Kelly, E.L.A., Y. Eynaud, S.M. Clements, M. Gleason, R.T. Sparks, I.D. Williams, and J.E. Smith (2016) Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes. Oecologia 182 (4). [pdf]

Nakajima, R., N. Nakatomi, H. Kurihara, M.D. Fox, J.E. Smith, and K. Okaji (2016) Crown-of-thorns starfish larvae feed on organic matter released from corals. Diversity, 8:4. [pdf]

Mullen, A.D., T. Treibitz, P.L.D. Roberts, E.L.A. Kelly,  R. Horwitz, J.E. Smith, and J.S. Jaffe (2016) Underwater microscopy for in situ studies of benthic ecosystems. Nat. Commun. 7:12093 doi:10.1038/ncomms12093 [pdf]

Kaplanis, N., J. Harris, and J.E. Smith (2016) Distribution patterns of the non-native seaweeds Sargassum horneri (Turner) C.Agardh and Undaria pinnatifida (Harvey) Suringar on the San Diego and Pacific coast of North America. Aquatic Invasions 11(2). [pdf]

Quinn, R., M.J.A. Vermeij, A.C. Hartmann, I. Galtier d’Auriac, S. Benler, A. Haas, S.D. Quistad, Y.W. Lim, M. Little, S.A. Sandin, J.E. Smith, P.C. Dorrestein, and F.L. Rohwer (2016) Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proc. R. Soc. B 20160469.

Haas, A.F., M.F.M. Fairoz, L.W. Kelly, C.E. Nelson, E.A. Dinsdale, R.A. Edwards, S. Giles, M. Hatay, N. Hisakawa, B. Knowles, Y.W. Lim, H. Maughan, O. Pantos, T.N.F. Roach, S.E .Sanchez, C.B. Silveira, S.A. Sandin, J.E. Smith, and F.L. Rohwer (2016) Global microbialization of coral reefs. Nature Microbiology, 16042, doi:10.1038/nmicrobiol.2016.42 [pdf]

Kram, S.L., N.N Price, E. Donham, M.D. Johnson, E.L.A. Kelly, S.L. Hamilton, and J.E. Smith (2016) Variable responses of temperate calcified and fleshy macroalgae to elevated pCO2 and warming. ICES Journal of Marine Science. Special Issue on Ocean Acidification. [pdf]

Smith, J.E., S.A. Sandin, P.S. Vroom, I. Williams, E. Sala, D. Obura, R. Brainard, A. Carter, S. Grillo, C. Edwards, L. Lewis, and J. Harris. (2016) Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific. Proc. R. Soc. B 283: 20151985. [pdf]

Knowles,B., C.B. Silveira, B.A. Bailey, K. Barott, V.A. Cantu, A.G. Cobián-Güemes, F.H. Coutinho, E.A. Dinsdale, B. Felts, K.A. Furby, E.E. George, K.T. Green, G.B. Gregoracci, A.F. Haas, J.M. Haggerty, E.R. Hester, N. Hisakawa, L.W. Kelly, Y.W. Lim, M. Little, A. Luque, T. McDole-Somera, K. McNair, L.S. de Oliveira, S.D. Quistad, N.L. Robinett, E. Sala, P. Salamon, S.E. Sanchez, S. Sandin, G.G.Z. Silva, J.E. Smith, C. Sullivan, C. Thompson, M.J.A. Vermeij, M. Youle, C. Young, B. Zgliczynski, R. Brainard, R.A. Edwards, J. Nulton, F. Thompson, and F. Rohwer (2016) Lytic to temperate switching of viral communities. Nature 531: 466-470. doi:10.1038/nature17193 [pdf]

Takeshita, Y., W. McGillis, E.M. Briggs, A. Carter, E. Donham, T.R. Martz, N.N. Price, and J. E. Smith (2016) Assessment of net community production and calcification of a coral reef using a boundary layer approach. J. Geophys. Res. Oceans. Accepted Author Manuscript. doi:10.1002/2016JC011886 [pdf]

Vargas-Ángel, B., C.L. Richards, P.S. Vroom, N.N. Price, T. Schils, C.W. Young, J.E. Smith, M.D. Johnson, and R. Branaird (2015) Baseline Assessment of Net Calcium Carbonate Accretion Rates on U.S. Pacific Reefs. PLoS ONE 10(12): e0142196. doi:10.1371/journal.pone.0142196 [pdf]

Haas, A.F., M. Guibert, A. Foerschner, S. Calhoun, E. George, M. Hatay, E. Dinsdale, S.A. Sandin, J.E. Smith, M.J.A. Vermeij, B. Felts, P. Dustan, P. Salamon, and F. Rohwer. (2015) Can we measure beauty? Computational evaluation of coral reef aesthetics. PeerJ 3:e1390 [pdf]

Takeshita, Y., C.A. Frieder, T.R. Martz, J.R. Ballard, R.A. Feely, S. Kram, S. Nam, M.O. Navarro, N.N. Price, and J.E. Smith (2015) Including high frequency variability in coastal ocean acidification projections. Biogeosciences. [pdf]

Beijbom, O., P.J. Edmunds, C. Roelfsema, J.E. Smith, D.I. Kline, B. Neal, M. Dunlap, V. Moriarty, T. Fan, C. Tan, S. Chan, T. Treibitz, A. Gamst, B.G. Mitchell, D.Kriegman (2015) Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation. PLoS One [pdf]

DeMartini, E.E. and J.E. Smith (2015) Effects of fishing on the fishes and habitat of coral reefs. In Ecology of Fishes on Coral Reefs. Cambridge University Press. Pp 135-144.

Harris, J.L., L.S. Lewis, and J.E. Smith (2015) Quantifying scales of spatial variability in algal turf assemblages on coral reefs. Marine Ecology Progress Series. doi:10.3354/meps11344 [pdf]

Bracken, M. E. S., H. Hillebrand,, E.T. Borer, E.W. Seabloom, J. Cebrian, E.E. Cleland, J.J. Elser, D.S. Gruner, W.S. Harpole, J. Ngai and J. E. Smith (2015) Signatures of nutrient limitation and co-limitation: responses of autotroph internal nutrient concentrations to nitrogen and phosphorus additions. Oikos. doi: 10.1111/oik.01215

Lim, Y.W., D.A. Cuevas, G.G.Z. Silva, K. Aguinaldo, E. Dinsdale, J.E. Smith, et al. (2014) Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ PrePrints 2:e433v1

Kelly, L.W., G.J. Williams, K.L. Barott, C.A. Carlson, E.A. Dinsdale, R.A. Edwards, A.F. Haas, M. Haynes,Y.W. Lim,T. McDole, JE Smith, et al. (2014) Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences 111(28), 10227-10232. (doi:10.1073/pnas.1403319111). [pdf]

Johnson, M.D., N.N. Price, and J.E. Smith (2014) Contrasting effects of ocean acidification on tropical fleshy and calcareous algae. PeerJ 2:e411.

Edwards, C.B., A. Green, A. Friedlander, M. Newman, E. Sala, S.A. Sandin, H. Sweatman, I. Williams, and J.E. Smith (2014) A global analysis of coral reef herbivorous fishes: Evidence for fishing impacts. PRSB [pdf]

Hamilton, S.L., J.E.Smith, N.N. Price, and S.A. Sandin (2014) Quantifying patterns of fish herbivory on an uninhabited predator-dominated central Pacific coral reef, Palmyra Atoll (USA). Marine Ecology Progress Series [pdf]

Williams, G.J., N.N. Price, G.S. Aeby, E.J. Conklin, S.K. Davy, J.M. Gove, I.S. Knapp, J.E. Smith, and T.M Work (2014) Ocean warming and acidification show interacting, complex effects on the dynamics of a marine fungal disease. PRSB [pdf]

Haas, A.F., A. Gregg, J.E. Smith, and F.L. Rohwer (2013) Visualization of oxygen distribution patterns facilitated by coral and algae. Peer J []

Haas, A., F.L. Rohwer, C. Carlson, C. Nelson, L. Wegley, J. Leichter, and J.E. Smith (2013) Influence of coral and alga exudates on microbially mediated reef metabolism. PeerJ []

 Williams, G., J.E. Smith, E. Conklin, J. Gove, S.A. Sandin, E. Sala (2013) Benthic communities at two remote Pacific coral reefs: effects of reef habitat, depth, and horizontal wave energy gradients on spatial patterns. PeerJ 1:e81

Smith, J.E., N.N Price, and A. Haas (2013) Coupled changes in dissolved oxygen and pH associated with metabolism of benthic reef organisms. Marine Biology 160(9): 2437-2447. doi: 10.1007/s00227-013-2239-z [pdf]

Borer, E.T, M.E S. Bracken, E.W. Seabloom, J.E. Smith, J. Cebrian, E.E. Cleland, J.J. Elser, W. Fagan, D.S. Gruner, W.S. Harpole, H. Hillebrand, A.J. Kerkhoff, and J.T. Ngai (2013) Global biogeography of autotroph chemistry: is insolation a driving force? Oikos [pdf]

Nelson, C.E., S.J. Goldberg, L. Wegely-Kelly, A.F. Haas, J.E. Smith, F.L. Rohwer, and C.A. Carlson (2013) Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. ISME 7: 962-979 [pdf]

Mcleod, E., K.R.N. Anthony, A. Andersson, R. Beeden, Y. Golbuu, J. Kleypas, K. Kroeker, D. Manzello, R. Salm, H. Schuttenberg, and J.E. Smith (2012) Preparing to manage coral reefs for ocean acidification: Lessons from coral bleaching. Frontiers in Ecology and the Environment 11: 20–27. doi:

Vermeij, M.A., R.A. van der Heijden, J.G. Olthuis, K.L. Marhaver, P.M. Visser, and J.E. Smith (2012) Survival and dispersal of turf algae and macroalgae consumed by herbivorous coral reef fishes. Oecologia 171(2):417-25. doi: 10.1007/s00442-012-2436-3  [pdf]

Price, N.N., T. Martz, R.E. Brainard, and J.E. Smith (2012) Diel variability in seawater pH relates to calcification and benthic community structure on coral reefs. PLoS ONE 7(8): e43843. doi:10.1371/journal.pone.0043843 [pdf]

Barott, K. G.J. Williams, M.A. Vermeij, J. Harris, J.E. Smith, F.L. Rohwer, and S.A. Sandin (2012) Natural history of competition between corals and algae across a gradient of human activity in the Line Islands of the Central Pacific. MEPS 460: 1-12 [pdf]

Choi H., S.J. Mascuch, F.A. Villa, T. Byrum, M.E. Teasdale, J.E. Smith, L.B. Preskitt,  D.C. Rowley, L. Gerwick, and W.H. Gerwick (2012) Honaucins A-C, potent inhibitors of eukaryotic inflammation and bacterial quorum  sensing: synthetic derivatives and structure-activity relationships. Biology and Chemistry 19(5): 589-598 [Link]

Dailer, M.L., J.E. Smith, and C.M Smith (2012) Responses of bloom forming and non-bloom forming macroalgae to nutrient enrichment in Hawaii, USA. Harmful Algae [pdf]

Barott, K., B.R. Brito, M. Youle, K. Marhaver, M. Vermeij, J.E. Smith, and F.L. Rohwer (2012) Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae. Proceedings of the Royal Society, Biology [pdf]

Kelly, L.W., K.L. Barott, E. Dinsdale, A.M. Friedlander, B. Nosrat, D. Obura, E. Sala, S.A. Sandin, J.E. Smith, M.J.A. Vermeij, G.J. Williams, D. Willner, and F. Rohwer. 2012. Black reefs: iron-induced phase shifts on coral reefs. ISME Journal 6:638-649. [pdf]

Freeman, L., A.J. Miller, R.D. Norris and J.E. Smith (2012) Classification of remote Pacific coral reefs by physical oceanographic environment. JGR117: C02007, DOI:10.1029/2011Jc007099 [pdf]

Hofmann, G.E.,  J.E. Smith, K.S. Johnson, U. Send, L.A. Levin, F. Micheli, A. Paytan, N.N. Price, B. Peterson, Y. Takeshita, P.G. Matson, E. Derse Crook, K.J. Kroeker, E.B. Rivest, C.A. Tanner, P.C. Yu, and T.R. Martz (2011) High frequency dynamics of ocean pH: A multi-ecosystem comparison. PlosOne DOI: 10.1371/journal.pone.0028983. [pdf]

Haas, A., F.L. Rohwer, C. Carlson, C. Nelson, L. Wegley, J. Leichter and J.E. Smith (2011) Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PLoSOne DOI: 10.1371/journal.pone.0027973. [pdf]

Price, N.P., S.L. Hamilton, J. Tootle and J.E. Smith (2011) Species specific consequences of ocean acidification for the calcareous tropical green algae Halimeda. MEPS 440: 67–78. [pdf]

Harpole,W.S., J. Ngai, E. Cleland, E. Seabloom, E. Borer, M. Bracken, J. Elser, D. Gruner, H. Hillebrand, J. Shurin, and J.E. Smith (2011) Nutrient co-limitation of plant communities. Ecology Letters 14: 852-862. [pdf]

Barott, K.L., B. Rodriguez-Brito, J. Janouškovec, K. Marhaver, J.E. Smith, P. Keeling, and  F.L. Rohwer (2011) Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environmental Microbiology 1192-1203. DOI: 10.1111/j.1462-2920.2010.02419.x

Knapp, I.S., L.S. Godwin, J.E. Smith, and J.J Bell (2011) Records of non-indigenous marine species at Palmyra Atoll in the US Line Islands. Marine Biodiversity Records 4:e30.[pdf]

Smith, J.E. (2011) Invasive Introduced Algae. Encyclopedia of Invasive Species. Edited by Simberloff and Rejamnek. University of California Press.[pdf]

Barott, K.L., J.E. Caselle, E.A. Dinsdale, A.M. Friedlander, J.E. Maragos, D. Obura, F.L. Rohwer, S.A. Sandin, J.E. Smith, and B. Zgliczynski (2010) The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem. PLoS ONE, 5(6), e10950. [pdf]

Carilli, J., J. Godfrey, R. Norris, S.A. Sandin, and J.E. Smith (2010) Periodic endolithic algal blooms in Montastraea faveolata corals may represent periods of low-level stress. Bulletin of Marine Science86 (3): 709-718. [pdf]

McCauley, D.J.,F. Micheli,H. Young,D.P. Tittensor, D.R. Brumbaugh, E. Madin, K.E. Holmes, R. Dunbar, J.E. Smith, H.K. Lotze, and B. Worm (2010) Acute effects of removing large fish from a near-pristine coral reef. Marine Biology 157(12):2739-2750. DOI: 10.1007/s00227-010-1533-2. [pdf]

Smith, J.E., C.L Hunter, and C.M Smith (2010) The effects of top-down and bottom-up factors on benthic coral reef community structure. Oecologia 163(2): 497-507. [pdf]

Dailer, M.L., R.S. Knox, J.E. Smith, M. Napier, and C.M. Smith (2010) Using delta-15N values in algal tissue to map locations and potential sources of anthropogenic nutrient inputs on the island of Maui, Hawai‘i. Marine Pollution Bulletin 60: 655-671. DOI: 10.1016/j.marpolbul.2009.12.021 [pdf]

Salomon, A.K., S.K. Gaichas, N.T. Shears, J.E. Smith, E.M.P. Madin, and S.D. Gaines (2010) Cascading Consequences of Fishing: Navigating Towards Resilient Marine Ecosystems. Conservation Biology 24(2): 382-394. [pdf]

Choi, H., N. Engene, J.E. Smith, L.B. Preskitt, and W.H. Gerwick (2010) Crossbyanols A-D, Toxic Brominated Polyphenyl Ethers from the Hawaiian Bloom-Forming Cyanobacterium Leptolyngbya crossbyana. Journal of Natural Products 73:517-522 [pdf]

Barott, K., J.E. Smith, E. Dinsdale, M. Hatay, S. Sandin, and F.L. Rohwer (2009) Hyperspectral and physiological analyses of coral-algal interactions. PLoS ONE 4(11): e8043. DOI:10.1371/journal.pone.0008043. [pdf]

Braun, C., P.S. Vroom, and J.E. Smith (2009) Examination of algal diversity and benthic community structure at Palmyra Atoll, U.S. Line Islands. Proceedings of the 11th Coral Reef Symposium. [pdf]

Hillebrand, H., D.S. Gruner, M.E. Bracken, E.E. Cleland, J.J. Elser, W.S. Harpole, J.T. Ngai, E.W. Seabloom, J.B. Shurin, and J.E. Smith (2009) Herbivore metabolism and stoichiometry each constrain herbivory at different organizational scales across ecosystems. Ecology Letters 12: 516-527. [pdf]

Smith, J.E., J. Kuwabara, J. Coney, K. Flanagan, J. Beets, D. Brown, F. Stanton, M. Takabayashi, S. duPlessis, B.K. Griesemer, S. Barnes, and J. Turner (2009) An unusual cyanobacterial bloom in Hawaii. Coral Reefs 27: 851. [pdf]

Vermeij, M.J.A., J.E. Smith, S.A. Sandin, and C.M. Smith (2009) Survival and settlement success of coral planulae: synergistic and independent effects of macroalgae and microbes. Oecologia 159(2):325-336. [pdf]

Smith, J.E., H. Spalding, R. Okano, and C.M. Smith (2009) Seaweed communities of Molokai. In An Atlas of Molokai’s Marine Ecosystems. USGS publication. [URL]

Gruner, D.S., J.E. Smith, E.W. Seabloom, S.A. Sandin, J.T. Ngai, H. Hillebrand, W.S. Harpole, J.J. Elser, E.E. Cleland, M.E.S. Bracken, E.T. Borer, and B.M. Bolker (2008) A cross-system synthesis of consumer and nutrient resource control on producer biomass. Ecology Letters 11: 740-755. [pdf]

Sandin, S.A., J.E. Smith, E.E. DeMartini, E.A. Dinsdale, S.D. Donner, A.M. Friedlander, T. Konotchick, M. Malay, J.E. Maragos, D. Obura, O. Pantos, G. Paulay, M. Richie, F.L. Rohwer, R.E. Schroeder, S. Walsh, J.B.C. Jackson, N. Knowlton, and E. Sala (2008) Changes in coral reef communities across a gradient of human disturbance. PLoS-One. [pdf]

Smith, J.E., E.J. Conklin, C.L. Hunter, and C.M. Smith (2008) Response to “Fighting alien algae in Kane’ohe Bay”. Science 319: 157-158. [pdf]

Elser, J.J., M.E. Bracken, E.E Cleland, , D.S Gruner, W.S. Harpole, Hillebrand, H., J.T. Ngai, E.W. Seabloom, J.B. Shurin, and J.E. Smith (2007) A global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine, and terrestrial ecosystems. Ecology Letters 10: 1135-1142. [pdf]

Williams, S.L. and J.E. Smith (2007) A global review of the distribution, taxonomy & ecological impacts of introduced seaweeds. Annual Review of Ecology Evolution and Systematics 38: 327-359. [pdf]

Diaz-Pulido G., L.J. McCook, A.W.D. Larkum, H.K. Lotze, J.A. Raven, B. Schaffelke, J.E. Smith, and R.S. Steneck (2007) Vulnerability of macroalgae of the Great Barrier Reef to climate change. Marshall PA, Johnson J (Ed) Climate change and the Great Barrier Reef. Great Barrier Reef Marine Park Authority, Townsville, pp 153-192. [pdf]

Hillebrand, H., D.S. Gruner, M.E. Bracken, E.E. Cleland, J.J. Elser, W.S. Harpole, J.T. Ngai, E.W. Seabloom, J.B. Shurin, and J.E. Smith (2007) Plant community structure and ecosystem productivity regulate the intrinsic control of plant diversity across major ecosystem types. Proceedings of the National Academy of Sciences 104: 10904-10905. [pdf]

Smith, J.E., M. Shaw, R.A. Edwards, D. Obura, D., O. Pantos, E. Sala, S. A. Sandin, S. Smriga, M. Hatay, and F.L. Rohwer (2006) Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. Ecology Letters 9: 835-845. [pdf]

Schaffelke, B., J.E. Smith, and C.L. Hewitt (2006) Introduced macroalgae – a growing concern. Proceedings of the International Seaweed Symposium. Journal of Applied Phycology 18: 529-541. [pdf]

Zuccarello, G.C., A.T. Critchley, J.E. Smith, and J.A. West (2006) Systematics and genetic variation in commercial Kappaphycus and Eucheuma (Solieriaceae, Rhodophyta). Proceedings of the International Seaweed Symposium. Journal of Applied Phycology 18: 643-651. [pdf]

Zemke-White, W.L. and J.E. Smith (2006) Environmental impacts of seaweed farming in the tropics. In: Editors A.T. Critchley, M. Ohno and D.B. Largo, World Seaweed Resources: An authoritative reference system. [URL]

Smith, J.E., J.W. Runcie, and C.M. Smith (2005) Bloom dynamics and physiological ecology of the invasive green alga Cladophora sericea on West Maui. Marine Ecology Progress Series 302: 77-91. [pdf]

Conklin, E.J. and J.E. Smith (2005) Increases in abundance and development of management options for the invasive red alga Kappaphycus in Kane’ohe Bay, Hawai’i. Biological Invasions7: 1029-1039. [pdf]

Friedlander, A., G. Aeby, E. Brown, A. Clark, S. Coles, S. Dollar, D. Gulko, C. Hunter, P. Jokiel, J.E. Smith, B. Walsh, I. Williams and W. Wiltse (2005) The Status of the Coral Reef Ecosystems of the Main Hawaiian Islands. In The Status of the Coral Reef Ecosystems of the United States and Pacific Freely Associated States: 2004. [pdf]

Smith, J.E., C. Smith, P. Vroom, K. Beach, S. Miller (2004) Nutrient dynamics of the green alga Halimeda tuna on Conch Reef, Florida Keys: possible influence of internal tides on nutrient status and physiology. Limnology and Oceanography. 49(6): 1923-1936. [pdf]

Smith, J.E., R. Most, T. Sauvage, C. Hunter, C. Squair and E. Conklin (2004) Ecology of the invasive red alga Gracilaria salicornia in Waikiki and possible mitigation strategies. Pacific Science 58(2) 325-343. [pdf]

Vroom, P.S., C.M. Smith, J.A. Coyer, L.J. Walters, C.L. Hunter, K.S. Beach, and J.E. Smith (2003) Field biology of Halimeda tuna (Bryopsidales, Chlorophyta) across a depth gradient: comparative growth, survivorship, recruitment, and reproduction.  Hydrobiologia 501(1): 149-166. [pdf]

Runcie, J.W. and J.E. Smith (2003) Introduction to special issue: Nutrient dynamics in coastal ecosystems-linking physical and biological processes. Journal of Marine Systems 42(3-4): 81-82. [pdf]

Smith, J.E., C.L. Hunter and C.M. Smith (2002) Distribution and reproductive characteristics of nonindigenous and invasive marine algae in the Hawaiian Islands. Pacific Science 56(3): 299-315. [pdf]

Vroom, P. S., J.E. Smith and C.M. Smith (2001) Observations of reproduction in Rhipidosiphon javensis (Halimedineae, Bryopsidales) in Hawai’i. Phycologia 40(1): 97-100. [pdf]

Smith, J.E., C.L. Hunter and C.M. Smith (2001) The effects of herbivory and nutrient enrichment on benthic community structure and development on a Hawaiian Reef. Coral Reefs 19: 332-342. [pdf]