eReefs Research Outputs – Publications
The peer-reviewed publications listed on this page reference, cite, acknowledge or are a direct output from eReefs research and projects.
For other related eReefs model input references, please see References
2024 – 2023 –2022 – 2021 – 2020 – 2019 – 2018 – 2017 – 2016 – 2015 – 2014 – 2013
If you use the eReefs model outputs, software or platforms in your research, please include the following acknowledgement:
“The eReefs model simulations were produced as part of the eReefs project (eReefs.info), a collaboration between the Science Industry Endowment Fund (SIEF), the Commonwealth Scientific Industrial Research Organisation (CSIRO), the Australian Institute of Marine Science (AIMS), the Bureau of Meteorology (BOM), and the Great Barrier Reef Foundation (GBRF), with support from BHP Billinton Mitsubishi Alliance, the Australian and Queensland governments, and with observations obtained through the Integrated Marine Observing System (IMOS).”
2024
[96] Álvarez-Noriega, M., Ortiz, J., Ceccarelli, D., Emslie, M., Fabricius, K., Jonker, M., Puotinen, M., Robson, B., Roelfsema, C., Sinclair-Taylor, T. and Ferrari, R. (2024), Spatial Variation in Upper Limits of Coral Cover on the Great Barrier Reef. Global Ecol Biogeogr e13928. https://doi.org/10.1111/geb.13928
[95] Cresswell, A.K., Haller-Bull, V., Gonzalez-Rivero, M. et al. Capturing fine-scale coral dynamics with a metacommunity modelling framework. Sci Rep 14, 24733 (2024). https://doi.org/10.1038/s41598-024-73464-y
[94] Rogers, J.G.D., Plagányi, É.E., Blamey, L.K. et al. Validating effectiveness of crown-of-thorns starfish control thresholds to limit coral loss throughout the Great Barrier Reef. Coral Reefs (2024). https://doi.org/10.1007/s00338-024-02560-2
[93] Scofield, J. M.P., E. L. Prime, F. Flores, A. Severati, M. Mongin, E. Bougeot, M. E. Baird, A. P. Negri, G. G. Qiao. (2024) The development of a floating mono-particle “Sun Shield” to protect corals from high irradiance during bleaching conditions. J. Mar. Sci. Eng. 12, 1809.
[92] Naugle, M.S., Denis, H., Mocellin, V.J.L. et al. Heat tolerance varies considerably within a reef-building coral species on the Great Barrier Reef. Commun Earth Environ 5, 525 (2024). https://doi.org/10.1038/s43247-024-01649-4.
[91] Harrison, D.P., 2024. An Overview of Environmental Engineering Methods for Reducing Coral Bleaching Stress. Oceanographic Processes of Coral Reefs, pp.403-418.
[90] Skinner C, Bozec YM, Matthews SA, Williamson DH, Beeden R, Mumby PJ. Advancing projections of crown-of-thorns starfish to support management interventions. Sci Total Environ. 2024 Aug 5;950:175282. doi: 10.1016/j.scitotenv.2024.175282.
[89] Ani, C.J., Haller-Bull, V., Gilmour, J.P. et al. Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters. Sci Rep 14, 13564 (2024). https://doi.org/10.1038/s41598-024-64388-8.
[88] Webster, E.G., Duce, S., Hamann, M., Murray, N., Shimada, T. and Limpus, C., 2024. Should I stay or should I go? The influence of environmental conditions on green turtle residence time and outward transit in foraging areas. Marine Biology, 171(7), pp.1-18.
[87] Matthews SA, Williamson DH, Beeden R, Emslie MJ, Abom RTM, Beard D, et al. (2024) Protecting Great Barrier Reef resilience through effective management of crown-of-thorns starfish outbreaks. PLoS ONE 19(4): e0298073. https://doi.org/10.1371/journal.pone.0298073
2023
[86] Mentzel, S., Nathan, R., Noyes, P., Brix, K.V., Moe, S.J., Rohr, J.R., Verheyen, J., Van den Brink, P.J. and Stauber, J. (2023), Evaluating the effects of climate change and chemical, physical, and biological stressors on nearshore coral reefs: A case study in the Great Barrier Reef, Australia. Integr Environ Assess Manag. https://doi.org/10.1002/ieam.4871
[85] Ani, C. J., M. Baird, B. Robson (2024). Modelling buoyancy-driven vertical movement of Trichodesmium application in the Great Barrier Reef. Ecological Modelling. 487: 110567.
[84] Ani, C.J., 2023. Biogeochemical modelling of tropical marine ecosystems in the context of climate change (jcu.edu.au) PhD thesis. James Cook University.
[83] Xiao, Z., Carlin, G., Steven, A. D. L., Livsey, D. N., Song, D., Crosswell, J. R. (2023). A measurement-to-modelling approach to understand catchment-to-reef processes: sediment transport in a highly turbid estuary. Frontiers in Marine Science, 10. https://www.frontiersin.org/articles/10.3389/fmars.2023.1215161
[82] Kroon, F. J., J. R. Crosswell and B. J. Robson (2023) The effect of catchment load reductions on water quality in the crown-of-thorn starfish outbreak initiation zone. Marine Pollution Bulletin 195 (2023) 115255. https://doi.org/10.1016/j.marpolbul.2023.115255
[81] Castro-Sanguino, C, Y-M, Bozec, S. A. Condie, C. S. Fletcher, K. Hock, C. Roelfsema, D. A. Westcott and P. J. Mumby (2023) Control Efforts of Crown-of-Thorns Starfish Outbreaks to Limit Future Coral Decline across the Great Barrier Reef.” Ecosphere 14( 6): e4580. https://doi.org/10.1002/ecs2.4580
[80] Patricio-Valerio L, Schroeder T, Devlin MJ, Qin Y, Smithers S. Meteorological Satellite Observations Reveal Diurnal Exceedance of Water Quality Guideline Thresholds in the Coastal Great Barrier Reef. Remote Sensing. 2023; 15(9):2335. https://doi.org/10.3390/rs15092335
[79] McGowan, H., Theobald, A. Atypical weather patterns cause coral bleaching on the Great Barrier Reef, Australia during the 2021–2022 La Niña. Sci Rep 13, 6397 (2023). https://doi.org/10.1038/s41598-023-33613-1.
[78] Skerratt, J. H, M. E Baird, M. Mongin, R. Ellis, R. A. Smith, A.D. L. Steven (2023) Dispersal of the pesticide diuron in the Great Barrier Reef. Science of the Total Environment. 879: 163041. https://doi.org/10.1016/j.scitotenv.2023.163041
[77] Ani, C. J., S. G. Smithers, S. Lewis, M. Baird, B. Robson (2023) eReefs modelling suggests Trichodesmium may be a major nitrogen source in the Great Barrier Reef. Est. Coast. Shelf. Sci. 108306, https://doi.org/10.1016/j.ecss.2023.108306.
[76] Blondeau-Patissier, D., Schroeder, T., Suresh, G., Li, Z., Diakogiannis, F.I., Irving, P., Witte, C. and Steven, A.D., 2023. Detection of marine oil-like features in Sentinel-1 SAR images by supplementary use of deep learning and empirical methods: Performance assessment for the Great Barrier Reef marine park. Marine Pollution Bulletin, 188, p.114598. https://doi.org/10.1016/j.marpolbul.2023.114598
[75] Page, C.A., Giuliano, C., Bay, L.K. and Randall, C.J., 2023. High survival following bleaching underscores the resilience of a frequently disturbed region of the Great Barrier Reef. Ecosphere, 14(2), p.e4280. https://doi.org/10.1002/ecs2.4280
[74] Fabricius, K.E., Crossman K, Jonker M, Mongin M, Thompson A (2023) Macroalgal cover on coral reefs: Spatial and environmental predictors, and decadal trends in the Great Barrier Reef. PLoS ONE 18(1): e0279699. https://doi.org/10.1371/journal.pone.0279699.
2022
[73] Gurdek-Bas, R., Benthuysen, J.A., Harrison, H.B., Zenger, K.R. and van Herwerden, L., 2022. The El Niño Southern Oscillation drives multidirectional inter-reef larval connectivity in the Great Barrier Reef. Scientific Reports, 12(1), p.21290.
[72] Andrews, E. L., A. D. Irving, C. C.H. Sherman, E. L. Jackson (2022) Spatio-temporal analysis of the environmental ranges and phenotypic traits of Zostera muelleri subpopulations in Central Queensland, Estuarine, Coastal and Shelf Science, 108191,
ISSN 0272-7714, https://doi.org/10.1016/j.ecss.2022.108191.
[71] Condie, S.A. (2022) Changing the climate risk trajectory for coral reefs. Front. Clim. 4:980035. https://doi.org/10.3389/fclim.2022.980035.
[70] Sun, C., A. J. Hobday, S. A. Condie, M. E. Baird, J. P. Eveson, J. R. Hartog, A. J. Richardson A. D. L. Steven, K. Wild-Allen, R. C. Babcock, D. Yang, R. Yu, M. Mongin (2022). Ecological forecasting and operational information systems support sustainable ocean management. Forecasting. Forecasting 2022, 4, 1051–1079. https://doi.org/10.3390/forecast4040057.
[69] Jahanbakht, M., Xiang, W., Robson, B. and Azghadi, M.R., 2022. Nitrogen prediction in the Great Barrier Reef using finite element analysis with deep neural networks. Environmental Modelling & Software, 150, p.105311.
[68] Jahanbakht, M., Xiang, W. and Azghadi, M.R., 2022. Sediment Prediction in the Great Barrier Reef using Vision Transformer with finite element analysis. Neural Networks, 152, pp.311-321. https://doi.org/10.1016/j.neunet.2022.04.022
[67] Schroeder, T., Schaale, M., Lovell, J. and Blondeau-Patissier, D., 2022. An ensemble neural network atmospheric correction for Sentinel-3 OLCI over coastal waters providing inherent model uncertainty estimation and sensor noise propagation. Remote Sensing of Environment, 270, p.112848. https://doi.org/10.1016/j.rse.2021.112848
[66] Bozec, Y.-M., Hock, K., Mason, R.A.B., Baird, M.E., Castro-Sanguino, C., Condie, S.A., Puotinen, M., Thompson, A. and Mumby, P.J. (2022), Cumulative impacts across Australia’s Great Barrier Reef: a mechanistic evaluation. Ecological Monographs. 92:e01494. https://doi.org/10.1002/ecm.1494
[65] Livsey, D. N., Crosswell, J. R., Turner, R. D. R., Steven, A. D. L., & Grace, P. R. (2022). Flocculation of riverine sediment draining to the Great Barrier Reef, implications for monitoring and modeling of sediment dispersal across continental shelves. Journal of Geophysical Research: Oceans, 127, e2021JC017988. https://doi.org/10.1029/2021JC017988
2021
[64] Cheung, M.W., Hock, K., Skirving, W. and Mumby, P.J., 2021. Cumulative bleaching undermines systemic resilience of the Great Barrier Reef. Current biology: CB, 31(23), pp.5385-5392. https://doi.org/10.1016/j.cub.2021.09.078
[63] Mumby, P. J., Mason, R. A., & Hock, K. (2021). Reconnecting reef recovery in a world of coral bleaching. Limnology and Oceanography: Methods, 19(10), 702-713. https://doi.org/10.1002/lom3.10455
[62] Natalie Stoeckl, N. S. A. Condie, K. R. N. Anthony (2021) Assessing changes to ecosystem service values at large geographic scale: A case study for Australia’s Great Barrier Reef,
Ecosystem Services, 51, 101352, https://doi.org/10.1016/j.ecoser.2021.101352.
[61] Condie, S. A., Anthony, K. R. N., Babcock, R. C., Baird, M. E., Beeden, R., Fletcher, C. S., Gorton R., Harrison, D., Hobday, A. J., Plagányi É. E., Westcott, D. A. (2021) Large-scale interventions may delay decline of the Great Barrier Reef. R. Soc. open sci.8:201296.201296. https://doi.org/10.1098/rsos.201296
[60] McNeil, M., Nothdurft, L., Erler, D., Hua, Q. and Webster, J.M., 2021. Variations in Mid‐to Late Holocene Nitrogen Supply to Northern Great Barrier Reef Halimeda Macroalgal Bioherms. Paleoceanography and Paleoclimatology, 36(2), p.e2020PA003871. https://doi.org/10.1029/2020PA003871
[57] Baird, M. E., M. Mongin, J, Skerratt, N. Margvelashvili, S. Tickell, A. D. L. Steven, C. Robillot, R. Ellis, D. Waters, P. Kaniewska, J. Brodie (2021) Impact of catchment loads of nutrients and sediments on marine water quality on the Great Barrier Reef: An application of the eReefs marine modelling system. Mar. Poll. Bull. 167, 112297. https://doi.org/10.1016/j.marpolbul.2021.112297
[56] Baird, M.E., M. Mongin, F. Rizwi, L. Bay, N. Cantin, L. Morris (2021) The effect of natural and anthropogenic nutrient and sediment loads on coral oxidative stress on runoff-exposed reefs. Mar. Poll. Bull. 168, 112409. https://doi.org/10.1016/j.marpolbul.2021.112409
[55] Castro-Sanguino, C. , J. C. Ortiz, A. Thompson, N. H. Wolff, R. Ferrari, B. Robson, M. M. Magno-Canto, M. Puotinen, K. E. Fabricius, S. Uthicke (2021) Reef state and performance as indicators of cumulative impacts on coral reefs,
Ecological Indicators, 123, 107335, ISSN 1470-160X, https://doi.org/10.1016/j.ecolind.2020.107335.
[54] Conroy, G. (2021) Can a cold water bath save the Great Barrier Reef. Hakai Magazine. https://www.hakaimagazine.com/news/can-a-cold-water-bath-save-the-great-barrier-reef/
2020
[53] Baird ME, Green R, Lowe R, Mongin M, Bougeot E (2020) Optimising cool-water injections to reduce thermal stress on coral reefs of the Great Barrier Reef. PLoS ONE 15(10): e0239978. https://doi.org/10.1371/journal.pone.0239978.
[52] Baird, M. E., K. Wild-Allen, J. Parslow, M. Mongin, B. Robson, J. Skerratt, F. Rizwi, M. Soja-Woźniak, E. Jones, M. Herzfeld, N. Margvelashvili, J. Andrewartha, C. Langlais, M. Adams, N. Cherukuru, S. Hadley, P. Ralph, T. Schroeder, A. Steven, U. Rosebrock, L. Laiolo, M. Gustafsson, and D. Harrison (2020). CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0). Geoscientific Model Development.13:4503-4553. https://doi.org/10.5194/gmd-13-4503-2020
[51] Frade, P.R., Glasl, B., Matthews, S.A. et al. Spatial patterns of microbial communities across surface waters of the Great Barrier Reef. Commun Biol 3, 442 (2020). https://doi.org/10.1038/s42003-020-01166-y.
[50] Khan, U., F. J. Cook, R. Laugesen, M. M. Hasan, K. Plastow, G. E. Amirthanathan, M. A. Bari, N. K. Tuteja (2020) Development of catchment water quality models within nowcasting system for the Great Barrier Reef. Env. Mod. Soft., 132, 104790. http://dx.doi.org/10.1016/j.envsoft.2020.104790
[49] Smith, J. N, M. Mongin, A. Thompson, M. J. Jonker G. De’ath, K. E. Fabricius (2020) Shifts in coralline algae, macroalgae, and coral juveniles in the Great Barrier Reef associated with present‐day ocean acidification. Glob Change Biol. 26: 2149– 2160. https://doi.org/10.1111/gcb.14985
[48] Robson, B., J. Skerratt, M. Baird, C. Davies, M. Herzfeld, E. Jones, M. Mongin, A. Richardson, F. Rizwi, K. Wild-Allen, A. D.L. Steven (2020) Enhanced assessment of the eReefs biogeochemical model for the Great Barrier Reef using the Concept/State/Process/System model evaluation framework. Environ. Mod. Soft. 129:104707. https://doi.org/10.1016/j.envsoft.2020.104707
[47] Steven, ADL, Baird, M, Crosswell, J, Carlin, G, Kenna, E., Rochester, W, Skerratt, J., Tickell, S., Wild, D. (2020). Continuous Monitoring and Model Parameterisation of Estuarine Water Quality entering the Great Barrier Reef. CSIRO Final Report to Great Barrier Reef Foundation, 84pp.
(14) (PDF) Continuous Monitoring and Model Parameterisation of Estuarine Water Quality entering the Great Barrier Reef. https://www.researchgate.net/publication/344990040_Continuous_Monitoring_and_Model_Parameterisation_of_Estuarine_Water_Quality_entering_the_Great_Barrier_Reef
2019
[46] Anthony KRN, Condie S, Bozec Y-M, Harrison D, Gibbs M, Baird M, Mumby PJ, Mead D (2019) Reef Restoration and Adaptation Program: Modelling Methods and Findings. A report provided to the Australian Government by the Reef Restoration and Adaptation Program (112 pp). https://gbrrestoration.org/wp-content/uploads/2020/09/T6-Modelling-Methods-and-Findings_26April_FINAL3.pdf
[45] Baird M, Mongin M, Bouget E (2019) Reef Restoration and Adaptation Program: Ultra-Thin Surface Films. A report provided to the Australian Government by the Reef Restoration and Adaptation Program (23 pp). https://gbrrestoration.org/wp-content/uploads/2020/09/T13-Ultra-Thin-Surface-Films3.pdf
[44] Baird ME, Green R, Lowe R (2019) Reef Restoration and Adaptation Program: Cool Water Injection. A report provided to the Australian Government by the Reef Restoration and Adaptation Program (15 pp). https://gbrrestoration.org/wp-content/uploads/2020/09/T12-Cool-Water-Injection3.pdf
[43] Baird, M. E., Margvelashvili, N and Cantin, N (2019) Historical context and causes of water quality decline in the Whitsunday region. CSIRO Report to Department of Environment and Energy. https://www.dcceew.gov.au/parks-heritage/great-barrier-reef/publications/historical-context-causes-water-quality-decline-whitsundays
[42] Brinkman, R., Baird, M., Boswood, P., Fearns, P., Gruber, R., Holmes, M., Honchin, C., Johnson, R., Lewis, S., Lonborg, C., Mueller, J., Robillot, C., Schroeder, T., Steinberg, C., and Treleaven, J. 2019, Monitoring the marine physical and chemical environment within the Reef 2050 Integrated Monitoring and Reporting Program: Final Report of the Marine Physical and Chemical Environment Expert Group, Great Barrier Reef Marine Park Authority, Townsville. http://hdl.handle.net/102.100.100/348749?index=1
[41] Harrison DP, Baird M, Harrison L, Utembe S, Schofield R, Escobar Correa R, Mongin M, Rizwi F (2019) Reef Restoration and Adaptation Program: Environmental Modelling of Large Scale Solar Radiation Management. A report provided to the Australian Government by the Reef Restoration and Adaptation Program (83pp). https://gbrrestoration.org/wp-content/uploads/2020/09/T14-Environmental-Modelling-of-Large-Scale-SRM_v3.03-3.pdf
[40] Herzfeld, M, F. Rizwi (2019) A two-way nesting framework for ocean models, Environmental Modelling & Software, 117, 200-213. https://doi.org/10.1016/j.envsoft.2019.03.015.
[39] Hock, K., Doropoulos, C., Gorton, R., Condie, S.A., Mumby, P.J. (2019) Split spawning increases robustness of coral larval supply and inter-reef connectivity Nature Communications, 10 (1), 3463. https://www.nature.com/articles/s41467-019-11367-7
[38] Pausina S, Greenwood J, Pitt K, Rissik D, Rochester W, Skerratt J, UribePalomino J, Richardson A.. 2019. Zooplankton of Moreton Bay. In: Tibbetts IR, Rothlisberg PC, Neil DT, Homburg TA, Brewer DT, & Arthington AH (Eds). Moreton Bay Quandamooka & Catchment: Past, present, and future. The Moreton Bay Foundation. Brisbane, Australia. Available from: https://moretonbayfoundation.org/books/moreton-bay-quandamooka-catchment-past-present-and-future/.
[37] Skerratt J.H., M. Mongin, K. A. Wild-Allen, M. E. Baird, B. J. Robson, B. Schaffelke, M. Soja-Wozniak, N Margvelashvili, C. H. Davies, A. J. Richardson, A. D. L. Steven (2019) Simulated nutrient and plankton dynamics in the Great Barrier Reef (2011-2016). J. Mar. Sys. 192, 51-74. https://doi.org/10.1016/j.jmarsys.2018.12.006
[36] Soja-Wozniak, M., M. Baird, T. Schroeder, Y. Qin, L. Clementson, B. Baker, D. Boadle, V. Brando, A. Steven (2019). Particulate backscattering ratio as an indicator of changing particle composition in coastal waters: Observations from Great Barrier Reef waters. Journal of Geophysical Research: Oceans, 124. https://doi.org/10.1029/2019JC014998.
[35] Andrew D. L. Steven, Mark E. Baird, Richard Brinkman, Nicholas J. Car, Simon J. Cox, Mike Herzfeld, Jonathan Hodge, Emlyn Jones, Edward King, Nugzar Margvelashvili, Cedric Robillot, Barbara Robson, Thomas Schroeder, Jenny Skerratt, Sharon Tickell, Narendra Tuteja, Karen Wild-Allen & Jonathan Yu (2019): eReefs: An operational information system for managing the Great Barrier Reef, Journal of Operational Oceanography, https://doi.org/10.1080/1755876X.2019.1650589
[34] Tickell, Sharon; Dowideit, Sven; Wild, Dan; Kenna, Erin; Steven, Andy; Baird, Mark; Schroeder, Thomas; Rizwi, Farhan; Mongin, Mathieu; Blondeau-Patissier, David; King, Edward. eReefs Infrastructure 2019: Capacity to facilitate user access and scale-up of services. Brisbane, Australia: CSIRO; 2019. https://doi.org/10.25919/5eea68383d375.
[33] Xiao, Y. , X. H Wang, E. A. Ritchie, F. Rizwi, L. Qiao 2019. The development and evolution of the Burdekin River estuary freshwater plume during Cyclone Debbie (2017) Estuarine, Coastal and Shelf Science, 224, 187-196, https://doi.org/10.1016/j.ecss.2019.04.037
2018
[32] Baird, M. E., M. Mongin, F. Rizwi, L. K. Bay, N. E. Cantin, M. Soja-Wozniak and J. Skerratt (2018) A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae. Ecol. Model 386: 20-37. https://doi.org/10.1016/j.ecolmodel.2018.07.013
[31] Condie, S. A., M. Herzfeld, K. Hock, J.R. Andrewartha, R. Gorton, R. Brinkman, M. Schultz (2018) System level indicators of changing marine connectivity, Ecological Indicators, 91, 531-541. https://doi.org/10.1016/j.ecolind.2018.04.036.
[30] Margvelashvili, N. M., J. Andrewartha, M. Baird, M. Herzfeld, E Jones, M. Mongin, F. Rizwi, B. Robson, J. Skerratt, K. Wild-Allen and A. Steven (2018) Simulated fate of catchment-derived sediment on the Great Barrier Reef shelf. Mar. Poll. Bull. 135: 954-962. https://doi.org/10.1016/j.marpolbul.2018.08.018
[29] Robillot, C., Logan, M., Baird, M., Waterhouse J., Martin, K. and Schaffelke, B. (2018) Testing and implementation of an improved water quality index for the 2016 and 2017 Great Barrier Reef Report Cards – Detailed technical report. Report to the National Environmental Science Program. Reef and Rainforest Research Centre Limited, Cairns (150pp.). https://nesptropical.edu.au/wp-content/uploads/2018/08/NESP-TWQ-Project-3.2.5-Final-Report.pdf
[28] Robson, B.J., Arhonditsis, G.B., Baird, M.E., Brebion, J., Edwards, K.F., Geoffroy, L., Hébert, M.P., van Dongen-Vogels, V., Jones, E.M., Kruk, C. and Mongin, M., 2018. Towards evidence-based parameter values and priors for aquatic ecosystem modelling. Environmental Modelling & Software, 100, pp.74-81. https://doi.org/10.1016/j.envsoft.2017.11.018
[27] Wolff, N. H., E. Teixeira da Silva, M. Devlin, K. R.N. Anthony, S. Lewis, H. Tonin, R. Brinkman, P. J. Mumby (2018) Contribution of individual rivers to Great Barrier Reef nitrogen exposure with implications for management prioritization, Marine Pollution Bulletin, 133, 30-43. https://doi.org/10.1016/j.marpolbul.2018.04.069.
2017
[26] Baird, M. E., J. Andrewartha, M. Herzfeld, E. Jones, N. Margvelashvili, M. Mongin, F. Rizwi, J. Skerratt, M. Soja-Wozniak, K. Wild-Allen, T. Schroeder, B. Robson, E. da Silva, M. Devlin (2017) River plumes of the Great Barrier Reef: freshwater, sediment and optical footprints quantified by the eReefs modelling system. In Syme, G., Hatton MacDonald, D., Fulton, B. and Piantadosi, J. (eds) MODSIM2017, 22nd International Congress on Modelling and Simulation. Modelling and Simulation Society of Australia and New Zealand, December 2017, pp.1892-1898. ISBN: 978-0-9872143-7-9. https://www.mssanz.org.au/modsim2017/L22/baird.pdf.
[25] Brodie, J., Baird, M., Waterhouse, J., Warne, M., Skerratt, J., Smith, R., Mann, R., Robillot, C. and Mongin, M., 2017. Development of basin-specific ecologically relevant water quality targets for the Great Barrier Reef. Australian Centre for Tropical Water and Aquatic Ecosystem Research.
[24] Brodie, J., Baird, M., Waterhouse, J., Mongin, M., Skerratt, J., Robillot, C., Smith, R., Mann, R., Warne, M., 2017. Development of basin-specific ecologically relevant water quality targets for the Great Barrier Reef. TropWATER Report No. 17/38, James Cook University, Published by the State of Queensland, Brisbane, Australia. 68 pp. https://www.reefplan.qld.gov.au/__data/assets/pdf_file/0025/46096/gbr-water-quality-targets-june2017.pdf
[23] Robson, B.J., Andrewartha, J., Baird, M.E., Herzfeld, M., Jones, E.M., Margvelashvili, N., Mongin, M., Rizwi, F., Skerratt, J. and Wild-Allen, K., 2017. Evaluating the eReefs Great Barrier Reef marine model against observed emergent properties. In MODSIM2017, 22nd International Congress on Modelling and Simulation (pp. 1976-1982). Modelling and Simulation Society of Australia and New Zealand. https://www.mssanz.org.au/modsim2017/L22/robson.pdf
2016
[22] Albright, R., Anthony, K.R., Baird, M., Beeden, R., Byrne, M., Collier, C., Dove, S., Fabricius, K., Hoegh-Guldberg, O., Kelly, R.P. and Lough, J., 2016. Ocean acidification: Linking science to management solutions using the Great Barrier Reef as a case study. Journal of environmental management, 182, pp.641-650. https://doi.org/10.1016/j.jenvman.2016.07.038
[21] BAIRD, M. E., ADAMS, M. P., BABCOCK, R. C., OUBELKHEIR, K., MONGIN, M., WILD-ALLEN, K. A., SKERRATT, J., ROBSON, B., PETROU, K., RALPH, P. J., O’BRIEN, K. R., CARTER, A. B., JARVIS, J. C. & RASHEED, M. A. 2016 A physical representation of seagrass growth for application in a complex shallow-water biogeochemical model Ecological Modelling. 325, 13-27. https://doi.org/10.1016/j.ecolmodel.2015.12.011
[20] BAIRD, M. E., CHERUKURU, N., JONES, E. M., MARGVELASHVILI, N., MONGIN, M., OUBELKHEIR, K., RALPH, P. J., RIZWI, F., ROBSON, B., SCHROEDER, T., SKERRATT, J., STEVEN, A. D. L. & WILD-ALLEN, K. A. 2016. Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with remotely-sensed data Environmental Modelling and Software 78, 79-96. https://doi.org/10.1016/j.envsoft.2015.11.025
[19] Benthuysen, J. A., Tonin, H., Brinkman, R., Herzfeld, M., and Steinberg, C. (2016), Intrusive upwelling in the Central Great Barrier Reef, J. Geophys. Res. Oceans, 121, 8395– 8416, https://doi.org/10.1002/2016JC012294.
[18] Jones, E.M., Baird, M.E., Mongin, M., Parslow, J., Skerratt, J., Lovell, J., Margvelashvili, N., Matear, R.J., Wild-Allen, K., Robson, B. and Rizwi, F., 2016. Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef. Biogeosciences, 13 (23), pp.6441-6469. https://doi.org/10.5194/bg-13-6441-2016
[17] GILLIBRAND, P. A. & HERZFELD, M. 2016 A mass-conserving advection scheme for offline simulation of tracer transport in coastal ocean models. Ocean Modelling. 101,1-16. https://doi.org/10.1016/j.ocemod.2016.02.008
[16] MARGVELASHVILI, N., HERZFELD, M., F. RIZWI, M. M., M. E. BAIRD, E. JONES, , E. KING, T. SCHROEDE, RIZWI, F., MONGIN, M., BAIRD, M. E., JONES, E. M., SCHAFFELKE, B., KING, E. & SCHROEDER, T. 2016. Emulator-assisted data assimilation in complex models. . Ocean Dynamics 66, 1109-1124. https://doi.org/10.1007/s10236-016-0973-8
[15] MONGIN, M., BAIRD, M. E., TILBROOK, B., MATEAR, R., LENTON, A., HERZFELD, M., WILD-ALLEN, K. A., SKERRATT, J., MARGVELASHVILI, N., ROBSON, B., DUARTE, C. M., GUSTAFSSON, M. S. M., RALPH, P. J. & STEVEN, A. D. L. 2016. The exposure of the Great Barrier Reef to ocean acidification. Nature Communications 7:10732. https://www.nature.com/articles/ncomms10732
[14a] MONGIN, M., BAIRD, M. E., LENTON, A & HADLEY, S. 2016. Optimising reef-scale CO2 removal by seaweed to buffer ocean acidification. Environ. Res. Lett. 11 034023. https://doi.org/10.1088/1748-9326/11/3/034023
[14] Yu, J., Leighton, B., Car, N., Seaton, S. and Hodge, J., 2016. The eReefs data brokering layer for hydrological and environmental data. Journal of Hydroinformatics, 18(2), pp.152-167. http://hdl.handle.net/102.100.100/155820?index=1
2015
[13] HERZFELD, M. 2015. Methods for freshwater riverine input into regional ocean models. Ocean Modelling, 90, 1-15. https://doi.org/10.1016/j.ocemod.2015.04.001
[12] HERZFELD, M. & GILLIBRAND, P. A. 2015. Active open boundary forcing using dual relaxation time-scales in downscaled ocean models. Ocean Modelling, 89, 71-83.
[11] JONES, E. M., DOBLIN, M. A., MATEAR, R. & KING, E. 2015. Assessing and evaluating the ocean-colour footprint of a regional observing system. Journal of Marine Systems, 143, 49-61. https://doi.org/10.1016/j.ocemod.2015.02.004
[10] ROBSON, B. J. & DOURDET, V. 2015. Prediction of sediment, particulate nutrient and dissolved nutrient concentrations in a dry tropical river to provide input to a mechanistic coastal water quality model. Environmental Modelling & Software, 63, 97-108. https://doi.org/10.1016/j.envsoft.2014.08.009
[9] SCHILLER, A., HERZFELD, M., BRINKMAN, R., RIZWI, F. & ANDREWARTHA, J. 2015. Cross-shelf exchanges between the Coral Sea and the Great Barrier Reef lagoon determined from a regional-scale numerical model. Continental Shelf Research, 109, 150-163. https://doi.org/10.1016/j.csr.2015.09.011
[8] STEVEN, A. D. L., HODGE, J., CANNARD, T., CARLIN, G., FRANKLIN, H., MCJANNET, D., MOESENEDER, C. & SEARLE, R. 2015. Continuous Water Quality Monitoring on the Great Barrier Reef. CSIRO Final Report to Great Barrier Reef Foundation. CSIRO, 159pp. https://doi.org/10.4225/08/5852de03a547a
2014
[7] MARGVELASHVILI, N., CAMPBELL, E., MURRAY, L. & JONES, E. M. 2014. Hierarchical emulation and data assimilation into the sediment transport model. Procedia Computer Science, 29, 2121-2126. https://doi.org/10.1016/j.procs.2014.05.196
[6] MONGIN, M. & BAIRD, M. 2014. The impact of photosynthesis, calcification and water circulation on carbon chemistry variability above a coral reef: a modelling study. Ecological Modelling, 284, 19-34. https://doi.org/10.1016/j.ecolmodel.2014.04.004
[5] ROBSON, B. 2014. When do aquatic systems models provide useful predictions, what is changing, and what is next? Environmental Modelling & Software, 61, 287-296. https://doi.org/10.1016/j.envsoft.2014.01.009
[4] ROBSON, B. J., SKERRATT, J., MONGIN, M., WILD-ALLEN, K. A. & BAIRD, M. E. 2014. Varying the temporal resolution of river nutrient boundary conditions to a coupled hydrodynamic-biogeochemical model of a coastal system has surprisingly little impact on model results. Proceedings – 7th International Congress on Environmental Modelling and Software: Bold Visions for Environmental Modeling, iEMSs Vol 1, 533-539. http://www.iemss.org/sites/iemss2014/papers/Volume_1_iEMSs2014_pp_1-602.pdf
[3] SCHILLER, A., HERZFELD, M., BRINKMAN, R. & STUART, G. 2014. Monitoring, Predicting, and Managing One of the Seven Natural Wonders of the World. Bulletin of the American Meteorological Society, 95, 23-30. https://doi.org/10.1175/BAMS-D-12-00202.1
2013
[2] MARGVELASHVILI, N., ANDREWARTHA, J., HERZFELD, M., ROBSON, B. & BRANDO, V. 2013. Satellite data assimilation and estimation of a 3d coastal sediment transport model using error-subspace emulators. Environmental Modelling and Software Journal 40, 191-201. https://doi.org/10.1016/j.envsoft.2012.09.009
[1] ROBSON, B. J., BAIRD, M. & WILD-ALLEN, K. 2013. A physiological model for the marine cyanobacteria, Trichodesmium. MODSIM2013, 20th International Congress on Modelling and Simulation, Modelling and Simulation Society of Australia and New Zealand, 1652-1658. https://www.mssanz.org.au/modsim2013/H3/robson.pdf