• Moore, K.D., and J.W. Moore. In press. Ecological restoration and enabling behavior: a new metaphoric lens? Conservation Letters (pdf)
• Heady, W.N., and J.W. Moore. In press. Tissue turnover and stable isotope clocks to quantify resource shifts in anadromous rainbow trout. Oecologia (pdf)
• Beakes, M.P., J.W. Moore, N. Retford, R. Brown, J.E. Merz, and S.M. Sogard. In press. Evaluating statistical approaches to quantifying juvenile Chinook salmon habitat in a regulated California River. River Research and Applications (pdf)
• Moore, J.W., S.M. Carlson, L.A. Twardochleb, J.L. Hwan, J.M. Fox, and S.A. Hayes. 2012. Trophic tangles through time? Opposing direct and indirect effects of an invasive omnivore on stream ecosystem processes. PLoS ONE 7: e50687. (pdf)
• Frechette, D., A.-M. Osterback, S.A. hayes, M.H. Bond, J.W. Moore, J.A. Shaffer, and J.T. Harvey. 2012. Assessing avian predation on juvenile salmonids using Passive Integrated Transponder Tag recoveries and mark-recapture methods. North American Journal of Fisheries Management 32: 1237-1250. (pdf)
• Moore, J.W., D.B. Herbst, W.N. Heady, and S.M. Carlson. 2012. Stream community and ecosystem responses to the boom and bust of an invading snail. Biological Invasions 14: 2435-2446. (pdf)
• Twardochleb, L.A., M. Novak, and J.W. Moore. 2012. Using the functional response of a consumer to predict biotic resistance to invasive prey. Ecological Applications 22: 1162-1171. (pdf)
• Moore, J.W., S.A. Hayes, W. Duffy, S. Gallagher, C.J. Michel, and D. Wright. 2011. Nutrient fluxes and the recent collapse of coastal California salmon populations. Canadian Journal of Fisheries and Aquatic Sciences 68: 1161-1170. (pdf)
• Novak, M., J.W. Moore, and R.A. Leidy. 2011. Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation-based approach. Global Change Biology 17: 3714-3724. (pdf)
• Yeakel, J.D., M. Novak, P.R. Guimaraes Jr., N.J. Dominy, P.L. Koch, E.J. Ward, J.W. Moore, and B.X. Semmens. 2011. Merging resource availability with isotope mixing models: the role of neutral interaction assumptions. PLoS ONE 6:e22015. (pdf)
• Ward, E.J., B.X. Semmens, D.L. Phillips, J.W. Moore, and N. Bouwees. 2011. A quantitative approach to combine sources in stable isotope mixing models. Ecosphere 2:art19. doi:10.1890/ES10-00190.1. (pdf)
• Moore, J.W., M. McClure, L.A. Rogers, and D.E. Schindler. 2010. Synchronization and portfolio performance of threatened salmon. Conservation Letters 3: 340-348. (pdf)
• Flecker, A.S., P.B. McIntyre, J.W. Moore, J.T. Anderson, B.W. Taylor, and R.O. Hall, Jr. 2010. Migratory fishes as material and process subsidies in riverine ecosystems. American Fisheries Society Symposium 73: 559-592. (pdf)
• Moore, J.W., and D.E. Schindler. 2010. Spawning salmon and the phenology of emergence in stream insects. Proceedings of the Royal Society B 277: 1695-1703. (pdf)
• Denton, K.P., H.B. Rich Jr., J.W. Moore, and T.P. Quinn. 2010. The utilization of a Pacific salmon Oncorhynchus nerka subsidy by three populations of charr Salvelinus spp. Journal of Fish Biology 77: 1006-1023. (pdf)
• Yeakel, J.D., B.D. Patterson, K. Fox-Dobbs, M.M. Okumura, T.E. Cerling, J.W. Moore, P.L. Koch, and N.J. Dominy. 2009. Cooperation and individuality among man-eating lions. Proceedings of the National Academy of Sciences 106: 19040-19043. (pdf)
• Semmens, B.X., E.J. Ward, J.W. Moore, and C.T. Darimont. 2009. Quantifying inter- and intra-population niche variability using hierarchical Bayesian stable isotope mixing models. PLoS ONE 4: e6187. (pdf).
• Zavaleta, E., J. Pasari, J.W. Moore, D. Hernandez, K.B. Suttle, and C.C. Wilmers. 2009. Ecosystems responses to community disassembly. The Year in Ecology and Conservation Biology 1162: 311-333. (pdf).
• Semmens, B.X., and J.W. Moore. 2009. Improving Bayesian isotope mixing models: a response to Jackson et al. (2009). Ecology Letters 12: E6-E8. (pdf).
• Moore, J.W., and B.X. Semmens**. 2008. Incorporating uncertainty and prior information in stable isotope mixing models. Ecology Letters. (pdf).
• Moore, J.W., and D.E. Schindler. 2008. Biotic disturbance and community dynamics in salmon-bearing streams. Journal of Animal Ecology 77: 275-284. (pdf).
• Moore, J.W., D.E. Schindler, and C.P. Ruff*. 2008. Habitat saturation drives thresholds in stream subsidies. Ecology 89: 306-312. (pdf).
• Moore, J.W., D.E. Schindler, J.L. Carter*, J.M. Fox*, J. Griffiths*, and G.W. Holtgrieve. 2007. Biotic control of stream ecosystem fluxes: spawning salmon drive nutrient and matter export. Ecology 88: 1278-1291. (pdf).
• Scheuerell, M.D., J.W. Moore, D.E. Schindler, C.J. Harvey. 2007. Varying effects of anadromous salmon on the trophic ecology of resident stream fishes in Alaska. Freshwater Biology 52: 1944-1956. (pdf).
• Moore, J.W. 2006. Animal ecosystem engineers of streams. BioScience 56: 237-246. (pdf).
• Francis, T.B., D.E. Schindler, and J.W. Moore. 2006. Aquatic insects play a minor role in dispersing salmon-derived nutrients into riparian forests in southwestern Alaska. Canadian Journal of Fisheries and Aquatic Sciences 63: 2543-2552. (pdf).
• Brock, C.P., P.R. Leavitt, D.E. Schindler, S.P. Johnson, J.W. Moore, and P.D. Quay. 2006. Spatial variability of stable isotopes and fossil pigments in surface sediments of Alaskan coastal lakes: constraints on quantitative estimates of past salmon abundance. Limnology and Oceanography 51: 1637-1647. (pdf).
• Payne, L.X., and J.W. Moore. 2006. Mobile scavengers create hotspots of biological productivity in freshwater ecosystems. Oikos 115: 69-80. (pdf).
• Winder, M., D.E. Schindler, J.W. Moore, S.P. Johnson, and W.J. Palen. 2005. Do bears facilitate transfer of salmon resources to aquatic macroinvertebrates? Canadian Journal of Fisheries and Aquatic Sciences 62: 2285-2293. (pdf).
• Moore, J.W., D.E. Schindler, and M.D. Scheuerell. 2004. Disturbance by spawning salmon of Alaskan stream and lake ecosystems. Oecologia 139: 298-308. (pdf).
• Moore, J.W., J.L. Ruesink, and K.A. McDonald. 2004. Impact of supply-side ecology on consumer-mediated coexistence. The American Naturalist 163: 480-487. (pdf).
• Moore, J.W., and D.E. Schindler. 2004. Nutrient export from freshwater systems by anadromous sockeye salmon. Canadian Journal of Fisheries and Aquatic Sciences 61: 1582-1589. (pdf).
• Moore, J.W., and J.L. Kenagy. 2004. Consumption of shrews, Sorex spp., by Arctic Grayling, Thymallus arcticus. Canadian Field-Naturalist 118: 111-114. (pdf).
• Schindler, D.E., M.D. Scheuerell, J.W. Moore, S.M. Gende, T.B. Francis, and W.J. Palen. 2003. Pacific salmon and the ecology of coastal ecosystems. Frontiers in Ecology and the Environment 1: 31-37. (pdf).
• Moore, J.W., D.E. Schindler, M.D. Scheuerell, J. Frodge, and D. Smith*. 2003. Lake eutrophication at the urban fringe: the Seattle region. Ambio 32: 13-18. (pdf).

*undergraduate at time of research
**shared first authorship