Hagihara, Rie, Jones, Rhondda E., Grech, Alana, Lanyon, Janet M., Sheppard, James K., and Marsh, Helene (2014) Improving population estimates by quantifying diving and surfacing patterns: a dugong example. Marine Mammal Science, 30 (1). pp. 348-366.

Grech, Alana, Sheppard, James, and Marsh, Helene (2011) Informing species conservation at multiple scales using data collected for marine mammal stock assessments. PLoS ONE, 6 (3). e17993. pp. 1-8.

Hagihara, Rie, Jones, Rhondda, Sheppard, James, Hodgson, Amanda, and Marsh, Helene (2011) Minimizing errors in the analysis of dive recordings from shallow-diving animals. Journal of Experimental Marine Biology and Ecology, 399 (2). pp. 173-181.

Sheppard, James K., Marsh, Helene, Jones, Rhondda E., and Lawler, Ivan R. (2010) Dugong habitat use in relation to seagrass nutrients, tides, and diel cycles. Marine Mammal Science, 26 (4). pp. 855-879.

Sheppard, James K., Jones, Rhondda E., Marsh, Helene, and Lawler, Ivan R . (2009) Effects of tidal and diel cycles on dugong habitat use. Journal of Wildlife Management, 73 (1). pp. 45-59.

Sheppard, James K., Carter, Alex B., McKenzie, Len J., Pitcher, C. Roland, and Coles, Robert G. (2008) Spatial patterns of sub-tidal seagrasses and their tissue nutrients in the Torres Strait, northern Australia: implications for management. Continental Shelf Research, 28 (16). pp. 2282-2291.

Sheppard, James K. (2008) The spatial ecology of dugongs: applications to conservation management. PhD thesis, James Cook University.

Sheppard, James K., Lawler, Ivan R ., and Marsh, Helene (2007) Seagrass as pasture for seacows: landscape-level dugong habitat evaluation. Estuarine, Coastal and Shelf Science , 71 (1-2). pp. 117-132.

Pitcher, Roland, Haywood, Mick, Hooper, John, Coles, Rob, Bartlett, Chris, Browne, Matthew, Cannard, Toni, Carini, Giovannella, Carter, Alexandra, Cheers, Sue, Chetwynd, Doug, Cook, Stephen, Davie, Peter, Ellis, Nick, Fellegara, Ida, Forcey, Karl, Furey, Melodyrose, Gledhill, Dan, Hendriks, Patricia, Jacobsen, Ian, Johnson, Jeff, Jones, Michelle, Last, Peter, Marks, Shona, McLeod, Ian, Sheils, Jacquie, Sheppard, James, Smith, Greg, Strickland, Colleen, Van der Geest, Claire, Venables, Bill, Wassenberg, Ted, and Yearsley, Gus (2007) Mapping and characterisation of key biotic and physical attributes of the Torres Strait ecosystem: CRC-TS task number: T2.1 final report. Report. CSIRO Marine and Atmospheric Research, Cleveland, QLD, Australia.

Carter, Alex B., Sheppard, James K., Coles, Robert G., and McKenzie, Len J. (2007) Sub-tidal seagrasses of the Torres Strait: spatial patterns and nutritional value for marine herbivores. Report. Department of Primary Industries and Fisheries (DPI&F), Cairns, QLD, Australia.

Sheppard, James K., Preen, Anthony R., Marsh, Helene, Lawler, Ivan R., Whiting, Scott D., and Jones, Rhondda E. (2006) Movement heterogeneity of dugongs, Dugong dugon (Müller), over large spatial scales. Journal of Experimental Marine Biology and Ecology, 334 (1). pp. 64-83.

Maitland, R.N., Lawler, I.R., and Sheppard, J.K. (2006) Assessing the risk of boat strike on dugongs (Dugong dugon) at Burrum Heads, Queensland, Australia. Pacific Conservation Biology, 12 (4). pp. 321-326.