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In press
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2008
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2007
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2006
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2005
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2004
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2003
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2002
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1997
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1996
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1985
Click the links to go to documents. Click the green arrow  to see metadata.
In press
Tyson, R., C. E. Jordan, J. Hebert. In press. Modelling anguilliform swimming at intermediate Reynolds number: A review and new approach using the immersed boundary method. Computer Methods in Applied Mechanics and Engineering.
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2008
Wainwright, T. C., M. W. Chilcote, P. W. Lawson, T. E. Nickelson, C. W. Huntington, J. S. Mills, K. M. Moores, G. H. Reeves, H. A. Stout, L. A. Weitkamp. 2008. Biological recovery criteria for the Oregon Coast coho salmon evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-91, 199 p.
Waples, R. S., and C. Do. 2008. LDNE: A program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resources 8:753-756.
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2007
Andrews, K. S., P. S. Levin, S. L. Katz, D. Farrer, V. Gallucci, G. Bargmann. 2007. Acoustic monitoring of sixgill shark movements in Puget Sound: evidence for localized movement. Canadian Journal of Zoology, 85(11):1136-1143.
Brodeur, R. D., E. A. Daly, M. V. Sturdevant, T. W. Miller, J. H. Moss, M. Thiess, M. Trudel, L. A. Weitkamp, J. L. Armstrong, E. C. Norton. 2007. Regional comparisons of juvenile salmon feeding in coastal marine waters off the West Coast of North America. American Fisheries Society Symposium, 57:183-203.
Good, T. P., M. M. McClure, B. P. Sandford, K. Barnas, D. M. Marsh, B. Ryan, E. Casillas. 2007. Quantifying the effect of Caspian tern predation on endangered and threatened Pacific salmonids in the Columbia River. Endangered Species Research, 3:11-21.
Gustafson, R. G., R. S. Waples, J. M. Myers, L. A. Weitkamp, G. J. Bryant, O. W. Johnson, J. J. Hard. 2007. Pacific salmon extinctions: quantifying lost and remaining diversity. Conservation Biology, 21(4):1009-1020. (Appendix S1 | Appendix S2 | Appendix S3)
Hauser, D. D., M. G. Logsdon, E. E. Holmes, G. R. VanBlaricom, R. W. Osborne. 2007.  Summer distribution patterns of Southern resident killer whales (Orcinus orca): core areas and spatial segregation of social groups. Marine Ecology Progress Series, 351:301-310.
Holmes, E. E., J. L. Sabo, S. V. Viscido, W. Fagan. 2007. A Statistical Approach to quasi-extinction forecasting. Ecology Letters, 10:1182--1198.
Katz, S.L., Barnas, K., Hicks,. R., Cowen, J. & Jenkinson, R., 2007. Freshwater habitat restoration actions in the Pacific Northwest: A 10 year census. Restoration Ecology 15:506-515.
Lawson, P. W., E. P. Bjorkstedt, M. W. Chilcote, C. W. Huntington, J. S. Mills, K. M. Moores, T. E. Nickelson, G. H. Reeves, H. A. Stout, T. C. Wainwright, L. A. Weitkamp. 2007. Identification of historical populations of coho salmon (Oncorhynchus kisutch) in the Oregon coast evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-79, 129 p.
McMillan, J. R., S. L. Katz, G. R. Pess. 2007. Observational Evidence of Spatial and Temporal Structure in a Sympatric Anadromous (Winter Steelhead) and Resident Rainbow Trout Mating System on the Olympic Peninsula, Washington. Transactions of the American Fisheries Society, 136(3):736-748.
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2006
Fagan, W., E. E. Holmes. 2006. Quantifying the extinction vortex. Ecology Letters, 9:51-60.
Fullerton, A.H., T.J. Beechie, S.E. Baker, J.E. Hall, and K.A. Barnas. 2006.0Regional Patterns of Riparian Characteristics in the Interior Columbia River Basin, Northwestern USA: Applications for Restoration Planning. Landscape Ecology 21:1347-1360.
Gustafson, R. G., J. Drake, M. J. Ford, J. M. Myers, E. E. Holmes, R. S. Waples. 2006. Status review of Cherry Point Pacific herring (Clupea pallasii) and updated status review of the Georgia Basin Pacific herring distinct population segment under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-76, 182 p.
Jenkinson, R., K. Barnas, J. Braatne, E. S. Bernhardt, M. A. Palmer, J. D. AllanNRRSS. 2006. Stream restoration databases and case studies: A guide to information resources and their utility in advancing the science and practice of restoration. Restoration Ecology, 14:177-186.
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2005
Bernhardt, E. S., M. A. Palmer, J. D. Allan, G. Alexander, K. Barnas, S. Brooks, J. Carr, S. Clayton, C. Dahm, J. Follstad-Shah, D. Galat, S. Gloss, P. Goodwin, D. Hart, B. Hassett, R. Jenkinson, S. L. Katz, G. M. Kondolf, P. S. Lake, R. Lave, J. L. Meyer, T. K. O'Donnell, L. Pagano, B. Powell, E. Sudduth. 2005. Synthesizing U.S. river restoration efforts. Science, 308(5722):636-637.
Bilby, R. E., W. Ehinger, T. P. Quinn, G. Volkhardt, K. Krueger, D. E. Seiler, G. R. Pess, C. E. Jordan, D. Poon. 2005. Study evaluates fish response to management actions. Western Forester, 50(2):14-15.
Good, T. P., K. Barnas, D. M. Marsh, M. M. McClure, B. Ryan, B. P. Sandford, E. Casillas. 2005. Caspian Tern Predation on Juvenile Salmonid Outmigrants in the Columbia River Estuary. In Caspian Tern Management to Reduce Predation of Juvenile Salmonids in the Columbia River Estuary. U.S. Fish and Wildlife Service Migratory Birds and Habitat Programs, Portland, OR..
Holmes, E. E., W. Fagan, J. J. Rango, A. Folarin, J. A. Sorensen, J. E. Lippe, N. E. McIntyre. 2005. Cross validation of quasi-extinction risks from real time series: An examination of diffusion approximation methods. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-67, 37 p.
Roni, P., M. Liermann, C. E. Jordan, E. A. Steel. 2005. Steps for Designing a Monitoring and Evaluation Program for Aquatic Restoration. Pages 13-34 in Roni, P. (Ed.) Methods for monitoring stream and watershed restoration. American Fisheries Society, Bethesda, Maryland.
Weitkamp, L. A. 2005. Quillfish Ptilichthys goodei, filiform prey for small coho and chinook salmon. Alaska Fishery Research Bulletin, 11:61-65.
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2004
Holmes, E. E. 2004. Beyond theory to application and evaluation: diffusion approximations for population viability analysis. Ecological Applications, 14:1272-1293. (Pre-Press Word | PDF | )
Holmes, E. E., B. Semmens. 2004. Population viability analysis for metapopulations: a diffusion approximation approach. Pages 565-598 in Hanski, I., O. E. Gaggiotti. (Eds.) Ecology, Genetics, and Evolution of Metapopulations. Elsevier Press.
Sabo, J. L., E. E. Holmes, P. Kareiva. 2004. The efficacy of simple viability models in ecological risk assessment: Does density dependence matter? Ecology, 85:328-341.
Weitkamp, L. A. 2004. Ocean conditions, marine survival, and performance of juvenile chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon in Southeast Alaska. Ph.D. Thesis University of Washington, vii, 223 p.
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2003
Holmes, E. E., A. E. York. 2003. Using age structure to detect impacts on threatened populations: A case study with steller sea lions
Using age structure to detect impacts on threatened populations: A case study with steller sea lions. Conservation Biology, 17:1794-1806.
McClure, M. M., E. E. Holmes, B. L. Sanderson, C. E. Jordan. 2003. A large-scale, multispecies status assessment: anadromous salmonids in the Columbia River Basin. Ecological Applications, 13:964-989. (Pre-Press Word | PDF)
Zabel, R. W., C. J. Harvey, S. L. Katz, T. P. Good, P. S. Levin. 2003. Ecologically Sustainable Yield. American Scientist, 91:150-157.
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2002
Holmes, E. E. 2002. Compute and Conserve, Book review of Quantitative methods for Conservation Biology. Conservation Biology, 16(1):275-276.
Holmes, E. E., W. Fagan. 2002. Validating population viability analysis for corrupted data sets. Ecology, 83:2379-2386. (PDF | Pre-Press Word)
Katz, S. L. 2002. Design of heterothermic muscle in fish. Journal of Experimental Biology, 205:2251-2266.
Weitkamp, L. A., K. Neely. 2002. Coho salmon (Oncorhynchus kisutch) ocean migration patterns: insight from marine coded-wire tag recoveries. Canadian Journal of Fisheries and Aquatic Sciences, 59:1100-1115.
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2001
Holmes, E. E. 2001. Estimating risks in declining populations with poor data. Proceedings of the National Academy of Sciences, USA, 98:5072-5077.
Waples, R. S., R. G. Gustafson, L. A. Weitkamp, J. M. Myers, O. W. Johnson, P. J. Busby, J. J. Hard, G. J. Bryant, F. W. Waknitz, K. Neely, D. J. Teel, W. S. Grant, G. A. Winans, S. Phelps, A. R. Marshall, B. M. Baker. 2001. Characterizing Diversity in Salmon From the Pacific Northwest. Journal of Fish Biology, 59(Suppl. A):1-41.
Weitkamp, L. A. 2001. Status review update for lower Columbia River coho. West Coast coho salmon Biological Review Team, 15 Mar. 2001. 52 p.
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2000
Holmes, E. E., P. Kareiva. 2000. Using single species measurements to anticipate community consequences of environmental contaminants. Page 344 in Albers, P., G. Heinz, H. Ohlendorf. (Eds.) Environmental Contaminants and Terrestrial Vertebrates: Effects on Populations, Communities, and Ecosystems. Special Publication of SETAC Press.
Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, D. J. Teel, R. G. Kope. 2000. Review of the status of coho salmon from Washington, Oregon, and California. Pages 111-118 in Knudsen, E. E., C. R. Steward, D. D. MacDonald, J. E. Williams, D. W. Reiser. (Eds.) Sustainable Fisheries Management: Pacific Salmon. Lewis Publishers, Boca Raton, FL.
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1998
Roni, P., L. A. Weitkamp, J. Scordino. 1998. Identification of essential fish habitat for salmon in the Pacific northwest: Initial efforts, information needs, and future direction. Pages 93-107 in Fish habitat: essential fish habitat and rehabilitation. American Fisheries Society Symposium 22.
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1997
Weitkamp, L. A. 1997. Artificial propagation and coho salmon along the Oregon coast. Restoration (Oregon Sea Grant), Summer 1997:1-6.
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1996
Roni, P., L. A. Weitkamp. 1996. Environmental monitoring of the Manchester Naval Fuel Pier replacement, Puget Sound, Washington, 1991-1994. Report to the U.S. Department of Navy, Naval Facilities Engineering Command, Western Division, Contract N62474-91-MP-00758, 40 p. plus appendices.
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1995
Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, R. S. Waples. 1995. Status review of coho salmon from Washington, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-24, 258 p. (PDF | HTML)
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1994
Waples, R. S., C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: Captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences, 51(Suppl. 1):310-329.
Weitkamp, L. A. 1994. A review of the effects of dams on the Columbia River estuarine environment, with special reference to salmonids. U.S. Dept. of Energy, Bonneville Power Administration and Coastal Zone and Estuarine Studies Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, ix, 148 p.
Weitkamp, L. A. 1994. Environmental monitoring of the Manchester Naval fuel pier replacement, Puget Sound, Washington. Report to the , Contract Contract N62474-91-MP-00758, 92 p.
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1993
Weitkamp, L. A., D. B. Dey. 1993. Environmental monitoring of the Manchester Naval Fuel Pier replacement, Puget Sound, Washington, 1992. Report to the Department of Navy, Contract N62474-91-MP-00758, 62 p.
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1985
Malins, D. C., B. B. McCain, M. M. Krahn, M. S. Myers, J. E. Stein, W. T. Roubal, D. W. Brown, U. Varanasi, H. O. Hodgins, S. Chan. 1985. Occurrence of hepatic neoplasms and other lesions in bottom-dwelling fish and relationships to pollution in Puget Sound, Washington. Pages 399-414 in Jolly, R. L., R. J. Bull, W. P. Davis, S. L. Katz, M. H. Roberts Jr., V. A. Jacobs. (Eds.) Effects, Vol. 5. Lewis Publishers, Inc., Chelsea, Michigan.
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