Journal Papers 
Lindenmayer, D., Pierson, J., Barton, P., Beger M., Branquinho C., Calhoun, A., Caro, T., Gross, J., Heino, J., Hunter, M., Lane, P, Longo, C., Martin K., McDowell, W.H., Camille Mellin11, Salo, H., Tulloch, A., and Westgate, M. (online 2015) A cross-disciplinary framework for the application of ecological surrogates. Science of the Total Environment. doi: 10.1016/j.scitotenv.2015.08.056.
Peirson W., Davey E., Jones A., Hadwen W., Bishop K., Beger M., Capon S., Fairweather P., Creese B., Smith T. F., Gray L., and Tomlinson R. (in press 2015). Opportunistic management of estuaries under climate change: a new adaptive decision-making framework and its practical application. Journal of Environmental Management.
Makino, A. Klein C.J., Possingham H.P., Yamano H., Yara Y., Ariga T., Matsuhasi K. and Beger M., (online 2014) The effect of applying alternate IPCC climate scenarios to marine reserve design for range changing species. Conservation Letters. DOI: 10.1111/conl.12147
Simpson C.J., Beger M., Colman J.G., Friedman K.J., Hill A.K., Kendrick A.J., Waples K.A., Whiting S.D. & Wilson S.K. (2015). Prioritisation of conservation research and monitoring for Western Australian protected areas and threatened species. 9 (3): 227-237 Conservation Science Western Australia.
Tulloch, V. J. D., Tulloch A. I. T., Visconti P., Halpern B. S., Watson J. E. M., Evans M. C., Auerbach N. A., Barnes M., Beger M., Chadès I., Giakoumi S., McDonald-Madden E., Murray N. J., Ringma J., and Possingham H. P. (2015). Why do we map threats? Linking threat mapping with actions to make good decisions for biodiversity conservation. Frontiers in Ecology and the Environment. 13(2): 91–99.
Tallis, H., and 218 authors, including M.Beger (2014) Towards a diverse conservation ethic. Nature. 515: 27-28
Hobbs JP., Beger M., De Brauwer M., Emslie M., (2014) Northeastern range extension of the anemone Stichodactyla haddoni to the Marshall Islands represents a new record of host use by the endemic anemonefish Amphiprion tricinctus. Marine Biodiversity Records. 7, e106.
Makino A., Yamano H., Beger M., Klein C. J., Yara Y. and Possingham H.P. (2014) Spatio-temporal marine conservation planning to support high-latitude coral range expansion under climate change, Diversity and Distributions, 20, 6-12
Beger M., Sommer B., Harrison P., Smith S. D. A. and Pandolfi J. M. (2014) Conserving potential coral reef refuges at high latitudes. Diversity and Distributions 20, 245-257. 
Beger M., Selkoe K. A., Treml E. A., Barber P. H., Von der Heyden S., Crandall E. D., Toonen R. J. and Riginos C. (2014) Evolving coral reef conservation with genetic information. Bulletin of Marine Science, 90 (1) 159-173 Special Issue on “Molecular Ecology and Evolution of the Indo-Pacific”.
Makino, A., Klein, C. J., Beger, M., Jupiter, S. D. & Possingham, H. P. (2013) Incorporating conservation zone effectiveness for protecting biodiversity in marine planning. PlosOne. 8(11): e78986. doi:10.1371/journal.pone.0078986
von der Heyden S., Beger M., Toonen R. J., van Herwerden L., Juinio-Meñez M. A., Ravago-Gotanco R., Fauvelot C. and Bernardi G. (2014) The application of genetics to marine management and conservation: examples from the Indo-Pacific. Bulletin of Marine Science, 90 (1) 123-158(36) Special Issue on “Molecular Ecology and Evolution of the Indo-Pacific”.
Sommer B., Harrison P., Beger M., and Pandolfi J. M. (2014) Trait-mediated environmental filtering drives assembly processes in biogeographic transition zones. Ecology, 95 (4) 1000-1009.
Ceccarelli, D. M., A. J. Frisch, N. A. J. Graham, A. M. Ayling, and M. Beger (2013) Habitat partitioning and vulnerability of sharks in the Great Barrier Reef Marine Park. Reviews in Fish Biology and Fisheries. (online early, Jul 2013, doi: 10.1007/s11160-013-9324-8).
Halpern B.S., Klein C., J., Brown C., Beger M., Grantham H., Ruckelshaus M., Tulloch V., White C. & Possingham H.P. (2013). Assessing the triple bottom line: inherent tradeoffs between equity and conservation. Proceedings of the National Academy of Sciences 110, 6229-6234, doi: 10.1073/pnas.1217689110.
Richards, Z. T.and Beger, M. (2013) Regional conservation status of scleractinian coral biodiversity in the Republic of the Marshall Islands. Diversity 5(3) 522-540, doi:10.3390/d5030522.
Lukoschek, V., Beger, M., Ceccarelli, D., Richards, Z. T. & Pratchett, M. S. (2013) Enigmatic declines of Australia’s sea snakes from a biodiversity hotspot. Biological Conservation 166, 191-202.
Makino, A., Beger, M., Klein, C. J., Jupiter, S. D. & Possingham, H. P. (2013) Integrated planning for land-sea ecosystem connectivity to protect coral reefs. Biological Conservation 165, 35-42.
Cvitanovic C., Wilson S.K., Fulton C.J., Almany G.R., Anderson P., Babcock R.C., Ban N.C., Beeden R.J., Beger M., Cinner J., Dobbs K., Evans L.S., Farnham A., Friedman K.J., Gale K., Gladstone W., Grafton Q., Graham N.A.J., Gudge S., Harrison P.L., Holmes T.H., Johnstone N., Jones G.P., Jordan A., Kendrick A.J., Klein C.J., Little L.R., Malcolm H.A., Morris D., Possingham H.P., Prescott J., Pressey R.L., Skilleter G.A., Simpson C., Waples K., Wilson D. & Williamson D.H. (2013). Critical research needs for managing coral reef marine protected areas: Perspectives of academics and managers. Journal of Environmental Management, 114, 84-91.
McClanahan, T.R., Donner, S.D., Maynard, J.A., MacNeil, M.A., Graham, N.A.J., Maina, J., Baker, A.C., Alemu I, J.B., Beger, M., Campbell, S.J., Darling, E.S., Eakin, C.M., Heron, S.F., Jupiter, S.D., Lundquist, C.J., McLeod, E., Mumby, P.J., Paddack, M.J., Selig, E.R. & van Woesik, R. (2012) Prioritizing key resilience indicators to support coral reef management in a changing climate. Plos One, 7, e42884. Plos1.
Beger, M., R. Babcock, D. J. Booth, D. Bucher, S. A. Condie, B. Creese, C. Cvitanovic, S. J. Dalton, P. Harrison, A. Hoey, A. Jordan, J. Loder, H. Malcolm, S. W. Purcell, C. Roelfsma, P. Sachs, S. D. A. Smith, B. Sommer, R. Stuart-Smith, D. Thomson, C. C. Wallace, M. Zann, and J. M. Pandolfi (2011) Research challenges to improve the management and conservation of subtropical reefs to tackle climate change threats. Ecological Management & Restoration 12:e7-e10.
Richards, Z. T., and M. Beger (2011) A quantification of the standing stock of macro-debris in Majuro lagoon and its effect on hard coral communities. Marine Pollution Bulletin 62:1693-1701.
Baker N., Beger M., McClennen C., Ishoda A. and Edwards F. (2011) Reimaanlok: A national framework for conservation area planning in the Marshall Islands. Journal of Marine Biology Article ID 273034, 11 pages, doi:10.1155/2011/273034.
Ceccarelli, D.M., Beger, M., Kospartov, M.C., Richards, Z.T., Birrell, C.L., Cvitanovic, C., (2011). Population trends of remote invertebrate resources in a marine reserve: trochus and holothurians at Ashmore Reef. Pacific Conservation Biology 17(1-2):132-140.
Kininmonth, S., M. Beger, M. Bode, E. Peterson, V. M. Adams, D. Dorfman, D. R. Brumbaugh, and H. P. Possingham. 2011. Dispersal connectivity and reserve selection for marine conservation. Ecological Modelling 222:1272-1282.
Mora C., Aburto-Oropeza O., Ayala Bocos A., Ayotte P. M., Banks S., Bauman A. G., Beger M., Bessudo S., Booth D. J., Brokovich E., Brooks A., Chabanet P., Cinner J., Cortés J., Cruz-Motta J. J., Cupul Magaña A., DeMartini E. E., Edgar G. J., Feary D. A., Ferse S. C. A., Friedlander A. M., Gaston K. J., Gough C., Graham N. A. J., Green A., Guzman H. M., Hardt M., Kulbicki M., Letourneur Y., López Pérez A., Loreau M., Loya Y., Martinez C., Mascareñas-Osorio I., Morove T., Nadon M.-O., Nakamura Y., Paredes G., Polunin N. V. C., Pratchett M. S., Reyes Bonilla H., Rivera F., Sala E., Sandin S., Soler G., Stuart-Smith R., Tessier E., Tittensor D. P., Tupper M., Usseglio P., Vigliola L., Wantiez L., Williams I. D., Wilson S. K. and Zapata F. A. (2011) Global human footprint on the linkage between biodiversity and ecosystem functioning in reef fishes. PLoS Biology 9. e1000606. doi:10.1371/journal.pbio.1000606.
Beger M., Grantham H., Pressey R.L., Wilson K.A., Peterson E.L., Dorfman D., Mumby P.J., Lourival R., Brumbaugh D.R. & Possingham H.P. (2010). Conservation planning for connectivity across marine, freshwater, and terrestrial realms. Biological Conservation, 143, 565-575.
Beger M., Simon L., Game E., Ball I., Treml E., Watts M. and Possingham H. P. (2010) Incorporating functional ecological connectivity into spatial decision making for conservation. Conservation Letters 3, 359–368.
Klein, C.J., Ban, N.C., Halpern, B., Beger, M., Game, E.T., Grantham, H., Green, A., Klein, T., Kininmonth, S., Treml, E., Wilson, K.A., Possingham, H.P. (2010). Prioritizing land and sea conservation investments to protect coral reefs. Plos One, 5, 8.
Conference papers
MacLeod I.D., Richards V. & Beger M. (2011). The effects of human and biological interactions on the corrosion of WWII iron shipwrecks in Chuuk Lagoon. In: 18th International Corrosion Congress 2011 Perth, WA; Australia, pp. 298-309. (1 citation)
Rasaiah B., Peterson E., Beger M. & Jones S.D. (2011). Bathymetry of near-shore zones in Rongelap Atoll, Marshall Islands using satellite imagery. In: 34th International Symposium on Remote Sensing of Environment – The GEOSS Era: Towards Operational Environmental Monitoring Sydney, NSW; Australia, 4p.
Roelfsema C., Phinn S., Jupiter S., Comley J., Beger M. & Peterson E.L. (2010). The application of object based analysis of high spatial resolution imagery for mapping large coral reef systems in the West Pacific at geomorphic and benthic community spatial scales. In: International Geoscience and Remote Sensing Symposium (IGARSS) Honolulu, pp. 4346-4349.
Reports and other publications
Beger, M., McGowan, J., Heron, S.F., Treml, E.A., Green, A., White, A.T., Wolff, N.H., Hock, K., van Hooidonk, R., Mumby, P.J. & Possingham, H.P. (2013). Identifying high priority gaps in the Coral Triangle Marine Protected Area System. Coral Triangle Support Program, The Nature Conservancy, and The University of Queensland Brisbane, Australia, p. 56.
Beger, M., McGowan, J., Polak, O., Tulloch, V.T. 2013. A Rapid Ecological Assessment of the reef fishes and coral reef health of the future Tun Mustapha Marine Park, Sabah, Malaysia. WWF Malaysia, The University of Queensland, Kota Kinabalu, Sabah, 78 pp.
Richards, Z.T. & Beger, M. (2011). Marshall Islands Coral Reef Monitoring Guide. College of the Marshall Islands, Australian Museum, The University of Queensland, Majuro, Republic of the Marshall Islands, p. 85.
Klein, C.J., Kark, S., Carvalho, S., Beger, M., Possingham, H.P. (2010) Conserving evolutionary novelty on the edge. Science, E-Letter (http://www.sciencemag.org/sciext/eletters/#13497).
Richards Z.T., Beger M., Hobbs J-P., Bowling T., Chong-seng K., Pratchett M. 2009. Ashmore Reef National Nature Reserve and Cartier Island Marine Reserve Marine Survey 2009. ARC Centre of Excellence for Coral Reef Studies. Produced for the Department of the Environment, Water, Heritage and the Arts.