A

Ani, Chinenye Jane (2023) Biogeochemical modelling of tropical marine ecosystems in the context of climate change. PhD thesis, James Cook University.

Ani, Chinenye J., Smithers, Scott G., Lewis, Stephen, Baird, Mark, and Robson, Barbara (2023) eReefs modelling suggests Trichodesmium may be a major nitrogen source in the Great Barrier Reef. Estuarine, Coastal and Shelf Science, 285. 108306.

B

Bainbridge, Zoe T., Olley, Jon M., Lewis, Stephen E., Stevens, Tom, and Smithers, Scott G. (2024) Tracing sources of inorganic suspended particulate matter in the Great Barrier Reef lagoon, Australia. Scientific Reports, 14. 15651.

Brunner, Christopher Andreas (2022) Cumulative impacts of climate change, sedimentation and light attenuation on coral recruits. PhD thesis, James Cook University.

Brunner, Christopher A., Ricardo, Gerard F., Uthicke, Sven, Negri, Andrew P., and Hoogenboom, Mia O. (2022) Effects of climate change and light limitation on coral recruits. Marine Ecology Progress Series, 690. pp. 65-82.

Brunner, Christopher, Uthicke, Sven, Ricardo, Gerard F., Hoogenboom, Mia O., and Negri, Andrew P. (2021) Climate change doubles sedimentation-induced coral recruit mortality. Science of the Total Environment, 768. 143897.

Berry, K.L.E., Hess, S., Clark, T.D., Wenger, A.S., Hoogenboom, M.O., and Negri, A.P. (2021) Effects of suspended coal particles on gill structure and oxygen consumption rates in a coral reef fish. Marine Pollution Bulletin, 169. 112459.

Bainbridge, Zoe, Lewis, Stephen, Stevens, Thomas, Petus, Caroline, Lazarus, Emily, Gorman, Jessica, and Smithers, Scott (2021) Measuring sediment grain size across the catchment to reef continuum: improved methods and environmental insights. Marine Pollution Bulletin, 168. 112339.

Bahadori, Mohammad, Chen, Chengrong, Lewis, Stephen, Rashti, Mehran Rezaei, Cook, Freeman, Parnell, Andrew, Esfandbod, Maryam, and Stevens, Thomas (2020) Tracing the sources of sediment and associated particulate nitrogen from different land uses in the Johnstone River catchment, Wet Tropics, northeastern Australia. Marine Pollution Bulletin, 157. 111344.

C

Canto, Marites Magno (2022) Benthic irradiance in the Great Barrier Reef: model, spatiotemporal patterns, and index of water quality. PhD thesis, James Cook University.

Chartrand, Kathryn M. (2021) Growth dynamics and drivers of deep-water seagrasses from the Great Barrier Reef lagoon. PhD thesis, University Technology Sydney.

Canto, Marites M., Fabricius, Katharina E., Logan, Murray, Lewis, Stephen, McKinna, Lachlan I.W., and Robson, Barbara J. (2021) A benthic light index of water quality in the Great Barrier Reef, Australia. Marine Pollution Bulletin, 169. 112539.

Chartrand, Katie, Rasheed, Michael, and Ralph, Peter (2016) Under pressure...how to succeed as a deepwater seagrass. In: [Presented at the 13th International Coral Reef Symposium]. From: 13th International Coral Reef Symposium, 19-24 June 2016, Honolulu, HI, USA.

Chartrand, Katie, Ralph, Peter, Petrou, Katherina, and Rasheed, Michael (2012) Development of a Light-Based Seagrass Management Approach for the Gladstone Western Basin Dredging Program. Report. Queensland Department of Agriculture, Fisheries and Forestry, Cairns, QLD, Australia.

D

Dierssen, Heidi M., Ackleson, Steven G., Joyce, Karen E., Hestir, Erin L., Castagna, Alexandre, Lavender, Samantha, and McManus, Margaret A. (2021) Living up to the hype of hyperspectral aquatic remote sensing: science, resources and outlook. Frontiers in Environmental Science, 9. 649528.

Drane, Kezia, Huerlimann, Roger, Power, Michelle, Ariel, Ellen, Sheehan, Madoc, and Kinobe, Robert (2021) Using Green sea turtles (Chelonia mydas) as essential bio-indicators for monitoring antibiotic resistance in marine environments worldwide: a critical appraisal. FASEB Journal, 35 (S1). 03303-03303.

Devlin, Michelle, Smith, Andy, Graves, Carolyn A., Petus, Caroline, Tracey, Dieter, Maniel, Michael, Hooper, Eryn, Kotra, Kryshna, Samie, Erie, Loubser, David, and Lyons, Brett P. (2020) Baseline assessment of coastal water quality, in Vanuatu, South Pacific: insights gained from in-situ sampling. Marine Pollution Bulletin, 160. 111651.

F

Fulton, Stella Elaine (2022) Effects of macroalgal removal on inshore coral reef communities and sedimentation dynamics. Masters (Research) thesis, James Cook University.

H

Ho, Yuen-Wa, Lim, Jin Yan, Yeoh, Yun Kit, Chiou, Jia-Chi, Zhu, Yuyan, Lai, Keng Po, Li, Lei, Chan, Paul Kay Sheung, and Fang, James Kar-Hei (2022) Preliminary Findings of the High Quantity of Microplastics in Faeces of Hong Kong Residents. Toxics, 10. 414.

J

Jahanbakht, Mohammad, Rahimi Azghadi, Mostafa, and Waltham, Nathan J. (2023) Semi-supervised and weakly-supervised deep neural networks and dataset for fish detection in turbid underwater videos. Ecological Informatics, 78. 102303.

Jahanbakht, Mohammad (2022) Deep learning for internet of underwater things and ocean data analytics. PhD thesis, James Cook University.

Jahanbakht, Mohammad, Xiang, Wei, Robson, Barbara, and Rahimi Azghadi, Mostafa (2022) Nitrogen prediction in the Great Barrier Reef using finite element analysis with deep neural networks. Environmental Modelling & Software, 150. 105311.

Jahanbakht, Mohammad, Xiang, Wei, and Azghadi, Mostafa Rahimi (2022) Sediment Prediction in the Great Barrier Reef using Vision Transformer with finite element analysis. Neural Networks, 152. pp. 311-321.

Jones, Ross, Wakeford, Mary, Currey-Randall, Leanne, Miller, Karen, and Tonin, Hemerson (2021) Drill cuttings and drilling fluids (muds) transport, fate and effects near a coral reef mesophotic zone. Marine Pollution Bulletin, 172. 112717.

L

Lloyd-Jones, Luke R., Kuhnert, Petra M., Lawrence, Emma, Lewis, Stephen E., Waterhouse, Jane, Gruber, Renee K., and Kroon, Frederieke J. (2022) Sampling re-design increases power to detect change in the Great Barrier Reef’s inshore water quality. PLoS ONE, 17 (7). e0271930.

M

Miller, Michaela E. (2022) Ecological fate of microplastics in a tropical marine environment. PhD thesis, James Cook University.

Miller, Michaela E., Santana, Marina F.M., Carsique, Madeline, Motti, Cherie A., Hamann, Mark, and Kroon, Frederieke J. (2022) Temporal patterns of plastic contamination in surface waters at the SS Yongala shipwreck, Great Barrier Reef, Australia. Environmental Pollution, 307. 119545.

N

Nair, Prashant (2022) Development and suitability assessment for elevated temperature accuracy of a novel high-throughput direct toxicity assay of chemically dispersed oil. PhD thesis, James Cook University.

P

Patricio-Valerio, Larissa, Schroeder, Thomas, Devlin, Michelle J., Yi, Qin, and Smithers, Scott (2023) Meteorological Satellite Observations Reveal Diurnal Exceedance of Water Quality Guideline Thresholds in the Coastal Great Barrier Reef. Remote Sensing, 15 (9). 2335.

Patricio Valerio, Larissa (2021) Exploring Himawari-8 geostationary observations for the advanced coastal monitoring of the Great Barrier Reef. PhD thesis, James Cook University.

S

Saint-Amand, A., Grech, A., Choukroun, S., and Hanert, E. (2022) Quantifying the environmental impact of a major coal mine project on the adjacent Great Barrier Reef ecosystems. Marine Pollution Bulletin, 179. 113656.

Santana, Marina F.M., Kroon, Frederieke J., van Herwerden, Lynne, Vamvounis, George, and Motti, Cherie A. (2022) An assessment workflow to recover microplastics from complex biological matrices. Marine Pollution Bulletin, 179. 113676.

Santana, Marina F.M., Dawson, Amanda L., Motti, Cherie, van Herwerden, Lynne, Lefevre, Carine, and Kroon, Frederieke (2021) Ingestion and depuration of microplastics by a planktivorous coral reef fish, Pomacentrus amboinensis. Frontiers in Environmental Science, 9. 641135.

Santana, Marina F. M. (2021) Presence, abundance and effects of microplastics on the Great Barrier Reef. PhD thesis, James Cook University.

T

Tol, Samantha J., Carter, Alexandra, York, Paul H., Grech, Alana, Situ, Rong, and Coles, Robert G. (2024) Estimates of Wind Drift Coefficient to Inform Biophysical Models of Seagrass Dispersal in the Great Barrier Reef. In: Wolanski, Eric, and Kingsford, Michael J., (eds.) Oceanographic Processes of Coral Reefs: Physical and Biological Links in the Great Barrier Reef. CRC Press, Boca Raton, Florida, USA, pp. 184-192.

Templeman, Michelle, and McDonald, Sarah (2024) Question 5.2 What are the primary sources of pesticides that have been found in Great Barrier Reef ecosystems and what are the key factors that influence pesticide delivery from source to ecosystem? [in 2022 Scientific Consensus Statement on land-based impacts on Great Barrier Reef water quality and ecosystem condition]. Report Section. Commonwealth of Australia and Queensland Government.

Terzin, Marko, Laffy, Patrick W., Robbins, Steven, Yeoh, Yun Kit, Frade, Pedro R., Glasl, Bettina, Webster, Nicole S, and Bourne, David G. (2024) The road forward to incorporate seawater microbes in predictive reef monitoring. Environmental Microbiome, 19. 5.

Thomas, Marie C., Waugh, Gretel, Vanwonterghem, Inka, Webster, Nicole S., Rinke, Christian, Fisher, Rebecca, Luter, Heidi M., and Negri, Andrew P. (2023) Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes. Science of the Total Environment, 904. 166658.

Tebbett, Sterling Bryn (2022) The functioning of future coral reefs: fishes, sediments and productivity. PhD thesis, James Cook University.

Tan Phong, Nguyen, and Van Tien, Huynh (2021) Water resource management and island tourism development: insights from Phu Quoc, Kien Giang, Vietnam. Environment, Development and Sustainability, 23. pp. 17835-17856.

Tebbett, Sterling B., and Bellwood, David R. (2020) Sediments ratchet-down coral reef algal turf productivity. Science of the Total Environment, 713. 136709.

Tien, Huynh Van, and Nguyen, Tan Phong (2019) Marine algal species and marine protected area management: A case study in Phu Quoc, Kien Giang, Vietnam. Ocean & Coastal Management, 178. 104816.

Tien, Huynh Van, and Nguyen, Tan Phong (2019) Marine algal species and their distribution in Phu Quoc marine protected area. Data in Brief, 25. 104200.

V

Vlaanderen, Eric J., Ghaly, Timothy M., Moore, Lisa R., Focardi, Amaranta, Paulsen, Ian T., and Tetu, Sasha G. (2023) Plastic leachate exposure drives antibiotic resistance and virulence in marine bacterial communities. Environmental Pollution, 327. 121558.

Velasquez Jimenez, Laura Marcela (2021) The effects of vessel noise on the antipredator behaviour of juvenile reef fishes. PhD thesis, James Cook University.

Velasquez Jimenez, Laura, Fakan, Eric P., and McCormick, Mark I. (2020) Vessel noise affects routine swimming and escape response of a coral reef fish. PLoS ONE, 15 (7). e0235742.