Collie, J.S., L.W. Botsford, A. Hastings, I.C. Kaplan, J.L. Largier, P.A. Livingston, E. Plagányi, K.A. Rose, B.K. Wells, F.E. Werner. 2014. Ecosystem models for fisheries management: finding the sweet spot. Fish and Fisheries, doi: 10.1111/faf.1209
Collie, J.S., C. Minto, B. Worm, and R. Bell. 2013. “Prerecruit predation can delay rebuilding of depleted cod stocks.” Bull. Mar. Sci. 89:107-122.
Collie, J.S., M.J. Rochet, and R. Bell. 2013. “Rebuilding fish communities: the ghost of fisheries past and the virtue of patience.” Ecological Applications 23:374-391.
Smith, B., J.S. Collie, and N.L. Lengyel. 2013. “Effects of chronic bottom fishing on the benthic epifauna and diets of demersal fish on northern Georges Bank.” Marine Ecology Progress Series 472:199-217.
Rochet, M.J., J.S. Collie, and V.M. Trenkel. 2013. “How do fishing and environmental effects propagate among and within functional groups?” Bulletin of Marine Science 89:285-315.
Collie, J.S., W.L. Adamowicz, M.W. Beck, B. Craig, T.E. Essington, D. Fluharty, J. Rice, and J.N. Sanchirico. 2013. “Marine spatial planning in practice.” Estuarine, Coastal and Shelf Science 117:1-11 (Invited feature).
Curti, K.L., J.S. Collie, C. Legault, and J.S. Link. 2013. “Evaluating the performance of a multispecies statistical catch-at-age model.” Canadian Journal of Fisheries and Aquatic Sciences 70(3):470-484.
J.S. Collie, R.M. Peterman, and B.M. Zuehlke. 2012. “A fisheries risk-assessment framework to evaluate trade-offs among management options in the presence of time-varying productivity.” Can. J. Fish. Aquat. Sci. 69:209-223.
Van Kirk, K., Quinn, T.J., Collie, J., and T. A’mar. 2012. “Multispecies age-structured assessment for groundfish and sea lions in Alaska.” In: G.H. Kruse, H.I. Browman, K.L. Cochrane, D. Evans, G.S. Jamieson, P.A. Livingston, D. Woodby, and C.I. Zhang (eds.), Global Progress in Ecosystem-Based Fisheries Management. Alaska Sea Grant, University of Alaska Fairbanks.
Bell, R.J., J.S. Collie, D. Jamu and M. Banda. 2012. “Changes in the biomass of chambo in the southeast arm of Lake Malawi: a stock assessment of Oceochromis spp.” Journal of Great Lakes Research 38:720-729.
Rochet, M.J., J.S. Collie, S. Jennings, and S.J. Hall. 2011. “Does selective fishing conserve community biodiversity? Predictions from a length-based multispecies model.” Canadian Journal of Fisheries and Aquatic Sciences 68:469-486.
Steele, J.H., Gifford, D.J., Collie, J.S. 2011. “Comparing species and ecosystem-based estimates of fisheries yields.” Fisheries Research 111, 139-144.
Collie, J.S. 2011. “What does ‘sustainable’ seafood mean?’ 41°N, Rhode Island’s Ocean and Coastal Magazine 6(2):22.
Fogarty, M.J., J.S. Collie. 2009. “Fisheries Overview.” P. 499-504, In Encyclopedia of ocean sciences. Edited by J. Steele, S. Thorpe, and K Turekian. Elsevier. 2010
Van Kirk, K.F., T.J. Quinn, and J.S. Collie. 2010. “A multispecies age-structured assessment model for the Gulf of Alaska.” Canadian Journal of Fisheries and Aquatic Sciencies 67:1135-1148.
Collie, J.S. and M.J. Rochet. Temporal changes in the diversity of shelf-se fish communities. ICES CM 2010/Q:03
Buckley, L., J.S. Collie, L.A.E. Kaplan, and J. Crivello. 2008. Winter flounder larval genetic population structure in Narragansett Bay, RI: Recruitment to juvenile young-of-the-year. Estuaries and Coasts 31:745–754. DOI 10.1007/s12237-008-9065-4.
Collie, J.S., D.J. Gifford, and J.H. Steele. 2009. “End-to-end food-web control of fish production on Georges Bank.” ICES J. Mar. Sci. 66:2223-2232.
Collie, J.S., J.M. Hermsen, and P.C. Valentine. 2009. “Recolonization of gravel habitats on Georges Bank (northwest Atlantic).” Deep-Sea Research II. 56:1846-1855. doi:10.1016/j.dsr2.2009.05.025.
Worm, B.R., Hilborn, J. Baum, T. Branch, J.S. Collie, C. Costello, M. Fogarty, E. Fulton, J. Hutchings, S. Jennings, O. Jensen, H. Lotze, P. Mace, T. McClanahan, C. Minto, S. Palumbi, A. Parma, D. Ricard, A. Rosenberg, R. Watson, D. Zeller. 2009. “Rebuilding global fisheries.” Science 325:578-585.
Gifford, D.J., J.S. Collie, and J.H. Steele. 2009. “Functional diversity in a marine fish community.” ICES Journal of Marine Science 66:791-796.
Wood, A.J., J.S. Collie, and J.A. Hare. 2009. “A comparison between warm-water fish assemblages of Narragansett Bay and those of Long Island Sound waters.” Fishery Bulletin 107:89-100.
Lengyel, N.L., J.S. Collie, and P.C. Valentine. 2009. “The invasive colonial ascidian Didemnum vexillum on Georges Bank—ecological effects and genetic identification.” Aquatic Invasions 4(1):143-152.
Collie, J.S., A.D. Wood, and H.P. Jeffries. 2008. Long-term shifts in the species composition of a coastal fish community. Can. J. Fish. Aquat. Sci. 65:1352-1365.
Asch, R.G. and J.S. Collie. 2008. Changes in a benthic megafaunal community due to disturbance from bottom fishing and the establishment of a fishery closure. Fishery Bulletin 106:438-456.
Bullard, S.G., G. Lambert, M.R. Carman, J. Byrnes, R.B. Witlach, G. Ruiz, R.J. Miller, L. Harris, P.C. Valentine, J.S. Collie, J. Pederson, D.C. McNaught, A.N. Cohen, R.G. Asch, J. Dijkstac, K. Heinonen. “The colonial ascidian Didemnum sp.: Current distribution, basic biology, and potential threat to marine communities of the northeast and west coasts of the United States.” Journal of Experimental Marine Biology and Ecology 342:99-108.
Valentine, P.C., J.S. Collie, R.N. Reid, R.G. Asch, and V.G. Guida. “The occurrence of the colonial ascidian Didemnum sp. on Georges Bank gravel habitat – ecological observations and potential effects on groundfish and scallop fisheries.” J. Exp. Mar. Biol. Ecol. 342:179-181.
Steele, J.H., J.S. Collie, J. Bisagni, M. Fogarty, D. Gifford, J. Link, M. Sieracki, B. Sullivan, A. Beet, D. Mountain, E. Durbin, D. Palka, and W. Stockhausen. “Balancing end-to-end budgets of the Georges Bank ecosystem.” Progress in Oceanography 74:423-448.
Wood, A.D., J.S. Collie, and N. Kohler. “Estimating survival of the short-fin mako, Isurus oxyrinchus, in the northwest Atlantic from tag-receptive data.” Journal of Fish Biology 71:1671-1695.
Safina, C., M.A. Rosenberg, R.A. Myers, T.J. Quinn, J.S. Collie. "U.S. Ocean fish recovery: staying the course." Science (Policy Forum) 309: 707-708.
Hall, S.J., J.S. Collie, D.E. Duplisea, S. Jennings, M. Brassington, and J. Link. “A Length-based multispecies model for evaluating community responses to fishing.” Can. J. Fish. Aquat. Sci. 63:1344-1359.
Collie, J.S., J.T. Anderson, P.C. Valentine, and J. Black. “A small hotspot of benthic biodiversity on the northwest Atlantic continental shelf. ICES CM 2006/D:13.
Collie, J.S., Hermsen, J.M., Valentine, P.C, and F.P. Almeida. "Effects of fishing on gravel habitats: assessment and recovery of benthic megafauna on Georges Bank,” American Fisheries Society Symposium 41:325-343.
Steele, J.H. and J.S. Collie. "Functional diversity and stability of coastal ecosystems". Chapter 22 In: A.R. Robinson and K. Brink (eds) The Sea: Vol 13, The global coastal ocean. pp. 785-819.
Quinn, T.Q. and J.S. Collie. "Sustainability in single-species populations models," Phil. Trans. R. Soc. B. 360:147-162.
Collie, J.S., A.K. DeLong and G.H. Kruse. "Three-stage catch-survey analysis applied to blue king crabs," In: Assessment and management of new and developed species in data-limited situations. Alaska Sea Grant College Program. AK-SG. P 683-714.
Steele, J.H., S.J. Roberts, D.L. Alverson, P.Auster, J.S. Collie, et al. “National Research Council study on the effects of trawling and dredging on seafloor habitat.” American Fisheries Society Symposium 41:91-99.
Collie, J.S., K. Richardson, and J.H. Steele. "Regime shifts: can theory illuminate the mechanisms?" Progress in Oceanography 60:281-302.
DeLong, A.K. and J.S. Collie. "Defining essential fish habitat: a model-based approach." Rhode Island Sea Grant, Narragansett, RI 4 pp.
Collie, J.S., K. Richardson, J.H. Steele, and L.T. Mouritsen. "Physical forcing and ecological feedbacks in marine regime shifts" ICES C.M. 2004.M:06.
Kaiser, M.J., J.S. Collie, S.J. Hall, and I.R. Poiner. "Impacts of fishing gear on marine benthic habitats," In M. Sinclair and G. Valdimusson [eds.] Responsible Fisheries in the Marine Ecosystem. FAO and CABI Publishing. p. 197-217.
Kaiser, M.J., J.S. Collie, S.J. Hall, and I.R. Poiner. "Long-term habitat changes and their implications for future fisheries management." In G. Wefer, F. Lamy and F. Mantoura [eds.] Marine Science Frontiers for Europe. Springer, Berlin, p. 189-201.
Collie, J.S., H. Gislason, and M. Vinther. "Using AMOEBAs to display multispecies, multifleet fisheries advice." ICES J. Mar. Sci. 60:709-720.
Hermsen, J.M., J.S. Collie, and P.C. Valentine. “Mobile fishing gear reduces benthic megafaunal production of Georges Bank.” Marine Ecology Progress Series 260:197-108.
Taylor, D.L. and J.S. Collie. “A temperature and size-dependent model of sand shrimp (Crangon septemspinosa) predation on juvenile winter flounder (Pseudopleuronectes americanus)” Can. J. Fish. Aquat. Sci. 60:1133-1148.
Taylor, D.L. and J.S. Collie. Effect of temperature on the functional response and foraging behavior of the sand shrimp (Crangon septemspinosa) preying on juvenile winter flounder.” Mar. Ecol. Prog. Ser. 263:217-234.
Kaiser, M.J., J.S. Collie, S.J. Hall, S. Jennings, and I.R. Poiner. "Modification of marine habitats by trawling activities: prognosis and solutions." Fish and Fisheries 3:114-136.
National Research Council (J.S. Collie was one of 12 committee members) "Effects of trawling and dredging on seafloor habitat." National Academy Press, Washington, D.C. 126 pp.
Collie, J.S. and A.K. DeLong. "Examing the decline of Narragansett Bay winter flounder." Final report to the Rhode Island Department of Environmental Management, Division of Fish and Wildlife.
Collie, J.S. “Fisheries: multispecies dynamics,” p. 1002-1009, In Encyclopedia of ocean sciences.” Edited by J. Steele, S. Thorpe, and K. Turekian. Academic Press, London, U.K.
Tsou, T.-S. and J.S. Collie. “Estimating predation mortality in the Georges Bank fish community,” Can. J. Fish. Aquat. Sci. 58:908-922.
Tsou, T.-S. and J.S. Collie. “Predation-mediated recruitment in the Georges Bank fish community,” ICES J. Mar. Sci. 58:994-1001.
Collie, J.S. (book review), “Effects of fishing on non-target species and habitats,” Edited by M. Kaiser and de Groot. J. Fish. Biol. 58:599-600.
Collie, J.S. and A.K. DeLong. “Examining the decline of Narragansett Bay winter flounder.” Year 1 Progress report to the Rhode Island Department of Environmental Management, Division of Fish and Wildlife.
Collie, J.S. and H. Gislason. "Biological reference points for fish stocks in a multispecies context." Can. J. Fish. Aquat. Sci. 58:2167-2176.
DeLong, A.K., J.S. Collie, C.J. Meise, and J.C. Powell. "Estimating growth and mortality of juvenile winter flounder (Pseudopleuronectes americanus)with a length-based model." Canadian Journal of Fisheries and Aquatic Sciences 58:2233-2246.
Hollowed, A.B., N.J. Bax, R.J. Beamish, J.S. Collie, M.J. Fogarty, P.A. Livingston, J.G. Pope, and J.C. Rice. “Are multispecies models an improvement on single-species models for measuring the fishing impacts on marine ecosystems?” ICES J. Mar. Sci. 57:707-719.
Collie, J.S., S.J. Hall, M.J. Kaiser, and I.R. Poiner. 2000. “A quantitative analysis of fishing impacts on shelf-sea benthos.” J. Anim. Ecol. 69: 987-1001.
Collie, J.S., G.A. Escanero, and P.C. Valentine. “Photographic evolution of the impacts of bottom fishing on benthic epifauna,” ICES J. Mar. Sci. 57: 987-1001.
Collie, J.S., S. Saila, C. Walters, and S. Carpenter. “Of salmon and dams,” Science 290:933-934 (Science’s Compass).
Meise, C.M., J.S. Collie, J. Widman, and P. Howell. "Growth and mortality of juvenile winter flounder in two New England estuaries," Estuaries, 22(2):297-303.
Collie, J.S. and A.K. DeLong. “Multispecies interactions in the Georges Bank fish community.” In Ecosystem approaches for fisheries management. Alaska Sea Grant College Program, AK-SG-99-01: 187-210.
Valentine, P.C., B. Barr, J.S. Collie, P. Auster, and B. Butman. “Habitat geology in the coastal ocean: examples from the northeastern United States.” Geological Society of America Abstracts with Program, 31(7):483.
National Research Council (J.S. Collie was one of 11 committee members) “Improving Fish Stock Assessments,” National Academy Press, Washington, D.C., 177pp.
Collie, J. S. “Predator-prey interactions on the New England Continental Shelf,” p. 38-40, In Prospects for multispecies fisheries management in Chesapeake Bay. STAC Publication 98-002, Edgewater, MD.
Collie, J.S. “Studies in new England of fishing gear impacts on the sea floor,” p. 53-62, In E.M. Dorsey and J. Peterson [eds.] Effects of fishing gear on the sea floor of New England. Conservation Law Foundation, Boston, MA, 160pp.
Collie, J.S. and G.H. Kruse. "Estimating king crab (Paralithodes camtschaticus) abundance from commercial catch and research survey data," In Proceedings of the North Pacific Symposium on Invertebrate Stock Assessment and Management. Edited by G.S. Jameison and A. Campbell, Can. Spec. Publ. Fish. Aquat. Sci. 125: 73-83.
Collie, J.S., G.A. Escanero and P.C. Valentine. "Effects of bottom fishing on the benthic megafauna of Georges Bank," Mar. Ecol. Prog. Ser., 155: 159-172.
Spencer, P.D. and J.S. Collie. "The effect of nonlinear predation rates on rebuilding the Georges Bank haddock (Melanogrammus aeglefinus) stock," Can. J. Fish. Aquat. Sci., 54: 2920-2929.
Spencer, P.D. and J.S. Collie. "Patterns of population variability in marine fish stocks. Fisheries Oceanography, 6(3): 188-204.
Collie, J.S. "Ecological effects of bottom fishing on Georges Bank," At the Bay Campus 15(1):1,12.
Mace, P., L. Botsford, J.S. Collie, and eight others. "Scientific review of definitions of overfishing in U.S. fishery management plans, Supplemental report prepared for the National Marine Fisheries Service, March 1996.
Collie, J.S. "Review of the surfclam assessement," Report to the Northeast Fisheries Science Center, 8p + xviii.
Templin, W.D., J. S. Collie, and T.J. Quinn, II. "Run reconstruction of wild pink salmon stocks in Prince William Sound, 1990-1991," American Fisheries Society Symposium 18:499-508.
Collie, J.S. and T.-S. Tsou. "Multispecies virtual population analysis of the Georges Bank fish community," ICES C.M. 1996/G:28, 16p.
Zebdi, A. and J.S. Collie. "Effects of climate on herring population dynamics in the northeast Pacific Ocean," p. 277-290. In R.J. Beamish [ed.], Climate change and northern fish populations. Can. Spec. Publ. Fish. Aquatic. Sci. 121.
Collie, J.S. "Predator-prey models in marine fisheries, " Source paper for the FAO World Conference on Security of Fish Supplies, Japan, December 1995.
Collie, J.S. "Reflections on multispecies fisheries models from altitude 10,000 m," MULTSPEC-News, Institute of Marine Research, Bergen, Norway, Winter 95-96.
Spencer, P.D. and J.S. Collie. "A simple predator-prey model of exploited marine fish populations incorporating alternative prey," ICES J. Mar. Sci. 53: 615-628.
Collie, J.S. "The changing face of New England fisheries," Maritimes, 37(1): 1-3.
Collie, J.S. and P.D. Spencer. "Modeling predator-prey dynamics in a fluctuating environment," Can. J. Fish. Aquat. Sci., 51:2665-2672.
Rosenberg, A. and 14 co-authors, including J.S. Collie. "Scientific review of definitions of overfishing in U.S. fishery management plans,” NOAA Technical Memorandum NMFS-F/SPO-17, 205p.
Fritz, L.W., V.G. Wespestad and J.S. Collie. "Distribution and abundance trends of forage fishes in the Bering Sea and Gulf of Alaska." In Proceedings of the workshop, Is it food? Addressing marine mammal and sea bird declines. Alaska Sea Grant College Program Rep. No. 93-01:30-44.
Collie, J.S. and C.J. Walters. "Models that 'learn' to distinguish among alternative hypotheses," Fisheries Research, 18: 259-275.
Collie, J.S. and P.D. Spencer. "Management strategies for fish populations subject to low-frequency environmental forcing," In Proceedings of the international symposium on management strategies for exploited populations, 21-24 October 1992, in Anchorage, AK. Alaska Sea Grant College Program Rep. No. 93-02: 629-650.
Geiger, H.J., T.J. Quinn II, J.S. Collie and W.D. Templin, "Run reconstruction and life history oil-spill injury model," State/Federal Natural Resources Damage Assessment Final Report. 46p.
Collie, J.S., "Salmon population and exploitation modeling," A Report to The Alaska State Legislature, Senate Special Committee on Domestic and International Commercial Fisheries, as part of the Legislative Review of the Alaska Salmon Enhancement Program Benefit-cost Analysis. JCFOS-9208:39p.
Kruse, G.H. and J.S. Collie. 1991. "Preliminary application of a population size estimation model to the Bristol Bay Stock of red king crabs," Alaska Department of Fish and Game, Regional Information Report No. 5J91-09. 25p.
Collie, J.S. "Recruitment of Pacific herring and the hydrography of Sitka Sound," Bulletin of the School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Vol IV(1):8-9.
Collie, J.S. "Population dynamics of Pacific herring." A report to the Alaska Department of Fish and Game, Commercial Fisheries Division. JCFOS-9002:31p.
Collie, J.S. and C.J. Walters, "Adaptive management of spatially replicated groundfish populations," Can J. Fish. Aquat. Sci. 48:1273-1284.
Collie, J.S., "Herring population dynamics and management in Sitka Sound, Alaska." In Proceedings of the International Herring Symposium, Alaska Sea Grant College Program Rep. No. 91-01:463-476.
Haldorson, L. and J.S. Collie, "Distribution of Pacific herring larvae in Sitka Sound, Alaska." In Proceedings of the International Herring Symposium, Alaska Sea Grant College Program Rep. No. 91-01:115-125.
Collie, J.S., "Adaptive strategies for management of fisheries resources in large marine ecosystems," p. 225-242. In K. Sherman, L.M. Alexander and B.D. Gold (eds.) Food chains, yields, models and management of large marine ecosystems, Westview Press, Boulder, CO.
Collie, J.S., R.M. Peterman and C.J. Walters, "Experimental harvest policies for a mixed-stock fishery: Fraser River sockeye salmon (Oncorhynchus nerka)," Can. J. Fish. Aquat. Sci. 47:145-155.
Quinn, T.J. II and J.S. Collie, "Alternative population models for eastern Bering Sea pollock," Int. North Pacific Fish. Comm. Bull. 50:243-257.
Walters, C.J., J.S. Collie and T. Webb, "Experimental designs for estimating transient responses to habitat alteration: is it practical to control for environmental interactions?" In Levings, D.D., L.B. Holtby and M.A. Henderson (eds.) Proceedings of the national workshop on effects of habitat alteration on salmonid stocks. Can. Spec. Publ. Fish. Aquat. Sci. 105: 13-20.
Walters, C.J. and J.S. Collie, "A strategy for groundfish management in the face of large uncertainty about stock size and production," In Beamish, R.J. and G. A. McFarlane (eds.) Effects of ocean variability on recruitment and an evaluation of parameters used in stock assessment models. Can. Spec. Publ. Fish. Aquat. Sci. 108: 13-25.
Collie, J.S., "Food consumption by the yellowtail flounder in relation to production of its benthic prey," Mar. Ecol. Prog. Ser. 36:205-213.1988
Collie, J.S. and C.J. Walters, "Alternative recruitment models of Adams River sockeye salmon, Oncorhynchus nerka," Can. J. Fish. Aquat. Sci. 44(9):1551-1561.1988
Walters, C.J., J.S. Collie and T. Webb, "Experimental designs for estimating transient responses to management disturbances," Can. J. Fish. Aquat. Sci. 45:530-538.
Collie, J.S. (book review), Dynamics of marine fish populations, by B.J. Rothschild. In Natural Resource Modeling 2:673-677.
Collie, J.S., "Evaluation of virtual population analysis tuning procedures as applied to Atlantic bluefin tuna, "Int. Comm. for the Conserv. of Atlantic Tunas, Col. Vol. Sci. Pap. 28:203-220.
Walters, C.J. and J.S. Collie, "Is research on environmental factors useful to fisheries management?" Can. J. Fish. Aquat. Sci. 45:1848-1854.
Collie, J.S., "Food selection by yellowtail flounder (Limanda ferruginea) on Georges Bank," Can. J. Fish. Aquat. Sci. 44(2):357-367.
Walters, C.J. , T. Webb and J.S. Collie, "Experimental designs for estimating transient responses to production enhancement measures in Columbia River streams," Northwest Power Planning Council, Portland, Oregon. 27p.
Collie, J.S., "Feeding habits of the yellowtail flounder and production of its invertebrate prey on Georges Bank," Ph.D. Thesis, Woods Hole Oceanographic Institution.
Collie, J.S. and M.C. Curran, "Production and fish feeding." p. 179-228 In: Battelle and Woods Hole Oceanographic Institution, Georges Bank Benthic Infauna Monitoring Program, Vol. 2: Final report, Year three. U.S. Dept. of Interior, Minerals Management Service, Washington, D.C.
Collie, J.S., "Life history and production of three amphipod species on Georges Bank," Mar. Ecol. Prog. Ser. 22:229-238.
Collie, J.S. and M.P. Sissenwine, "Estimating population size from relative abundance data measured with error," Can. J. Fish. Aquat. Sci. 40:1871-1879