Frid, A., L.M. Dill, R.E. Thorne, and G.M. Blundell. 2007. Inferring Prey Perception of Relative Danger in Large-Scale Marine Systems. Evolutionary Ecology Research 9(4):635-649.

Kline, T.K., C.A. Woody, M.A. Bishop, S.P. Powers, and E.E. Knudsen. 2007. Assessment of Marine-Derived Nutrients in the Copper River Delta, Alaska, Using Natural Abundance of the Stable Isotopes of Nitrogen, Sulfur, and Carbon. In: C.A. Woody, editor. Sockeye salmon evolution, ecology and management. American Fisheries Society Symposium 54, Bethesda, MD. p 51-72.

Powers, S.P., M.A. Bishop, S. Moffitt, and G.H. Reeves. 2007. Variability in Freshwater, Estuarine and Marine Residence of Sockeye Salmon (Oncorhynchus nerka) within the Copper and Bering River Deltas, Alaska. In: C.A. Woody, editor. Sockeye salmon evolution, ecology and management. American Fisheries Society Symposium 54, Bethesda, MD. p 87-99.

Thorne, R.E. 2007. When endangered species collide: Ecosystem restoration in Prince William Sound, Alaska. Proceedings Ocean ’07, Aberdeen, Scotland, June 18-21, 2007. IEEE Publications.

Williams, T.D., N. Warnock, J. Y. Takekawa, and M.A. Bishop. 2007. Flyway Scale Variation in Plasma Triglyceride Levels as an Index of Refueling Rate in Spring-Migrating Western Sandpipers (Calidris mauri). Auk 124(3):886-897.

Bishop, M. A., N. Warnock, and J. Y. Takekawa. 2006. Spring Migration Patterns in Western Sandpipers (Calidris mauri). In: G.C. Boere, C.A. Galbraith, and D.A. Stroud, editors. Waterbirds around the world. Edinburgh, U.K: The Stationery Office. p 545-550.

Powers, S.P., M.A. Bishop, J.H. Grabowski, and C.H. Peterson. 2006. Distribution of the invasive bivalve Mya arenaria L. on intertidal flats of southcentral Alaska. Journal of Sea Research 55:207-216.

Thorne, R.E. and G.L. Thomas. 2006. Herring and Oil Don't Mix: A lesson from the Exxon Valdez Oil Spill. Proceedings Ocean ’06, Boston, MA, Sept 18-21, 2006. IEEE Publications.

Thorne, R.E., G.L. Thomas and M.A. Bishop. 2006. Alternative seafood waste disposal procedure for Alaskan waters. Proceedings Ocean ‘06 Boston, MA, Sept 18-21, 2006. IEEE Publications.

Bishop, M.A. and D. Tsamchu. 2005. History and Influence of a Nature Reserve On a Local Population of Wintering Black-necked Cranes in Tibet. In: Wang Qishan and Li Fengshan, editors. Crane Research in China. Kunming: Yunnan Education Publishing House p 155-160.

Churnside, J.H. and R.E. Thorne. 2005. Comparison of airborne lidar measurements with 420 kHz echos-sounder measurements of zooplankton. Applied Optics 44(26):5504-5511.

Thorne, R.E. 2005. Monitoring Pacific herring abundance with combined acoustic and optical technologies. Proceedings Ocean ‘05, Washington D.C., Sept 19-23, 2005.

Thorne, R.E. 2005. Effectively addressing ecosystem understanding: solutions to the limitations of current fisheries and oceans policy. Proceedings Ocean ‘05, Washington D.C., Sept 19-23, 2005.

Thorne, R.E. 2005. Acoustic monitoring of the juvenile pink salmon food supply and predators in Prince William Sound, Alaska. Proceedings Ocean ‘05, Washington D.C., Sept 19-23, 2005.

Tsamchu, D. and Bishop, M.A. 2005. Population and habitat use by Black-necked Cranes wintering in Tibet. In: Wang Qishan and Li Fengshan, editors. Crane Research in China. Kunming: Yunnan Education Publishing House. p 44-48.

Bishop, M.A., N. Warnock, and J. Takekawa. 2004. Differential spring migration of male and female Western Sandpipers at interior and coastal stopover sites. Ardea 92:185-196.

Johnson, O.W., D. Adler, L.A. Ayres, M.A. Bishop, J.E. Doster, P.M. Johnson, R.J. Kienholz, and S.E. Savage. 2004. Radio-tagged Pacific Golden-Plovers: Further insight concerning the Hawaii-Alaska migratory link. Wilson Bulletin 116:158-162.

Thorne, R.E. 2004. Acoustic Surveying of Pelagic Fish in Shallow Water. IGARSS04 (Electronic). IEEE Publications, Escondido, CA. 4 p.

Thorne, R.E. 2004. Factors Governing Pink Salmon Survival in Prince William Sound, Alaska. In: V. Keong, editor. Proceedings of the 21st Northeast Pink and Chum Salmon Workshop, Victoria, B.C. Feb 26-28, 2004. Pacific Salmon Commission, Vancouver, B.C. p 67-72.

Warnock, N., J.Y. Takekawa, and M.A. Bishop. 2004. Migration and stopover strategies of individual Dunlin along the Pacific Flyway. Canadian Journal Zoology 82:1687-1697.

Kline, T.C. Jr. 2003. Implications of trophic level when assessing the role of salmon-derived nutrients for lacustrine juvenile sockeye ecology using the natural abundance of 15N/14N. In: J. Stockner, editor. Nutrients in salmonid ecosystems: sustaining production and biodiversity. American Fisheries Society Symposium 34, Bethasda, Maryland. p 229-236.

Thomas, G.L. and R.E. Thorne. 2003. Acoustical-optical assessment of pacific herring and their predator assemblage in Prince William Sound, Alaska. Aquatic Livings Resources 16:247-253.

Thorne, R.E. and G.L. Thomas. 2003. Application of combined optical and acoustic technologies for fisheries and marine mammal research in Prince William Sound and Kodiak, Alaska. Proceedings Ocean ’03, Escondido, CA: Holland Publications. MTS/IEEE (Electronic).

Bishop, M.A. and Fengshan Li. 2002. Effects of farming practices in Tibet on wintering Black-necked Crane (Grus nigricollis) diet and food availability. Biodiversity Science 10:393-398 (in Chinese).

Bishop, M.A. 2002. Great possessions: Leopold's good oak. In: R.L. Knight and S. Reidel, editors. Aldo Leopold and the Ecological Conscience. New York: Oxford University Press. p 72-87.

Kline, T.C. Jr. 2002. Implications of Trophic Level when Assessing the Role of Salmon-Derived Nutrients for Lacustrine Juvenile Sockeye Ecology using the Natural Abundance of 15N/14N. In: J. Stockner, editor. Restoring Nutrients to Salmonid Ecosystems. American Fisheries Society, Bethesda, Maryland.

Kline, T.C. Jr. 2002. The relative trophic position of Cancer magister Megalopae within the planktonic community of the sub-polar northeastern Pacific Ocean. In: A.J. Paul, E.G. Dawe, R. Elner, G.S. Jamieson, G.H. Kruse, R.S. Otto, B. Sainte-Marie, T.C. Shirley and D. Woodby, editors. Crabs in cold water regions: Biology, management and economics. University of Alaska Sea Grant, Fairbanks, AK. AK-SG-02-01, p. 645-649.

Kline, T.C. Jr. and T.M. Willette. 2002. Pacific salmon (Oncorhynchus) early marine feeding patterns based on 15N/14N and 13C/12C in Prince William Sound, Alaska. Can. J. Fish. Aquat. Sci. 59: 1626–1638.

Powers, S.P., M.A. Bishop, J.H. Grabowski, and C.H. Peterson. 2002. Intertidal benthic resources of the Copper River Delta, Alaska, USA. Journal of Sea Research 47:13-23.

Thomas, G.L. and R.E. Thorne. 2002. Ex-situ target strength measurements of Pacific herring and Pacific sandlance. North American Journal of Fisheries Management 22:1136-1145.

Bishop, M.A. and S.P. Green. 2001. Predation on Pacific herring (Clupea pallasi) spawn by birds in Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):149-158.

Cooney, R.T., J.R. Allen, M.A. Bishop, D.L. Eslinger, T. Kline,B.L. Norcross, C.P. McRoy, J. Milton, J. Olsen, E.V. Patrick, A.J. Paul, D. Salmon, D. Scheel, G.L. Thomas, S.L. Vaughan, and T.M. Willette. 2001. Ecosystem controls of juvenile pink salmon (Onchorynchus gorbuscha) and Pacific herring (Clupea pallasi) populations in Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):1-13.

Eslinger, D.L., R.T. Cooney, C.P. McRoy, A. Ward, T.C. Kline Jr., E.P. Simpson, J. Wang and J.R. Allen. 2001. Plankton dynamics: observed and modeled responses to physical conditions in Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):81-96.

Gay III, S.M. and S.L. Vaughan. 2001. Seasonal hydrography and tidal currents of bays and fjords in Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):159-193.

Kline, T.C. Jr. 2001. The trophic position of Pacific herring in Prince William Sound, Alaska based on their stable isotope abundance. In: F. Funk, J. Blakkburn, D. Hay, A.J. Paul, R. Stephenson, R. Toresen and D. Witherell, editors. Herring: Expectations for a New Millenium. University of Alaska Sea Grant, Fairbanks, AK. AK-SG-01-04. p. 69-80.

Kline, T.C. Jr. 2001. Evidence of biophysical coupling from shifts in natural stable carbon and nitrogen isotopes in Prince William Sound, Alaska. In: Kruse, G.H., N. Bez, T. Booth, M. Dorn, S. Hills, R. Lipcius, D. Pelletier, C. Roy, S.J. Smith and D. Witherell, editors. Spatial processes and management of marine populations. University of Alaska Sea Grant, Fairbanks, AK. AK-SG-01-02. p 363-375.

Norcross, B.L., E.D. Brown, R.J. Foy, M. Frandsen, S.M. Gay III, T.C. Kline Jr., D.M. Mason, E.V. Patrick, A.J. Paul and K.D.E. Stokesbury. 2001. A synthesis of the life history and ecology of juvenile Pacific herring in Prince William Sound, Alaska. Fisheries Oceanography 10, (Suppl. 1):42-57.

Paul, A.J., J.M. Paul and T.C. Kline, Jr. 2001. Estimating whole body energy content for juvenile Pacific herring from condition factor, dry weight, and carbon/nitrogen ratio. In: F. Funk, J. Blakkburn, D. Hay, A.J. Paul, R. Stephenson, R. Toresen and D. Witherell, editors. Herring: Expectations for a New Millenium. University of Alaska Sea Grant, Fairbanks, AK. AK-SG-01-04. p 121-133.

Thomas, G.L. and R.E. Thorne. 2001. Night-time predation by Steller sea lions: new insight into the feeding habits of these mammals will help conservation attempts. Nature 411:1013.

Vaughan, S.L., C.N.K. Mooers, and S.M. Gay III. 2001. Physical variability in Prince William Sound during the SEA study (1994-1998). Fisheries Oceanography 10 (Suppl. 1):58-80.

Wang, J., M. Jin, E.V. Patrick, J.R. Allen, D.L. Eslinger, C.N.K. Mooers and R.T. Cooney. 2001. Numerical simulations of the seasonal circulation patterns and thermohaline structures of Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):132-148.

Willette, T.M., R.T. Cooney, E.V. Patrick, D.M. Mason, G.L. Thomas and D. Scheel. 2001. Ecological processes influencing mortality of juvenile pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Fisheries Oceanography 10 (Suppl. 1):14-41.

Bishop, M.A., P. Meyers, and P.F. McNeley. 2000. A method to estimate shorebird numbers on the Copper River Delta, Alaska. Journal Field Ornithology 71(4): 627-637.

Bishop, M.A., J. Harris, and Z. Canjue. 2000. Agricultural management zones for Bar-headed Geese and Black-necked Cranes in Tibet. In: Wu Ning, D. Miller, Lu Zhi and J. Springer, editors. Tibet's Biodiversity Conservation and Management. China Forestry Publishing House, Bejing.

Kirsch, Jay, G.L. Thomas and R.T. Cooney. 2000. Acoustic estimates of zooplankton distributions in Prince William Sound, spring 1996. Fisheries Research. 47 (2000) 245-260.

McClatchie, S., R. Thorne, P. Grimes and S. Hanchet. 2000. Ground truth and target identification for fisheries acoustics. Fisheries Research 47:173-191.

Stokesbury, Kevin D.E., Jay Kirsch, Evelyn D. Brown, Gary L. Thomas and Brenda L. Norcross. 2000. Spatial distributions of Pacific herring, Clupea pallasi, and walleye pollock, Theragra chalcogramma, in Prince William Sound, Alaska. Fisheries Bulletin, 98:400-409.

Thomas, G.L. and Jay Kirsch. (Guest Editors) 2000. Nekton and Plankton Acoustics: An Overview. Fisheries Research 47 (2000) 107-113.

Thomas, G.L. and Walter Cox. 2000. A Nowcast-Forecast Information System for PWS. Proceedings of the 23rd Arctic and Marine Oil Spill Program (AMOP) Technical Seminar June 14-16, 2000. Environment Canada, Vancouver, British Columbia. Volume 1, 247-255.

Brown, E.D., J. Wang, S.L. Vaughan and B.L. Norcross. 1999. Identifying seasonal spatial scale for the ecological analysis of herring and other forage fish in Prince William Sound, Alaska. Proceedings of the Symposium on Ecosystem Considerations in Fisheries Management. AK-SG-99-01, Fairbanks, Alaska. Alaska Sea Grant College Program. Lowell Wakefield Fisheries Symposium.

Dodge, R. and D. Scheel. 1999. Remains of the prey: recognizing the middens of Octopus dofleini. The Veliger. 42(3):260-266.

Kline, T.C., Jr. 1999. Temporal and spatial variability of 13C/12C and 15N/14N in pelagic biota of Prince William Sound, Alaska. Canadian Journal of Fisheries and Aquatic Sciences. Vol. 56, Suppl. 1, pg. 94-117.

Kline, T.C., Jr. and Ralph A. Lewin. 1999. Natural 15N/14N Abundance as Evidence for N2 Fixation by Prochloron (Prochlorophyta) Endosymbiotic with Didemnid Ascidians. Symbiosis, 26: 193-198.

Wang, J., V. Patrick, J.R. Allen, S.L. Vaughan, C.N.K. Mooers and M. Jin. 1999. Modeling seasonal ocean circulation of Prince William Sound, Alaska using freshwater of a line source. Brebbia, C.A. and Anagnostopoulos, P. Fourth International Conference on Computer Modeling of Seas and Coastal Regions Coastal Engineering 99 Incorporating the International Seminar on Marina Planning Design and Operation Marina 99. 57-66. 99. Coastal Engineering and Marina Developments.

Kline, T.C. Jr. and D. Pauly. 1998. Cross-validation of trophic level estimates from a mass-balance model of Prince William Sound using 15N/14N data. In: Funk, F., T.J. Quinn II, J. Heifetz, J.N. Ianelli, J.E. Powers, J.F. Schweigert, P.J. Sullivan, and C.I. Zhang (eds.), Fishery Stock Assessment Models. University of Alaska Sea Grant, AK-SG-98-01. Fairbanks, Alaska. p. 693-702.

Kline, T.C. Jr., William J. Wilson and John J. Goering. 1998. Natural isotope indicators of fish migration at Prudhoe Bay, Alaska. Canadian Journal of Fisheries and Aquatic Sciences, Vol. 55: 1494-1502.

Thorne, Richard E. 1998. Review: experiences with shallow water acoustics. Fisheries Research 35:137-141, Elsevier Science, Amsterdam.

Vincent, T.L.S., D. Scheel, K. Hough. 1998. Some aspects of diet and foraging behavior of Octopus dofleini in its northernmost range. Marine Ecology, 19(1): 13-29.

Kline, T.C. Jr., J.J. Goering, and R. Piorkowski. 1997. The effect of salmon carcasses on freshwater systems. In: A. Milner and M. Oswood (eds.), Alaskan Freshwaters of Alaska, Ecological Synthesis. Ecological Studies 119179-204, Springer-Verlag. New York.

Scheel, D. and K.R. Hough. 1997. Salmon fry predation by seabirds near an Alaskan hatchery. Marine Ecology Progress Series, Vol. 150:35-48.

Thomas, G. L., E. V. Patrick, J. Kirsch, and J. R. Allen. 1997. Development of a multi-species model for managing the fisheries resources of Prince William Sound. In D.A. Hancock, D.C. Smith, A. Grant, and J.P. Beumer [eds.], Developing and Sustaining World Fisheries Resources – the State of Science and Management. 2nd World Fisheries Congress. CSIRO Publishing, Collingwood, Australia. Pages 606-613.

Vaughan, S. L. and R. L. Molinari, 1997: Temperature and Salinity Variability in the Deep Western Boundary Current. J. Phys. Oceanog., 27(5) 749-761.

Wang, J. Christopher N.K. Mooers and E. Vincent Patrick. 1997. A three-dimensional tidal model for Prince William Sound, Alaska. Computer Modeling of Seas and Coastal Regions III (eds. J.R. Acinas and C.A. Brebbia), Computational Mechanics Publications, Southampton. Pages 95-104.

Beauchamp, D.A., M.G. LaRiviere and G.L. Thomas. 1995. An evaluation of competition and predation as limits to juvenile kokanee and sockeye production in Lake Ozette, Washington. North American Journal of Fisheries Management. 15(1):193-207.

Vaughan, Shari L. and Kevin D. Leaman. 1995. The role of small-scale cells in the Mediterranean convection process. Journal of Physical Oceanography. 25(10) 2423-2436.

Bodnar, S.A., G.L. Thomas, Steven L. Thiesfeld, Gilbert B. Pauley and T. Brock Stables. 1993. Effect of triploid white amur (Ctenopharyngodon idella) on the qautic macrophyte community of Devils Lake, Oregon. North American Journal of Fisheries Management. 13:757-765.

Kline, T.C. Jr., J.J. Goering, O.A. Mathisen, P.H. Poe, P.L. Parker and R.S. Scalan. 1993. Recyling of elements transported upstream by runs of Pacific salmon: II. ?15N and ?13C evidence in the Kvichak River watershed, southwestern Alaska. Canadian Journal of Fisheries and Aquatic Sciences 50:2350-2360.

Thomas, G.L. and Ole Mathisen. 1993. Biological interactions between enhanced and wild salmon in Alaska. Fisheries Research. 18(1-2):1-17.

Beauchamp, D.A., Sharron Vecht, and G.L. Thomas. 1992. Distribution and feeding of Cutthroat Trout (Oncorhynchus clarkii) in Lake Washington. Northwest Science. 66(3):149-159.

Crittenden, Robert and G.L. Thomas. 1992. The importance of statistical analysis to determining the accuracy and precision of acoustical estimates of fish abundance. Fisheries Research. 14:197-208.

Stables, Brock and G.L. Thomas. 1992. Acoustic measurement of trout distributions in Spada Lake, Washington, using stationary transducers. Journal of Fish Biology. 40:191-203.

Thomas, G.L. 1992. Successes and failures of fisheries acoustics – An international, national and regional perspective. Fisheries Research. 14:95-105.

Washington, Percy, G.L. Thomas and David A. Marino. 1992. Successes and failures of fisheries acoustics in the evaluation of environmental impact. Fisheries Research. 14:239-250.

Kline, T.C. Jr., J.J. Goering, O.A. Mathisen, P.H. Poe, and P.L. Parker. 1990. Recyling of elements transported upstream by runs of Pacific salmon: I. ?15N and ?13C evidence in the Sashin Creek, southeastern Alaska. Canadian Journal of Fisheries and Aquatic Sciences 47:136-144.

Thorne, Richard E. and G.L. Thomas. 1990. Acoustic observation of gas bubble release by Pacific herring. Canadian Journal of Fisheries & Aquatic Sciences 47(10):1920-1928.