Pratchett, Morgan S., Chandler, Josie F., Choukroun, Severine M., Doll, Peter C., Lang, Bethan J., Kwong, Sarah, Chen, Carla C.M., Emslie, Mike J., Caballes, Ciemon F., Uthicke, Sven, and Matthews, Sam A. (2024) Biophysical Processes Involved in the Initiation and Spread of Population Irruptions of Crown-of-Thorns Starfish on 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. 290-305.

Pell, T.J., McClure, E.C., Emslie, M.J., and Hoey, A.S. (2024) Limited susceptibility of Lobophora to browsing fishes on inshore reefs of the Great Barrier Reef. Coral Reefs, 43. pp. 5-17.

Benthuysen, Jessica A., Emslie, Michael J., Currey-Randall, Leanne M., Cheal, Alistair J., and Heupel, Michelle R. (2022) Oceanographic influences on reef fish assemblages along the Great Barrier Reef. Progress in Oceanography, 208. 102901.

Cheal, Alistair J., Emslie, Michael J., Currey-Randall, Leanne M., and Heupel, Michelle R. (2021) Comparability and complementarity of reef fish measures from underwater visual census (UVC) and baited remote underwater video stations (BRUVS). Journal of Environmental Management, 289. 112375.

Ceccarelli, Daniela M., McLeod, Ian M., Boström-Einarsson, Lisa, Bryan, Scott E., Chartrand, Kathryn M., Emslie, Michael J., Gibbs, Mark T., Gonzalez Rivero, Manuel, Hein, Margaux Y., Heyward, Andrew, Kenyon, Tania M., Lewis, Brett M., Newlands, Maxine, Mattocks, Neil, Schläppy, Marie-Lise, Suggett, David J., and Bay, Line K. (2020) Substrate stabilisation and small structures in coral restoration: state of knowledge, and considerations for management and implementation. PLoS ONE, 15 (10). e0240846.

Pratchett, Morgan, Bridge, Thomas, Brodie, Jon, Cameron, Darren, Day, Jonathan, Emslie, Mike, Grech, Alana, Hamann, Mark, Heron, Scott, Hoey, Andrew, Hoogenboom, Mia, Lough, Janice, Morrison, Tiffany, Osborne, Kate, Read, Mark, Schauble, Chloe, Smithers, Scott, Sweatman, Hugh, and Waterhouse, Jane (2019) Australia's Great Barrier Reef. In: Sheppard, Charles, (ed.) World Seas: an environmental evaluation. Elsevier, London, UK, pp. 333-362.

Johns, Kerryn A., Emslie, Michael J., Hoey, Andrew S., Osborne, Kate, Jonker, Michelle J., and Cheal, Alistair J. (2018) Macroalgal feedbacks and substrate properties maintain a coral reef regime shift. Ecosphere, 9 (7). e02349.

Emslie, Michael J. (2016) Effects of habitat versus fisheries management on spatio-temperal variation in fish assemblages on the Great Barrier Reef. PhD thesis, James Cook University.

Emslie, Michael J., Logan, Murray, Williamson, David H., Ayling, Anthony M., MacNeil, M. Aaron, Ceccarelli, Daniela, Cheal, Alistair J., Evans, Richard D., Johns, Kerryn A, Jonker, Michelle J., Miller, Ian R., Osborne, Kate, Russ, Garry R., and Sweatman, Hugh P.A. (2015) Expectations and outcomes of reserve network performance following re-zoning of the Great Barrier Reef Marine Park. Current Biology, 25 (8). pp. 983-992.

Feary, David A., Pratchett, Morgan S., Emslie, Michael J., Fowler , Ashley M., Figueira, Will F., Luiz, Osmar J., Nakamura, Yohei, and Booth, David J. (2014) Latitudinal shifts in coral reef fishes: why some species do and others don't shift. Fish and Fisheries, 15 (4). pp. 593-615.

Baird, Andrew H., Emslie, Michael J., and Lewis, Andrew R. (2012) Extended periods of coral recruitment on the Great Barrier Reef. In: Proceedings of the 12th International Coral Reef Symposium. 12A_1. pp. 1-5. From: 12th International Coral Reef Symposium, 9-13 July 2012, Cairns, QLD, Australia.

Emslie, M.J., Logan, M., Ceccarelli, D.M., Cheal, A.J., Hoey, A.S., Miller, I., and Sweatman, H.P.A. (2012) Regional-scale variation in the distribution and abundance of farming damselfishes on Australia's Great Barrier Reef. Marine Biology, 159 (6). pp. 1293-1304.

Emslie, M.J., Pratchett, M.S., and Cheal, A.J. (2011) Effects of different disturbance types on butterflyfish communities of Australia's Great Barrier Reef. Coral Reefs, 30 (2). pp. 461-471.

Emslie, M.J., Pratchett, M.S., Cheal, A.J., and Osborne, K. (2010) Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type. Coral Reefs, 29 (3). pp. 705-715.

Wilson, S.K., Dolman, A.M., Cheal, A.J., Emslie, M.J., Pratchett, M.S., and Sweatman, H.P.A. (2009) Maintenance of fish diversity on disturbed coral reefs. Coral Reefs, 28 (1). pp. 3-14.

Cheal, Alistair J., Wilson, Shaun K., Emslie, Michael J., Dolman, Andrew M., and Sweatman, Hugh (2008) Responses of reef fish communities to coral declines on the Great Barrier Reef. Marine Ecology Progress Series, 372. pp. 211-223.

Russ, Garry R., Cheal, Alistair J., Dolman, Andrew M., Emslie, Michael J., Evans, Richard D., Miller, Ian, Sweatman, Hugh, and Williamson, David H. (2008) Rapid increase in fish numbers follows creation of world's largest marine reserve network. Current Biology, 18 (12). pp. 514-515.

Wilson, Shaun K., Burgess, Scott C., Cheal, Alistair J., Emslie, Mike, Fisher, Rebecca, Miller, Ian, Polunin, Nicholas V.C., and Sweatman, Hugh P.A. (2008) Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment. Journal of Animal Ecology, 77 (2). pp. 220-228.

Emslie, Michael J., and Jones, Geoffrey P. (2001) Patterns of embryo mortality in a demersally spawning coral reef fish and the role of predatory fishes. Environmental Biology of Fishes, 60 (4). pp. 363-373.