Quan WM, Fan R, Wang Y, Humphries AT (in press) Long-term oyster recruitment and growth are not influenced by substrate type in China: implications for sustainable oyster reef restoration. Journal of Shellfish Research.
 Coen LT, Humphries AT (in press) Bivalve-generated marine habitats: their value and related monitoring, restoration, and enhancement efforts. In S Stuart and S Murphy (Ed.) Routledge Handbook of Ecological and Environmental Restoration. Routledge, Oxon.
 Oczkowski AJ, Gumbley T, Carter BJ, Carmichael RH, Humphries AT. (2016) Establishing an anthropogenic nitrogen baseline using Native American shell middens. Frontiers in Marine Science 3:79. [doi] [art]
 Humphries AT, Ayvazian SG, Carey J, Hancock BT, Grabbert S, Cobb D, Strobel CJ and Fulweiler RW (2016) Directly measured denitrification reveals oyster aquaculture and restored oyster reefs remove nitrogen at comparable high rates. Frontiers in Marine Science 3:74. [doi]
 Humphries AT, McQuaid CD, McClanahan TR (2015) Context-dependent diversity-effects of seaweed consumption on coral reefs in Kenya. PLoS ONE 10(12):e0144204. [doi]
 La Peyre MK, Serra KT, Joyner TA, Humphries AT (2015) Assessing shoreline exposure and oyster habitat suitability maximizes potential success for restored oyster reefs. PeerJ 3:e1317. [doi]
 Humphries AT, La Peyre MK (2015) Oyster reef restoration supports increased nekton biomass and potential commercial fishery value. PeerJ 3:e1111. [doi]
 Humphries AT, McClanahan TR, McQuaid CD (2014) Differential impacts of coral reef herbivores on algal succession in Kenya. Marine Ecology Progress Series 504:119-132. [pdf]
 La Peyre MK, Humphries AT, Casas SM, La Peyre JL (2014) Temporal variation in the development of ecosystem services from oyster reef restoration. Ecological Engineering 63:34-44. [pdf]
 Cinner JE, Huchery C, Darling ES, Humphries AT, Graham NAJ, Hicks CC, Marshall N, McClanahan TR (2013) Evaluating social and ecological vulnerability of coral reef fisheries to climate change. PLoS ONE 8(9):e74321. [doi]
 Cinner JE, McClanahan TR, Wamukota A, Darling ES, Humphries AT, Hicks CC, Huchery C, Marshall N, Hempson T, Graham NAJ, Bodin O, Daw T, Allison E (2013) Social-ecological vulnerability of coral reef fisheries to climate shocks. FAO Fisheries and Aquaculture Circular No. 1082. Rome, FAO. 64 pp. [doi]
 McClanahan TR, Humphries AT (2012) Differential and slow life history responses of fishes to coral reef closures. Marine Ecology Progress Series 469:121-131. [pdf]
 Quan WM, Humphries AT, Shi LY, Chen YQ (2012) Oyster and benthic macrofaunal development on a restored oyster reef in the Yangtze River estuary, China. Journal of Shellfish Research 31(3):1-12. [pdf]
 Quan WM, Humphries AT, Shi LY, Chen YQ (2012) Trophic transfer at a restored intertidal oyster reef in the Yangtze River estuary using stable isotope analysis. Estuaries and Coasts 35(1):109-120. [pdf]
 Humphries AT, La Peyre MK, Decossas GA (2011) The effect of structural complexity, prey density, and predator-free space on prey survivorship at oyster reef mesocosms. PLoS ONE 6(12):e28339. [doi]
 Humphries AT, La Peyre MK, Kimball ME, Rozas LP (2011) Testing the effect of habitat structure and complexity on nekton assemblages using experimental oyster reefs. Journal of Experimental Marine Biology and Ecology 409(1):172-179. [pdf]