Muscatine L (1999) The influence of an anthozoan "host factor" on the physiology of a symbiotic dinoflagellate. Journal of Experimental Marine Biology and Ecology 232(2): 241-259.


Muscatine L, Ferrier-Pages C, Blackburn A, Gates RD, Baghdasarian G, and Allemand D (1998) Cell-specific density of symbiotic dinoflagellates in tropical anthozoans. Coral Reefs 17(4): 329-337.


Gates RD, Hoegh-Guldberg O, McFall Ngai M, Bil KY and Muscatine L (1995) Free amino exhibit anthozoan “host factor” activity: They induce the release of photosynthate from symbiotic dinoflagellates in vitro. Proceedings of the National Academy of Sciences, USA 92 (16): 7430-7434.


Muscatine L, Gates RD, and LaFontaine I (1994) Do symbiotic dinoflagellates secrete lipid droplets? Limnology and Oceanography 39 (4): 925-929.


Gates RD, Baghdasarian G, and Muscatine L (1992) Temperature stress causes host cell detachment in symbiotic cnidarians: implications for coral bleaching. Biological Bulletin 182: 324-332.
Gates RD and Muscatine L (1992) Three methods for isolating viable anthozoan endoderm cells with their intracellular symbiotic dinoflagellates. Coral Reefs 11: 143-145.


Bean B, Fogle T and Gates RD (1991) Rapid Hoechst staining for the sperm penetration assay. Fertility and Sterility 55 (1): 214-216.


Gates RD (1990) Seawater temperature and sublethal coral bleaching in Jamaica. Coral Reefs 8: 193-197.