Sheppard, Charles, Davy, Simon, Pilling, Graham, and Graham, Nicholas (2018) The Biology of Coral Reefs. Biology of Habitats . Oxford University Press, Oxford, UK, pp. 1-370.

Roche, R.C., Pratchett, M.S., Carr, P., Turner, J.R., Wagner, D., Head, C., and Sheppard, C.R.C (2015) Localized outbreaks of Acanthaster planci at an isolated and unpopulated reef atoll in the Chagos Archipelago. Marine Biology, 162 (8). pp. 1695-1704.

Harris, Alasdair, Wilson, Shaun, Graham, Nicholas, and Sheppard, Charles (2014) Scleractinian coral communities of the inner Seychelles 10 years after the 1998 mortality event. Aquatic Conservation: marine and freshwater ecosystems , 24 (5). pp. 667-679.

Sale, Peter F., Agardy, Tundi, Ainsworth, Cameron H., Feist, Blake E., Bell, Johann D., Christie, Patrick, Hoegh-Guldberg, Ove, Mumby, Peter H., Feary, David A., Saunders, Megan I., Daw, Tim M., Foale, Simon J., Levin, Phillip S., Lindeman, Kenyon C., Lorenzen, Kai, Pomeroy, Robert S., Allison, Edward H., Bradbury, R.H., Corrin, Jennifer, Edwards, Alasdair J., Obura, David O., Sadovy de Mitcheson, Yvonne J., Samoilys, Melita A., and Sheppard, Charles R.C. (2014) Transforming management of tropical coastal seas to cope with challenges of the 21st century. Marine Pollution Bulletin, 85 (1). pp. 8-23.

Feary, David A., Burt, John A., Bauman, Andrew G., Al Hazeem, Shaker, Abdel-Moati, Mohamed A., Al-Khalifa, Khalifa A., Anderson, Donald M., Amos, Carl, Baker, Andrew, Bartholomew, Aaron, Bento, Rita, Cavalcante, Geórgenes H., Chen, Chaolun Allen, Coles, Steve L., Dab, Koosha, Fowler, Ashley M., George, David, Grandcourt, Edwin, Hill, Ross, John, David M., Jones, David A., Keshavmurthy, Shashank, Mahmoud, Huda, Tapeh, Mahdi Moradi Och, Mostafavi, Pargol Ghavam, Naser, Humood, Pichon, Michel, Purkis, Sam, Riegl, Bernhard, Samimi-Namin, Kaveh, Sheppard, Charles, Samiei, Jahangir Vajed, Voolstra, Christian R., and Wiedenmann, Joerg (2013) Critical research needs for identifying future changes in Gulf coral reef ecosystems. Marine Pollution Bulletin, 72 (2). pp. 406-416.

Keshavmurthy, Shashank, Yang, Sung-Yin, Alamaru, Ada, Chuang, Yoo-Yang, Pichon, Michel, Obura, David, Fontana, Silvia, De Palmas, Stephane, Stefani, Fabrizio, Benzoni, Francesca, MacDonald, Angus, Noreen, Annika M.E., Chen, Chienshun, Wallace, Carden C., Pillay, Ruby Moothein, Denis, Vianney, Amri, Affendi Yang, Reimer, James D., Mezaki, Takuma, Sheppard, Charles, Loya, Yossi, Abelson, Avidor, Mohammed, Mohammed Suleiman, Baker, Andrew C., Mostafavi, Pargol Ghavam, Suharsono, Budiyanto A., and Chen, Chaolun Allen (2013) DNA barcoding reveals the coral "laboratory-rat", Stylophora pistillata encompasses multiple identities. Scientific Reports, 3. 1520. pp. 1-7.

Pratchett, M.S., Pisapia, C., and Sheppard, C.R.C. (2013) Background mortality rates for recovering populations of Acropora cytherea in the Chagos Archipelago, central Indian Ocean. Marine Environmental Research, 86. pp. 29-34.

Sheppard, C.R.C., Ateweberhan, M., Bowen, B.W., Carr, P., Chen, C.A., Clubbe, C., Craig, M.T., Ebinghaus, R., Eble, J., Fitzsimmons, N., Gaither, M.R., Gan, C-H., Gollock, M., Guzman, N., Graham, N.A.J., Harris, A., Jones, R., Keshavmurthy, S., Koldewey, H., Lundin, C.G., Mortimer, J.A., Obura, D., Pfeiffer, M., Price, A.R.G., Purkis, S., Raines, P., Readman, J.W., Riegl, B., Rogers, A., Schleyer, M., Seaward, M.R.D., Sheppard, A.L.S., Tamelander, J., Turner, J.R., Visram, S., Vogler, C., Vogt, S., Wolschke, H., Yang, J. M-C., Yang, S-Y., and Yesson, C. (2012) Reefs and islands of the Chagos Archipelago, Indian Ocean: why it is the world's largest no-take marine protected area. Aquatic Conservation: marine and freshwater ecosystems , 22 (2). pp. 232-261.

Ateweberhan, M., McClanahan, T.R., Graham, N.A.J., and Sheppard, C.R.C. (2011) Episodic heterogeneous decline and recovery of coral cover in the Indian Ocean. Coral Reefs, 30 (3). pp. 739-752.

Pratchett, M.S., Graham, N.A.J., Sheppard, C.R.C., and Mayes, B. (2010) Are infestations of Cymo melanodactylus killing Acropora cytherea in the Chagos archipelago? Coral Reefs, 29 (4). p. 941.

Graham, Nicholas, Spalding, Mark D., and Sheppard, Charles R.C. (2010) Reef shark declines in remote atolls highlight the need for multi-faceted conservation action. Aquatic Conservation: marine and freshwater ecosystems , 20 (5). pp. 543-548.

Graham, Nicholas A.J., McClanahan, Timothy R., MacNeil, M. Aaron, Wilson, Shaun K., Polunin, Nicholas V.C., Jennings, Simon, Chabanet, Pascale, Clark, Susan, Spalding, Mark D., Letourneur, Yves, Bigot, Lionel, Galzin, René, Öhman, Marcus C., Garpe, Kajsa C., Edwards, Alasdair J., and Sheppard, Charles R.C. (2008) Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems. PLoS ONE, 3 (8). e3039. - .

Carpenter, Kent E., Abrar, Muhammad, Aeby, Greta, Aronson, Richard B., Banks, Stuart, Bruckner, Andrew , Chiriboga, Angel, Cortés, Jorge, Delbeek, J. Charles, DeVantier, Lyndon, Edgar, Graham J., Edwards, Alasdair J., Fenner, Douglas, Guzmán, Héctor M., Hoeksema, Bert W., Hodgson, Gregor, Johan, Ofri, Licuanan, Wilfredo Y., Livingstone, Suzanne R., Lovell, Edward R., Moore, Jennifer A., Obura, David O., Ochavillo, Domingo, Polidoro, Beth A., Precht, William F., Quibilan, Miledel C., Reboton, Clarissa, Richards, Zoe T., Rogers, Alex D., Sanciangco, Jonnell, Sheppard, Anne, Sheppard, Charles, Smith, Jennifer, Stuart, Simon, Turak, Emre, Veron, John E. N., Wallace, Carden, Weil, Ernesto, and Wood, Elizabeth (2008) One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science, 321 (5888). pp. 560-563.