A

Andutta, Fernando P. , Ridd, Peter V., and Wolanski, E. (2013) The age and the flushing time of the Great Barrier Reef Waters. Continental Shelf Research, 53. pp. 11-19.

Andutta, Fernando P., Kingsford, Michael J., and Wolanski, Eric (2012) 'Sticky water' enables the retention of larvae in a reef mosaic. Estuarine, Coastal and Shelf Science , 101. pp. 54-63.

Andutta, Fernando Pinheiro, dos Santos, Michael R.M., De Miranda, Luiz Bruner, Ancona, Cintia M., Saldanha-Corrêa, Flávia M.P., and Gianesella, Sônia M.F. (2006) Monthly variations of physical and chemical properties observed in Santos Bay and Santos Estuarine channel. In: Proceedings of the Environmental and Health World Congress. pp. 80-84. From: EHWC 2006: Environmental and Health World Congress, 16-19 July 2006, Santos, Brazil.

B

Beaman, R.J., and Webster, J.M. (2008) The Great Barrier Reef margin revealed: implications for deep-water biodiversity distribution. In: Western Pacific Geophysics Meeting. From: 2008 Western Pacific Geophysics Meeting, 29 July -1 August 2008, Cairns, QLD, Australia.

Bird, James C. (2005) Modelling sub-reef thermodynamics to predict coral bleaching: a case study at Scott Reef, WA. Masters (Research) thesis, James Cook University.

C

Chen, Y., Minchin, S.A., Seaton, S., Joehnk, K.D., Robson, B. J., and Bai, Q. (2011) eReefs - a new perspective on the Great Barrier Reef. In: Proceedings of the 19th International Congress on Modelling and Simulation. pp. 1195-1201. From: MODSIM 2011: 19th International Congress on Modelling and Simulation, 12-16 December 2011, Perth, WA, Australia.

Clarke, Allan J., Van Gorder, Stephen, and Everingham, Yvette (2010) Forecasting long-lead rainfall probability with application to Australia's Northeastern coast. Journal of Applied Meteorology and Climatology, 49 (7). pp. 1443-1453.

Cooper, Timothy F., Ridd, Peter V., Ulstrup, Karin E., Humphrey, Craig, Slivokoff, Matthew, and Fabricius, Katharina E. (2008) Temporal dynamics in coral bioindicators for water quality on coastal coral reefs of the Great Barrier Reef. Marine and Freshwater Research, 59 (8). pp. 703-716.

D

Dao, Hoc Tan, Smith-Keune, Carolyn, Wolanski, Eric, Jones, Clive M., and Jerry, Dean R. (2015) Oceanographic currents and local ecological knowledge indicate, and genetics does not refute, a contemporary pattern of larval dispersal for the ornate spiny lobster, Panulirus ornatus in the south-east Asian archipelago. PLoS ONE, 10 (5). e0124568. pp. 1-19.

de Miranda, Luiz Bruner, Olle, Eugenio Dalle, Bergamo, Alessandro Luvizon, dos Santos Silva, Lourval, and Pinheiro Andutta, Fernando (2012) Circulation and salt intrusion in the Piacaguera Channel, Santos (SP). Brazilian Journal of Oceanography, 60 (1). pp. 11-23.

Devney, Carol Ann (2012) Climate variation and population dynamics in tropical seabirds. PhD thesis, James Cook University.

Devlin, M.J., Barry, J., Mills, D.K., Gowen, R.J., Foden, J., Sivyer, D., Greenwood, N., Pearce, D., and Tett, P. (2009) Estimating the diffuse attenuation coefficient from optically active constituents in UK marine waters. Estuarine, Coastal and Shelf Science , 82 (1). pp. 73-83.

Devlin, M.J., Barry, J., Mills, D.K., Gowen, R.J., Foden, J., Sivyer, D., and Tett, P. (2008) Relationships between suspended particulate material, light attenuation and Secchi depth in UK marine waters. Estuarine, Coastal and Shelf Science , 79 (3). pp. 429-439.

Devlin, Michelle (2005) Spatial and temporal patterns of flood plumes in the Great Barrier Reef, Australia. PhD thesis, James Cook University.

F

Ferrira, Ines M., Kasuya, Toshio, Marsh, Helene, and Best, Peter B. (2014) False killer whales (Pseudorca crassidens) from Japan and South Africa: differences in growth and reproduction. Marine Mammal Science, 30 (1). pp. 64-84.

Foden, J., Sivyer, D.B., Mills, D.K., and Devlin, M.J. (2008) Spatial and temporal distribution of chromophoric dissolved organic matter (CDOM) fluorescence and its contribution to light attenuation in UK waterbodies. Estuarine, Coastal and Shelf Science , 79 (4). pp. 707-717.

Fulton, Christopher J., and Bellwood, David R. (2005) Wave-induced water motion and the functional implications for coral reef fish assemblages. Limnology and Oceanography, 50 (1). pp. 255-264.

G

Gove, Jamison M., Williams, Gareth J., McManus, Margaret A., Heron, Scott F., Sandin, Stuart A., Vetter, Oliver J., and Foley, David G. (2013) Quantifying climatological ranges and anomalies for Pacific coral reef ecosystems. PLoS ONE, 8 (4). e61974. pp. 1-14.

Gowen, R.J., Tett, P., Kennington, K., Mills, D.K., Shammon, T.M., Stewart, B.M., Greenwood, N., Flanagan, C., Devlin, M., and Wither, A. (2008) The Irish Sea: Is it eutrophic? Estuarine, Coastal and Shelf Science , 76 (2). pp. 239-254.

H

Heron, M.L., Heron, S.F., and Skirving, W.J. (2008) Mitigation of coral bleaching on the reef front by wave mixing. In: Proceedings of the Western Pacific Geophysics Meeting. OS51B-02. From: 2008 Western Pacific Geophysics Meeting, 29 July - 1 August 2008, Cairns, QLD, Australia.

Hendy, Erica J., Gagan, Michael K., Alibert, Chantal A., McCulloch, Malcolm T., Lough, Janice M, and Isdale, Peter J. (2002) Abrupt decrease in tropical Pacific sea surface salinity at end of Little Ice Age. Science, 295 (5559). pp. 1511-1514.

K

Kingsford, M.J., and Wolanski, E. (2008) Oceanography. In: Hutchings, Pat, Kingsford, Mike, and Hoegh-Guldberg, Ove, (eds.) The Great Barrier Reef: biology, environment and management. CSIRO Publishing, Collingwood, VIC, Australia, pp. 28-39.

L

Liu, Gang, Heron, Scott F., Eakin, C. Mark, Muller-Karger, Frank E., Vega-Rodriguez, Maria, Guild, Liane S., De La Cour, Jacqueline L., Geiger, Erick F., Skirving, William J., Burgess, Timothy F.R., Strong, Alan E., Harris, Andy, Maturi, Eileen, Ignatov, Alexander, Sapper, John, Li, Jianke, and Lynds, Susan (2014) Reef-scale thermal stress monitoring of coral ecosystems: new 5-km global products from NOAA coral reef watch. Remote Sensing, 6 (11). pp. 11579-11606.

Lacroix, Geneviève, Maes, Gregory E., Bolle, Loes J., and Volckaert, Filip A.M. (2013) Modelling dispersal dynamics of the early life stages of a marine flatfish (Solea solea L.). Journal of Sea Research, 84. pp. 13-25.

Luick, John L., Mason, Luciano, Hardy, Thomas, and Furnas, Miles J. (2007) Circulation in the Great Barrier Reef Lagoon using numerical tracers and in situ data. Continental Shelf Research, 27 (6). pp. 757-778.

M

Munk, Peter, Hansen, Michael M., Maes, Gregory E., Nielsen, Torkel G., Castonguay, Martin, Riemann, Lasse, Sparholt, Henrik, Als, Thomas D., Aarestrup, Kim, Andersen, Nikolaj G., and Bachler, Mirjam (2010) Oceanic fronts in the Sargasso Sea control the early life and drift of Atlantic eels. Proceedings of the Royal Society of London Series B, Biological Sciences, 277 (1700). pp. 3593-3599.

McKinna, Lachlan I.W. (2010) Optical detection and quantification of Trichodesmium spp. within the Great Barrier Reef. PhD thesis, James Cook University.

Majdi bin Pehin Dato Hj Abdul Aziz, Muhammad, Purwati, Sri Unon, Zainuddin, Norazma Binti, Demonstrator, Aung Aye Latt, Cabading, Vilma T., Cruz, Renato T., Rivera, Marcelino N., Rajaram, Indrani C., Wainipee, Wimolporn, Nga, Pham Thuy, and Anh, Tran Thi Le (2008) ASEAN Marine Water Quality: Monitoring Manual. Manual. Association of Southeast Asian Nations (ASEAN), Jakarta, Indonesia.

McCulloch, Malcolm, Fallon, Stewart, Wyndham, Timothy, Hendy, Erica, Lough, Janice, and Barnes, David (2003) Coral record of increased sediment flux to the inner Great Barrier Reef since European settlement. Nature, 421 (6924). pp. 727-730.

P

Pollock, F. Joseph, Lamb, Joleah B., Field, Stuart N., Heron, Scott F., Schaffelke, Britta, Shedrawi, George, Bourne, David G., and Willis, Bette L. (2014) Sediment and turbidity associated with offshore dredging increase coral disease prevalence on nearby reefs. PLoS ONE, 9 (7). e102498. pp. 1-9.

Pinheiro Andutta, Fernando, de Miranda, Luiz Bruner, de Castro, Belmiro Mendes, Fontes, Roberto Fioravanti Carelli, and Ramos e Silva, Carlos Augusto (2008) Numerical simulation of the hydrodynamic in the Curimataú estuary, RN Brazil. In: Proceedings of the III Simposio Brasileiro de Oceanografia. pp. 545-558. From: III Simposio Brasileiro de Oceanografia, 2006, Sao Paulo, Brazil.

Pujolar, J.M., Maes, G.E., and Volckaert, F.A.M. (2006) Genetic patchiness among recruits in the European eel Anguilla anguilla. Marine Ecology Progress Series, 307. pp. 209-217.

Pelejero, Carles, Calvo, Eva, McCulloch, Malcolm T, Marshall, John F, Gagan, Michael K, Lough, Janice M, and Opdyke, Bradley N (2005) Preindustrial to modern interdecadal variability in coral reef pH. Science, 309 (5744). pp. 2204-2207.

Puotinen, Marjetta Lee (2004) Tropical cyclone impacts on coral reef communities: modelling the disturbance regime in the Great Barrier Reef region, 1969-2003. PhD thesis, James Cook University.

R

Robson, Barbara J., and Dourdet, Vincent (2013) Incorporating a generalised additive model of river nutrient concentrations into a mechanistic receiving water model. In: Proceedings of the 20th International Conference on Modelling and Simulation. pp. 373-379. From: MODSIM2013: 20th International Congress on Modelling and Simulation, 1-6 December 2013, Adelaide, SA, Australia.

Robson, Barbara J., Baird, Mark, and Wild-allen, Karen (2013) A physiological model for the marine cyanobacteria, Trichodesmium. In: Proceedings of the 20th International Congress on Modelling and Simulation. pp. 1652-1658. From: MODSIM 2013: 20th International Congress on Modelling and Simulation, 1-6 December 2013, Adelaide, SA, Australia.

S

Smithers, Scott G., and Woodroffe, Colin D. (2001) Coral microatolls and 20th century sea level in the eastern Indian Ocean. Earth and Planetary Science Letters, 191 (1-2). pp. 173-184.

T

Thomas, Christopher J., Bridge, Thomas C.L., Figueiredo, Joana, Deleersnijder, Eric, and Hanert, Emmanuel (2015) Connectivity between submerged and near-sea-surface coral reefs: can submerged reef populations act as refuges? Diversity and Distributions, 21 (10). pp. 1254-1266.

Thomas, Christopher J., Lambrechts, Jonathan, Wolanski, Eric, Traag, Vincent A, Blondel, Vincent D, Deleersnijder, Eric, and Hanert, Emmanuel (2014) Numerical modelling and graph theory tools to study ecological connectivity in the Great Barrier Reef. Ecological Modelling, 272. pp. 160-174.

Tan, C.H., and Heron, S.F (2011) First observed severe mass bleaching in Malaysia, Greater Coral Triangle. Galaxea, Journal of Coral Reef Studies, 13 (1). pp. 27-28.

Tudhope, Alexander W., Colin P., Chilcott, McCulloch, Malcolm T., Cook, Edward R., Chappell, John, Ellam, Robert M., Lea, David W., Lough, Janice M., and Graham B., Shimmield (2001) Variability in the El Niño-Southern Oscillation through a glacial-interglacial cycle. Science, 291 (5508). pp. 1511-1517.

V

Vandamme, S.G., Maes, G.E., Raeymaekers, J.A.M., Cottenie, K., Imsland, A.K., Hellemans, B., Lacroix, G., Mac Aoidh, E., Martinsohn, J.T., Martínez, P., Robbens, J., Vilas, R., and Volckaert, F.A.M. (2014) Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus). Molecular Ecology, 23 (3). pp. 618-636.

W

Weijerman, Mariska, Fulton, Elizabeth A., Janssen, Annette B.G., Kuiper, Jan J., Leemans, Rik, Robson, Barbara J., Van De Leemput, Ingrid A., and Mooij, Wolf M. (2015) How models can support ecosystem-based management of coral reefs. Progress in Oceanography, 138 (B). pp. 559-570.

Wang, X.H., and Andutta, F.P. (2013) Sediment transport dynamics in ports, estuaries and other coastal environments. In: Manning, Andrew J., (ed.) Sediment Transport Processes and their Modelling Applications. InTech, Croatia, pp. 3-36.

Wolanski, Eric, Andutta, Fernando, and Delhez, Eric (2012) Estuarine hydrology. In: Bengtsson, Lars, Herschy, Reginald W., and Fairbridge, Rhodes W., (eds.) Encyclopedia of Lakes and Reservoirs. Encyclopedia of Earth Sciences Series . Springer-Verlag, pp. 238-249.

Woolsey, Erika, Bainbridge, Scott J., Kingsford, Michael J., and Byrne, Maria (2012) Impacts of cyclone Hamish at One Tree Reef: integrating environmental and benthic habitat data. Marine Biology, 159 (4). pp. 793-803.

Wolanski, Eric, Fabricius, Katharina E., Cooper, Timothy F., and Humphrey, Craig (2008) Wet season fine sediment dynamics on the inner shelf of the Great Barrier Reef. Estuarine, Coastal and Shelf Science , 77 (4). pp. 755-762.

Webster, Nicole S., Negri, Andrew P., Webb, Richard I., and Hill, Russell T. (2002) A spongin-boring α-proteobacterium is the etiological agent of disease in the Great Barrier Reef sponge Rhopaloeides odorabile. Marine Ecology Progress Series, 232. pp. 305-309.

Y

Young, Jock W., McKinnon, A. David, Ceccarelli, Daniela, Brinkman, Richard, Bustamante, Rodrigo H., Cappo, Mike, Dichmont, Cathy, Doherty, Peter, Furnas, Miles, Gledhill, Daniel, Griffiths, Shane, Hutton, Trevor, Ridgway, Ken, Smith, David, Skewes, Tim, Williams, Alan, and Richardson, Anthony J. (2012) Workshop on the ecosystem and fisheries of the Coral Sea: an Australian perspective on research and management. Reviews in Fish Biology and Fisheries, 22 (3). pp. 827-834.