Heintz, T., Haapkylä, J., and Gilbert, A. (2015) Coral health on reefs near mining sites in New Caledonia. Diseases of Aquatic Organisms, 115 (2). pp. 165-173.

Haapkylä , J., Melbourne-Thomas, J., and Flavell, M. (2015) The association between coral communities and disease assemblages in the Wakatobi Marine National Park, south-eastern Sulawesi, Indonesia. Marine and Freshwater Research, 66 (10). pp. 948-955.

Haapkylä, J., Melbourne-Thomas, J., Flavell, M., and Willis, B.L. (2013) Disease outbreaks, bleaching and a cyclone drive changes in coral assemblages on an inshore reef of the Great Barrier Reef. Coral Reefs, 32 (3). pp. 815-824.

Muller, Erinn M., Raymundo, Laurie J., Willis, Bette L., Haapkylä, Jessica, Yusuf, Syafyudin, Wilson, Joanne R., and Harvell, Drew C. (2012) Coral health and disease in the Spermonde Archipelago and Wakatobi, Sulawesi. Journal of Indonesian Coral Reefs, 1 (3). pp. 147-159.

Pisapia, C., Hennige, S.J., Haapkylä, J., Matteucci, R., and Smith, D.J. (2012) Morphological changes in polyp structure of massive coral species in clear and turbid waters. Bulletin of Marine Science, 88 (1). pp. 183-191.

Aeby, Greta S., Williams, Gareth J., Franklin, Erik C., Haapkyla, Jessica, Harvell, C. Drew, Neale, Stephen, Page, Cathie A., Raymundo, Laurie, Vargas-Ángel, Bernardo, Willis, Bette L., Work, Thierry M., and Davy, Simon K. (2011) Growth anomalies on the coral genera Acropora and Porites are strongly associated with host density and human population size across the Indo-Pacific. PLoS ONE, 6 (2). e16887. pp. 1-9.

Haapkylä, Jessica, Unsworth, Richard K.F., Flavell, Mike, Bourne, David G., Schaffelke, Britta, and Willis, Bette L. (2011) Seasonal rainfall and runoff promote coral disease on an inshore reef. PLoS ONE, 6 (2). e16893. pp. 1-10.

Scaps, P, and Haapkyla, J (2011) Focal white spots on Porites spp. from the north Andaman Sea, Western Thailand and the Wakatobi Marine National Park, Indonesia. Galaxea, Journal of Coral Reef Studies, 13. pp. 3-4.

Haapkylä, Jessica (2011) Dynamics and drivers of coral disease on Indo-Pacific reefs. PhD thesis, James Cook University.

Clifton, Julian, Cullen, Leanne C., Haapkyla, Jessica, and Unsworth, Richard K.F. (2010) Ensuring appropriate and proportionate responses to environmental threats: a response to Caras and Pasternak. Ocean & Coastal Management, 53 (11). pp. 700-702.

Haapkylä, J., Melbourne-Thomas, J., Flavell, M., and Willis, B.L. (2010) Spatiotemporal patterns of coral disease prevalence on Heron Island, Great Barrier Reef, Australia. Coral Reefs, 29 (4). pp. 1035-1045.

Haapkyla, Jessica, Seymour, Adrian S., Barneah, Orit, Brickner, Itzchak, Hennige, Sebastian, Suggett, David, and Smith, David (2009) Association of Waminoa sp. (Acoela) with corals in the Wakatobi Marine Park, South-East Sulawesi, Indonesia. Marine Biology, 156. pp. 1021-1027.

Haapkyla, Jessica, Unsworth, Richard K.F., Seymour, Adrian S., Melbourne-Thomas, Jessica, Flavell, Mike, Willis, Bette L., and Smith, David J. (2009) Spatio-temporal coral disease dynamics in the Wakatobi Marine National Park, South-East Sulawesi, Indonesia. Diseases of Aquatic Organisms, 87 (1-2). pp. 105-115.