Anderson MJ, Thompson AA (2004) Multivariate control charts for ecological and environmental monitoring. Ecological Applications 14: 1921-1935.
Sweatman HPA, Thompson AA, Neale SJ and Thomson DP (2006) Inshore coral reefs monitoring. (pp.171-236) Water quality and ecosystem monitoring programs - Reef Water Quality Protection Plan. Final report August 2006. An unpublished report to the Great Barrier Reef Marine Park Authority. CRC Reef Research Centre. 138 p.
Cheal AJ, Delean S, Sweatman HPA and Thompson AA (2007) Spatial synchrony in coral reef fish populations and the influence of climate. Ecology 88(1): 158-169.
Uthicke S, Thompson AA and Schaffelke B (2010) Effectiveness of benthic foraminiferal and coral assemblages as water quality indicators on inshore reefs of the Great Barrier Reef, Australia. Coral Reefs 29: 209-225.
Thompson AA, Dolman A (2010) Coral bleaching: one disturbance too many for near-shore reefs of the Great Barrier Reef. Coral Reefs 29: 637-648.
Thompson A, Schroeder T, Brando VE, Schaffelke B (2014) Coral community responses to declining water quality: Whitsunday Islands, Great Barrier Reef, Australia. Coral Reefs 33(4): 923-938
Petus C, Devlin M, Thompson A, McKenzie L, da Silva ET, Collier C, Tracey D, Martin K (2016) Estimating the exposure of coral reefs and seagrass meadows to land-sourced contaminants in river flood plumes of the Great Barrier Reef: Validating a simple satellite risk framework with environmental data. Remote Sensing 8(3): 210
Osborne K, Thompson AA, Cheal AJ, Emslie MJ, Johns KA, Jonker MJ, Logan M, Miller IR, Sweatman HP (2017) Delayed coral recovery in a warming ocean. Global Change Biology 23(9):3869-81.
Thompson A, Costello P, Davidson J, Logan M, Coleman G, Gunn K (2018) Marine Monitoring Program. Annual for coral reef monitoring: 2016 to 2017. Australian Institute of Marine Science, Townsville (148 p)