Publications & Papers by CBR Faculty, Students, and Staff Organized by Title


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Publications by Title Author Date Theses/Dissertations

An agent-based event driven foraging model. 2002. Anderson, James J.

Final Publication: Anderson, James J. 2002. An agent-based event driven foraging model. Natural Resource Modeling 15(1): 55-82.

Analysis of Fish Response to Flows in the 1991 Pasco Flume Experiments. 1991. Anderson, James J.

Analysis of reported release and collection results from Cramer (1996) in comparison to CRiSP v1.5.3. 1997. Hayes, Joshua A.

An analysis of smolt survival with implications to flow management. 2003. Anderson, James J. and Chris Van Holmes.

Analysis of Snake River Spill: Information based on the CRiSP research project. Testimony before the Subcommittee on Water and Power of the Senate Energy and Natural Resources Committee June 1995. 1995. Anderson, James J.

Application of a Computer Model to the Sacramento River and Major Tributaries in Regard to Chinook Salmon (Oncorhynchus tshawytscha) Juvenile Migration. 1996. White, Paula J.

Application of an Eulerian-Lagrangian-Agent method (ELAM) to rank alternative designs of a juvenile fish passage facility. 2006. Weber, L. J., R. A. Goodwin, S. Li, J. M. Nestler, J. J. Anderson.

Final Publication: Weber, L. J., R. A. Goodwin, S. Li, J. M. Nestler, J. J. Anderson. 2006. Application of an Eulerian-Lagrangian-Agent method (ELAM) to rank alternative designs of a juvenile fish passage facility. J. Hydroinformatics 8(4):271-295.

Application of the Out-Migrant Survival Simulator (OMSS) using the SWARM modeling environment to study smolt-predator interactions. 2000. Beer, W. Nicholas and James J. Anderson. Presented at SwarmFest 2000, March 11-13, 2000, Utah State University, Logan, Utah.

Application of the Out-Migrant Survival Simulator using the SWARM modeling environment to study smolt-predator interactions: Modeling Support to Army Corps of Engineers Columbia River Fisheries Programs, DRAFT. 1999. Beer, W. Nicholas.

Assessing compliance with fish survival standards: a case study at Rock Island Dam, Washington. 2012. John R. Skalski, Tracey W. Steig, Steven Hemstrom. .

Final Publication: Skalski, J.R., T.W. Steig and S. Hemstrom. 2012. Assessing compliance with fish survival standards: a case study at Rock Island Dam, Washington. Environmental Science & Policy 18:45-51.

Assessment of the risk of pile driving to juvenile fish. 1990. Anderson, James J. Presented at the 15th Annual Meeting of Deep Foundations Institute, October 10-12, 1990, Seattle, WA.

Chinook Salmon Harvesting Model CRiSP Harvest Manual. 1997. Norris, James G.

Climate Indicators of Salmon Survival. 1996. Anderson, James J. and Richard A. Hinrichsen. Presented at the PICES meeting, October 18, 1996, Nanaimo, B.C.

Coast Model Documentation Manual. 1999. Norris, James G., Troy Frever, and Susannah Iltis. Prepared for U.S. Dept. of Commerce, NOAA, NMFS, NWFSC.

Columbia River Salmon Passage Model CRiSP.1.5 Theory, Calibration and Validation for SUNOS. 1996. Anderson, James J., Joshua A. Hayes, Pamela Shaw, and Richard W. Zabel.

Columbia River Salmon Passage Model CRiSP.1.5 User manual for SUNOS. 1996. Anderson, James J., Joshua A. Hayes, and Richard W. Zabel.

Columbia River Salmon Passage Model CRiSP.1.6 Theory and Calibration. 2000. Anderson, James J., W. Nicholas Beer, Troy Frever, Joshua A. Hayes, Susannah Iltis, Matthew P. Moore, David Salinger, Pamela Shaw, Chris Van Holmes, and Richard W. Zabel.

Columbia River World Wide Web Group. 1995. Anderson, James J. :JJAnderson.

Comparing methods for inferring site biological condition from a sample of site biota. 2002. Brinck, Kevin W. Thesis.

Final Publication: Brinck, K.W. 2002. Comparing methods for inferring site biological condition from a sample of site biota. Master of Science Thesis. University of Washington. Seattle, Washington.

Comparison of Mainstem Recovery Options Recover-1 and DFOP. 1994. Anderson, James J.

Comparison of mechanistic and empirical methods for modeling embryo and alevin development in Chinook salmon. 1999. Beer, W. Nicholas.

Final Publication: Beer, W.N. 1999. Comparison of mechanistic and empirical methods for modeling embryo and alevin development in Chinook salmon. North American Journal of Aquaculture 61:126-134.

A comparison of methods for measuring visual water clarity, DRAFT. 2001. Steel, E. Ashley, and Steve Neuhausser.

Final Publication: Steel, E.A., and S. Neuhausser. 2002. Comparison of methods for measuring visual water clarity. Journal of the North American Benthological Society 21(2): 326-335.

Comparison of Two Alternative Approaches for Estimating Dam Passage Survival of Salmon Smolts. 2010. John R. Skalski, Richard L. Townsend, Tracey W. Steig, Steven Hemstrom. .

Final Publication: Skalski, J.R., R.L. Townsend, T.W. Steig and S. Hemstrom. 2010. Comparison of Two Alternative Approaches for Estimating Dam Passage Survival of Salmon Smolts. North American Journal of Fisheries Management 30(3):831-839.

Comprehensive Passage (COMPASS) Model: a model of downstream migration and survival of juvenile salmonids through a hydropower system. 2008. Zabel, R. W., J. Faulkner, S. G. Smith, J. J. Anderson, C. Van Holmes, N. Beer, S. Iltis, J. Krinke, G. Fredicks, B. Bellerud, J. Sweet and A. Giorgi.

Final Publication: Zabel, R. W., J. Faulkner, S. G. Smith, J. J. Anderson, C. Van Holmes, N. Beer, S. Iltis, J. Krinke, G. Fredicks, B. Bellerud, J. Sweet and A. Giorgi. 2008. Comprehensive Passage (COMPASS) Model: a model of downstream migration and survival of juvenile salmonids through a hydropower system. Hydrobiologia 609(1):289-300.

Contaminants as viral cofactors: assessing indirect population effects. 2005. Springman, K.R., G. Kurath, J.J. Anderson, and J.M. Emlen. Abstract.

Final Publication: Springman, K.R., G. Kurath, J.J. Anderson, and J.M. Emlen. 2005. Contaminants as viral cofactors: assessing indirect population effects. Aquatic Toxicology 71(1): 13-23.

Correcting Bias in Survival Estimation Resulting From Tag Failure in Acoustic and Radiotelemetry Studies. 2006. Richard L. Townsend, John R. Skalski, Peter Dillingham, Tracey W. Steig. .

Final Publication: Townsend, R.L., J.R. Skalski, P. Dillingham and T.W. Steig. 2006. Correcting bias in survival estimation resulting from tag failure in acoustic and radiotelemetry studies . Journal of Agricultural, Biological, and Environmental Statistics 11(2):183-196.

CRiSP validation against preliminary 1996 NMFS survival results. 1996. Hayes, Joshua A. Memo to William Stelle, NMFS.

Decadal climate cycles and declining Columbia River salmon. 1997. Anderson, James J.

Final Publication: Anderson, J.J. 2000. Decadal climate cycles and declining Columbia River salmon. In Sustainable Fisheries Management: Pacific Salmon, ed. E.E. Knudsen et al., 467-484. New York : CRC Press LLC.

Decadal Scale Climate Pattern and Salmon Survival: Indicators, Interactions and Implications. 1997. Anderson, James J.

Final Publication: Anderson, J.J. 1997. Decadal scale climate pattern and salmon survival: Indicators, interactions and implications. In Estuarine and Ocean Survival of Northeastern Pacific Salmon: Proceedings of the Workshop, March 20-22, 1996, Newport, Oregon, ed. R.L. Emmett and M.H. Schiewe. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSC-29.

Decline and Recovery of Snake River Salmon. 1995. Anderson, James J.

Decoding 3-D movement patterns of fish in response to hydrodynamics and water quality for forecast simulation. 2004. Goodwin, R. Andrew, James J. Anderson, and John M. Nestler. Submitted to the 6th International Conference on Hydroinformatics 2004, 21-24 June 2004, Singapore.

Defining equivalent exploitation rate reduction policies for endangered salmon stocks. 2000. Norris, James G.

Final Publication: Norris, J.G. 2000. Defining equivalent exploitation rate reduction policies for endangered salmon stocks. In Sustainable Fisheries Management: Pacific Salmon, ed. E.E. Knudsen et al., 451-466. New York : CRC Press LLC.

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume IX: A Comparison of Statistical Methods of Estimating Treatment-Control Ratios (Transportation Benefit Ratios) Based on Spring Chinook Salmon on the Columbia River, 1986-1988. 1997. Townsend, Richard L. and John R. Skalski.

Final Publication: Townsend, R.L. and J.R. Skalski. 2000. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume IX: A Comparison of Statistical Methods of Estimating Treatment-Control Ratios (Transportation Benefit Ratios) Based on Spring Chinook Salmon on the Columbia River, 1986-1988. Technical Report DOE/BP-02341-11. Portland, OR : Bonneville Power Administration.

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume VII: Monte-Carlo Comparison of Confidence Interval Procedures for Estimating Survival in a Release-Recapture Study, with Applications to Snake River Salmonids. 1996. Lowther, Alan B. and John R. Skalski.

Final Publication: Lowther, A.B. and J.R. Skalski. 1996. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume VII: Monte-Carlo Comparison of Confidence Interval Procedures for Estimating Survival in a Release-Recapture Study, with Applications to Snake River Salmonids. Technical Report DOE/BP-02341-5. Portland, OR : Bonneville Power Administration.

Design and analysis of salmonid tagging studies in the Columbia Basin, Volume VIII: A new model for estimating survival probabilities and residualization from a release-recapture study of fall chinook salmon (Oncorhynchus tschawytscha) smolts in the Snake River. 1997. Lowther, Alan B. and John R. Skalski.

Final Publication: Lowther, A.B. and J.R. Skalski. 1997. Design and analysis of salmonid tagging studies in the Columbia Basin, Volume VIII: A new model for estimating survival probabilities and residualization from a release-recapture study of fall chinook salmon (Oncorhynchus tschawytscha) smolts in the Snake River. Technical Report DOE/BP-02341-6. Portland, OR : Bonneville Power Administration.

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XX: Evaluation and Recommendations on Alternative Hydroacoustic Array Deployments for the Mouth of the Columbia River to Provide Estimates of Salmonid Smolt Survival and Movements. 2006. John R. Skalski.

Final Publication: Skalski, J.R. "Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XX; Evaluation and Recommendations on Alternative Hydroacoustic Array Deployments for the Mouth of the Columbia River to Provide Estimates of Salmonid Smolt Survival and Movements", 2006 Technical Report, Project No. 198910700, 38 electronic pages, (BPA Report DOE/BP-00025091-1).

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXI: A Summary of Methods for Conducting Salmonid Fry Mark-Recapture Studies for Estimating Survival in Tributaries. 2006. John R. Skalski, Jim Griswold.

Final Publication: Skalski, J.R. and Jim Griswold "Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXI; A Summary of Methods for Conducting Salmonid Fry Mark-Recapture Studies for Estimating Survival in Tributaries", 2005-2006 Technical Report, Project No. 198910700, 50 electronic pages, (BPA Report DOE/BP-00025091-2).

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXII: Evaluating Wetland Restoration Projects in the Columbia River Estuary using Hydroacoustic Telemetry Arrays to Estimate Movement, Survival, and Residence Times of Juvenile Salmonids. 2008. Russell W. Perry, John R. Skalski.

Final Publication: Perry, R.W. and J.R. Skalski. "Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXII; Evaluating Wetland Restoration Projects in the Columbia River Estuary using Hydroacoustic Telemetry Arrays to Estimate Movement, Survival, and Residence Times of Juvenile Salmonids", Technical Report, Project No. 198910700, 24 electronic pages, (BPA Report DOE/BP-P107849).

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXIII: Effects of Array Configuration on Statistical Independence of Replicated Telemetry Arrays used in Smolt Survival Studies. 2008. Russell W. Perry, John R. Skalski.

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXIV: A Statistical Critique of Estimating Salmon Escapement in the Pacific Northwest. 2009. Amber L. Parsons, John R. Skalski. BPA P112130.

Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXV: A Bibliography of Literature on Estimating Salmon Escapement with Focus on the Pacific Northwest. 2009. Amber L. Parsons, John R. Skalski.

Dynamic splitting: An algorithm for deterministic and stochastic multiperiod optimization. 2003. Salinger, David H., and R.T. Rockafellar. Abstract.

Final Publication: Salinger, D.H., and R.T. Rockafellar. 2003. Dynamic splitting: An algorithm for deterministic and stochastic multiperiod optimization. Stochastic Programming E-Print Series 6.

The Dynamics and Effects of Bacterial Kidney Disease in Snake River Spring Chinook Salmon (Oncorhynchus tshawytscha). 2001. Hamel, Owen S. Dissertation.

Final Publication: Hamel, O.S. 2001. The Dynamics and Effects of Bacterial Kidney Disease in Snake River Spring Chinook Salmon (Oncorhynchus tshawyscha). Ph.D. diss., Quantitative Ecology and Resource Management, University of Washington, Seattle.

Effect of Multiple Turbine Passage on Juvenile Snake River Salmonid Survival. 2005. Ham, K.D., J.J. Anderson, and J.A. Vucelick. Executive Summary.

Final Publication: Ham, K.D., J.J. Anderson, and J.A. Vucelick. 2005. Effect of Multiple Turbine Passage on Juvenile Snake River Salmonid Survival. PNNL-15450. Richland, WA: Pacific Northwest National Laboratory.

Effect of spawning day and temperature on salmon emergence: interpretations of a growth model for Methow River chinook. 2001. Beer, W. Nicholas and James J. Anderson.

Final Publication: Beer, W. Nicholas and James J. Anderson. 2001. Effect of spawning day and temperature on salmon emergence: interpretations of a growth model for Methow River chinook. Can. J. Fish. Aquat. Sci. 58(5): 943-949.

Effects of Flow Augmentation on Snake River Fall Chinook. 2000. Anderson, James J., Richard A. Hinrichsen, and Chris Van Holmes. Report to the Committee of Nine and the Idaho Water Users Association.

Effects of the ocean and river environments on the survival of Snake River stream-type chinook salmon. 1997. Hinrichsen, R.A., J.J. Anderson, G.M. Matthews, and C.C. Ebbesmeyer.

Final Publication: Hinrichsen, R.A., J.J. Anderson, G.M. Matthews, and C.C. Ebbesmeyer. 1998. Effects of the ocean and river environments on the survival of Snake River stream-type chinook salmon. In Plan for Analyzing and Testing Hypotheses (PATH): Retrospective and prospective analyses of spring/summer chinook reviewed in fiscal year 1997, ed. D.R. Marmorek, C.N. Peters, and I. Parnell. Vancouver, BC, Canada: ESSA Technologies Ltd.

Effects of Turbine Operating Efficiency on Smolt Passage Survival. 2002. John R. Skalski, Dilip Mathur, and Paul G. Heisey. .

Final Publication: Skalski, J.R., D. Mathur, and P.G. Heisey. 2002. Effects of Turbine Operating Efficiency on Smolt Passage Survival. North American Journal of Fisheries Management 22(4):1193-1200.

Effects of Water Temperature and Flow on Adult Salmon Migration Swim Speed and Delay. 2006. Salinger, D.H., and J.J. Anderson. Abstract.

Final Publication: Salinger, D.H., and J.J. Anderson. 2006. Effects of Water Temperature and Flow on Adult Salmon Migration Swim Speed and Delay. Transactions of the American Fisheries Society 135(1): 188-199.

Effects of water temperature on adult salmon migration swim speed. 2004. Salinger, David H., and James J. Anderson. Abstract.

Estimating the Effects of Smolt Transportation from Different Vantage Points and Management Perspectives. 2006. Rebecca A. Buchanan, John R. Skalski, Steven G. Smith. .

Final Publication: Buchanan, R.A., J.R. Skalski and S.G. Smith. 2006. Estimating the Effects of Smolt Transportation from Different Vantage Points and Management Perspectives. North American Journal of Fisheries Management 26:460-472.

Estimators of stream residence time of Pacific salmon (Oncorhynchus spp.) based on release-recapture data. 1998. Lady, James M. and John R. Skalski.

Final Publication: Lady, J.M. and J.R. Skalski. 1998. Estimators of stream residence time of Pacific salmon (Oncorhynchus spp.) based on release-recapture data. Can. J. Fish. Aquat. Sci. 55(12): 2580-2587.

Evaluating Surrogacy of Hatchery Releases for the Performance of Wild Yearling Chinook Salmon from the Snake River Basin. 2010. Rebecca A. Buchanan, John R. Skalski, Albert E. Giorgi. .

Final Publication: Buchanan, R.A., J.R. Skalski and A.E. Giorgi. 2010. Evaluating Surrogacy of Hatchery Releases for the Performance of Wild Yearling Chinook Salmon from the Snake River Basin. North American Journal of Fisheries Management 30(5):1258–1269.

Evaluation of the 1994 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin. 1995. Townsend, Richard L., Peter Westhagen, and Dean Yasuda.

Final Publication: Townsend, R.L., P. Westhagen, and D. Yasuda. 1995. Evaluation of the 1994 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin. Technical Report DOE/BP-D35885-8. Portland, OR : Bonneville Power Administration.

Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. 1996. Townsend, Richard L., Peter Westhagen, Dean Yasuda, John R. Skalski, and Kristen Ryding.

Final Publication: Townsend, R.L., P. Westhagen, D. Yasuda, J.R. Skalski, and K. Ryding. 1996. Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. Technical Report DOE/BP-35885-9. Portland, OR : Bonneville Power Administration.

Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Yearling Chinook at Multiple Locations in the Snake and Columbia River Basins using CRiSP/RealTime. 1996. Hayes, Joshua A., Richard Zabel, Pamela Shaw, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. 1997. Townsend, Richard L., John R. Skalski, and Dean Yasuda.

Final Publication: Townsend, R.L., J.R. Skalski, and D. Yasuda. 1997. Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. Technical Report DOE/BP-91572-1. Portland, OR : Bonneville Power Administration.

Evaluation of the 1998 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 1999. Beer, W. Nicholas, Joshua A. Hayes, Pamela Shaw, Richard W. Zabel, and James J. Anderson.

Final Publication: Beer, W.N., J.A. Hayes, P. Shaw, R.W. Zabel, and J.J. Anderson. 1999. Evaluation of the 1998 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. Technical Report DOE/BP-02347-1. Portland, OR : Bonneville Power Administration.

Evaluation of the 1999 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2000. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2000 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2001. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2001 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2002. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2002 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2003. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2003 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon returning to the Columbia and Snake Rivers. 2004. Beer, W. Nicholas, David Salinger, Susannah Iltis, and James J. Anderson.

Evaluation of the 2003 Predictions of the Run-Timing of Wild Migrant Yearling Chinook, Subyearling Chinook and Steelhead and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2004. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2004 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) returning to the Columbia and Snake Rivers. 2006. Beer, W. Nicholas, David Salinger, Susannah Iltis, and James J. Anderson.

Final Publication: Beer, W.N, D. Salinger, S. Iltis, and J.J. Anderson. 2006. Evaluation of the 2004 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) returning to the Columbia and Snake Rivers. Technical Report DOE/BP-00005396-1. Portland, OR : Bonneville Power Administration.

Evaluation of the 2004 Predictions of the Run-Timing of Wild Migrant Yearling Chinook, Subyearling Chinook and Steelhead and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2006. Beer, W. Nicholas, Susannah Iltis, Chris Van Holmes, and James J. Anderson.

Final Publication: Beer, W.N, S. Iltis, C. Van Holmes, and J.J. Anderson. 2006. Evaluation of the 2004 Predictions of the Run-Timing of Wild Migrant Yearling Chinook, Subyearling Chinook and Steelhead and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. Technical Report DOE/BP-00005396-2. Portland, OR : Bonneville Power Administration.

Evaluation of the 2005 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) returning to the Columbia and Snake Rivers. 2006. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson.

Final Publication: Beer, W.N, S. Iltis, and J.J. Anderson. 2006. Evaluation of the 2005 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) returning to the Columbia and Snake Rivers. Technical Report DOE/BP-00025162-3. Portland, OR : Bonneville Power Administration.

Evaluation of the 2005 Predictions of the Run-Timing of Wild Migrant Yearling Chinook, Subyearling Chinook and Steelhead and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime. 2006. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Environment, Fish and Wildlife.

Evaluation of the 2008 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. 2009. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 2008 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. 2009. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 2009 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. 2010. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 2009 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. 2010. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 2010 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. 2011. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of the 2010 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. 2011. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Evaluation of Wanapum Dam Bypass Configurations for Outmigrating Juvenile Salmon Using Virtual Fish: Numerical Fish Surrogate (NFS) Analysis. 2005. Goodwin, R.A., J.M. Nestler, J.J. Anderson, J. Kim, and T. Toney. Abstract.

Final Publication: Goodwin, R.A., J.M. Nestler, J.J. Anderson, J. Kim, and T. Toney. 2005. Evaluation of Wanapum Dam Bypass Configurations for Outmigrating Juvenile Salmon Using Virtual Fish: Numerical Fish Surrogate (NFS) Analysis. ERDC/EL TR-05-7 June 2005. Washington, DC: U.S. Army Corps of Engineers.

Exposure of migrating salmon populations in the Columbia/Snake River basins to environmental factors. 2003. Beer, W. Nicholas, Susannah Iltis, and James J. Anderson. white paper.

Extension of the Vitality Model and Its Application. 2008. Li, Ting. Thesis.

Final Publication: Li, Ting 2008. Extension of the Vitality Model and Its Application. Master of Science Thesis. University of Washington. Seattle, Washington.

Factors Associated with Travel Time and Survival of Migrant Yearling Chinook Salmon and Steelhead in the Lower Snake River. 2002. Steven G. Smith, William D. Muir, John G. Williams, John R. Skalski. .

Final Publication: Smith, S.G., W.D. Muir, J.G. Williams, and J.R. Skalski. 2002. Factors Associated with Travel Time and Survival of Migrant Yearling Chinook Salmon and Steelhead in the Lower Snake River. North American Journal of Fisheries Management 22:385-405.

The Flow Survival Relationship and Flow Augmentation Policy in the Columbia River Basin. 2002. Anderson, James J.

Forecasting 3-D fish movement behavior using a Eulerian-Lagrangian-agent method (ELAM). 2006. Goodwin, R. Andrew, John M. Nestler, James J. Anderson, Larry J. Weber, and Daniel P. Loucks. Abstract.

Final Publication: Goodwin, R.A., J.M. Nestler, J.J. Anderson, L.J. Weber, and D.P. Loucks. 2006. Forecasting 3-D fish movement behavior using a Eulerian-Lagrangian-agent method (ELAM). Ecological Modelling 192: 197-223.

Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin. 2007. Lindley, S. T., R. S. Schick, E. Mora, P. B. Adams, J. J. Anderson, S. Greene, C. Hanson, B. P. May, D. McEwan, R. B. MacFarlane, C. Swanson, and J. G. Williams.

Final Publication: Lindley, S. T., R. S. Schick, E. Mora, P. B. Adams, J. J. Anderson, S. Greene, C. Hanson, B. P. May, D. McEwan, R. B. MacFarlane, C. Swanson, and J. G. Williams. 2007. Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin. San Francisco Estuary and Watershed Science. Vol. 5, Issue 1 (February), Article 4. http://repositories.cdlib.org/jmie/sfews/vol5/iss1/art4.

Gas Saturation and Sensitivity Analysis Using CRiSP. 1997. Shaw, Pamela.

A growth model for larval salmon with application to field and laboratory observations of chinook salmon. 1996. Beer, W. Nicholas. Thesis.

Final Publication: Beer, W.N. 1996. A growth model for larval salmon with application to field and laboratory observations of chinook salmon. Master of Science Thesis. University of Washington. Seattle, Washington.

Growth of Snake River chinook salmon, DRAFT. 1998. Beer, W. Nicholas.

Guidelines and Suggested Protocols for Conducting, Analyzing, and Reporting Juvenile Salmonid Survival Studies in the Columbia River Basin. 2005. Peven, Chuck, Al Giorgi, John Skalski, Mike Langeslay, Andrew Grassell, Steve Smith, Tim Counihan, Russell Perry, and Shane Bickford. white paper.

Heat Budget of Water Flowing through Hells Canyon and the Effect of Flow Augmentation on Snake River Water Temperature DRAFT. 2000. Anderson, James J.

Historical population structure of Central Valley steelhead and its alteration by dams. 2006. Lindley, S. T., R. S. Schick, A. Agrawal, M. Goslin, T. E. Pearson, E. Mora, J. J. Anderson, B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R. B. MacFarlane, C. Swanson, and J. G. Williams. JJAnderson.

Final Publication: Lindley, S. T., R. S. Schick, A. Agrawal, M. Goslin, T. E. Pearson, E. Mora, J. J. Anderson, B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R. B. MacFarlane, C. Swanson, and J. G. Williams. 2006. Historical population structure of Central Valley steelhead and its alteration by dams. San Francisco Estuary and Watershed Science. Vol. 4, Issue 1 (February), Article 3. http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art3.

Historical Population Structure of Central Valley Steelhead and its Alteration by Dams. 2006. Lindley, S.T., R.S. Schick, A. Agrawal, M. Goslin, T.E. Pearson, E. Mora, J.J. Anderson, B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R.B. MacFarlane, C. Swanson and J.G. Williams. Abstract.

Final Publication: Lindley, S.T., R.S. Schick, A. Agrawal, M. Goslin, T.E. Pearson, E. Mora, J.J. Anderson, B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R.B. MacFarlane, C. Swanson and J.G. Williams. 2006. Historical Population Structure of Central Valley Steelhead and its Alteration by Dams. San Francisco Estuary & Watershed Science 4(1).

History of the Flow Survival Relationship and Flow Augmentation Policy in the Columbia River Basin. 2001. Anderson, James J. working paper.

In-stream factors affecting juvenile salmonid migration, DRAFT. 1999. Steel, E. Ashley. Dissertation.

Final Publication: Steel, E. Ashley. 1999. In-stream factors affecting juvenile salmonid migration. Ph.D. diss., Quantitative Ecology and Resource Management, University of Washington, Seattle.

An individual-based fishery model and assessing fishery stability DRAFT. 1999. S. Langitoto Helu, James J. Anderson and David B. Sampson. :JJAnderson.

Final Publication: Helu, S.L., J.J. Anderson, and D.B. Sampson. 1999. An individual-based fishery model and assessing fishery stability. Natural Resource Modeling. 12(2) 213-247.

Inseason Forecasts of Sockeye Salmon Returns to the Bristol Bay Districts of Alaska. 2002. Hyun, Saang-Yoon. Dissertation.

Final Publication: Hyun, S. 2002. Inseason Forecasts of Sockeye Salmon Returns to the Bristol Bay Districts of Alaska. Ph.D. diss., Quantitative Ecology and Resource Management, University of Washington, Seattle.

Learning and animal behavior: exploring the dynamics of simple models. 2006. Steele-Feldman, Abran M. Thesis.

Final Publication: Steele-Feldman, A.M. 2006. Learning and animal behavior: exploring the dynamics of simple models. Master of Science Thesis. University of Washington. Seattle, Washington.

Linking growth, survival and heterogeneity through vitality. 2008. J. J. Anderson, M. C. Gildea, D. W. Williams, and T. Li.

Final Publication: Anderson, J. J., M. C. Gildea, D. W. Williams, and T. Li. 2008. Linking growth, survival and heterogeneity through vitality. American Naturalist 171: E20-E43.

Mathematical & Conceptual Framework for the New Discipline of Ecohydraulics. 2008. Nestler, J. M., Goodwin, R. A., Smith, D. L., and Anderson, J. J.

Final Publication: Nestler, J. M., Goodwin, R. A., Smith, D. L., and Anderson, J. J. 2008. Mathematical & Conceptual Framework for the New Discipline of Ecohydraulics. In Hydroecology and Ecohydrology: Past, Present and Future, ed. P. Wood, D. Hannah, and J. Sadler, 205-224, New York: Wiley.

Mean free-path length theory of predator-prey interactions: Application to juvenile salmon migration. 2005. Anderson, J.J., E. Gurarie, R.W. Zabel. Abstract.

Final Publication: Anderson, J.J., E. Gurarie, R.W. Zabel. 2005. Mean free-path length theory of predator-prey interactions: Application to juvenile salmon migration. Ecological Modelling 186(2): 196-211.

Measurement of Low Frequency Sound at Bonneville, McNary and Lower Granite Dams--1988. 1989. Anderson, James J., Blake E. Feist, Robert T. Miyamoto, and Steven O. McConnell.

Final Publication: Anderson, J.J., B.E. Feist, R.T. Miyamoto, and S.O. McConnell. 1989. Measurement of Low Frequency Sound at Bonneville, McNary and Lower Granite Dams--1988. FRI-UW-8906. Seattle, WA : Fisheries Research Institute, School of Fisheries, University of Washington.

The Merging of Empirical and Modeling Research: Columbia River Models and Beyond. 1994. Norris, James G. Presented at the 75th Anniversary Celebration, School of Fisheries, University of Washington, Seattle, WA.

Migration and bioenergetics of juvenile Snake River fall Chinook salmon. 2012. Widener, Daniel. Thesis.

Final Publication: Widener, D. 2012. Migration and bioenergetics of juvenile Snake River fall Chinook salmon. Master of Science Thesis. University of Washington. Seattle, Washington.

A Migratory Life-Cycle Release-Recapture Model for Salmonid PIT-Tag Investigations. 2007. Rebecca A. Buchanan, John R. Skalski. .

Final Publication: Buchanan, R.A. and J.R. Skalski. 2007. A Migratory Life-Cycle Release-Recapture Model for Salmonid PIT-Tag Investigations. Journal of Agricultural, Biological, and Environmental Statistics 12(3):325-345.

A model of the ocean migration of Pacific salmon. 2010. Bracis, Chloe. Thesis.

Final Publication: Bracis, C. 2010. A model of the ocean migration of Pacific salmon. Master of Science Thesis. University of Washington. Seattle, Washington.

A model of the travel time of migrating juvenile salmon, with an application to Snake River spring chinook. 1997. Zabel, Richard W. and James J. Anderson.

Final Publication: Zabel, R.W. and J.J. Anderson. 1997. A model of the travel time of migrating juvenile salmon, with an application to Snake River spring chinook. North American Journal of Fisheries Management 17(1):93-100.

Modeling Juvenile Salmon Migration Using a Simple Markov Chain, DRAFT. 2001. Steel, E. Ashley, Peter Guttorp, James J. Anderson and David C. Caccia.

Final Publication: Steel, E.A., P. Guttorp, J.J. Anderson and D.C. Caccia. 2001. Modeling Juvenile Salmon Migration Using a Simple Markov Chain. Journal of Agricultural, Biological & Environmental Statistics 6(1): 80-88.

Modeling the impacts of John Day drawdown on the survival of salmonid stocks. 2000. Anderson, James J., Richard W. Zabel, and Richard A. Hinrichsen. JJAnderson,RWZabel,RAHinrichsen.

Modelling the Growth of Salmonid Embryos. 1997. Beer, W. Nicholas and James J. Anderson.

Final Publication: Beer, W.N. and J.J. Anderson. 1997. Modelling the Growth of Salmonid Embryos. Journal of Theoretical Biology 189(3): 297-306.

Models and analysis of animal movements: From individual tracks to mass dispersal. 2008. Gurarie, Eli. Dissertation.

Final Publication: Gurarie, E. 2008. Models and analysis of animal movements: From individual tracks to mass dispersal. Ph.D. diss., University of Washington, Seattle.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume II: Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. 1997. Townsend, Richard L., John R. Skalski, and Dean Yasuda.

Final Publication: Townsend, R.L., J.R. Skalski, and D. Yasuda. 1998. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume II: Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. Technical Report DOE/BP-91572-2. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume III: Evaluation of the 1997 predictions of run-timing of wild migrant yearling and subyearling chinook and sockeye in the Snake River Basin using program RealTime. 1999. Townsend, Richard L., John R. Skalski, and Dean Yasuda.

Final Publication: Townsend, R.L., J.R. Skalski, and D. Yasuda. 1999. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume III: Evaluation of the 1997 predictions of run-timing of wild migrant yearling and subyearling chinook and sockeye in the Snake River Basin using program RealTime. Technical Report DOE/BP-91572-6. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume IV: Evaluation of the 1998 Predictions of the Run-Timing of Wild Migrant Yearling and Subyearling Chinook and Steelhead, and Hatchery Sockeye in the Snake River Basin using Program RealTime. 1999. Burgess, Caitlin, Richard L. Townsend, and John R. Skalski.

Final Publication: Burgess, C., R.L. Townsend, and J.R. Skalski. 1999. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume IV: Evaluation of the 1998 Predictions of the Run-Timing of Wild Migrant Yearling and Subyearling Chinook and Steelhead, and Hatchery Sockeye in the Snake River Basin using Program RealTime. Technical Report DOE/BP-91572-7. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume IX: Evaluation of the 2001 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. 2001. Burgess, Caitlin and John R. Skalski.

Final Publication: Burgess, C. and J.R. Skalski. 2001. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume IX: Evaluation of the 2001 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. Technical Report DOE/BP-00004134-1. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume V: Evaluation of the 1999 Predictions of the Run-Timing of Wild Migrant Yearling and Subyearling Chinook Salmon & Steelhead Trout, & Hatchery Sockeye Salmon in the Snake River Basin using Program RealTime. 2000. Burgess, Caitlin and John R. Skalski.

Final Publication: Burgess, C. and J.R. Skalski. 2000. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume V: Evaluation of the 1999 Predictions of the Run-Timing of Wild Migrant Yearling and Subyearling Chinook Salmon & Steelhead Trout, & Hatchery Sockeye Salmon in the Snake River Basin using Program RealTime. Technical Report DOE/BP-91572-4. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VI: Evaluation of the 2000 Predictions of the Run-Timing of Wild Migrant Chinook Salmon & Steelhead Trout, & Hatchery Sockeye Salmon in the Snake River Basin, & Combined Wild & Hatchery Salmonids migrating to Rock Island & McNary Dams Using Program RealTime. 2001. Burgess, Caitlin and John R. Skalski.

Final Publication: Burgess, C. and J.R. Skalski. 2001. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VI: Evaluation of the 2000 Predictions of the Run-Timing of Wild Migrant Chinook Salmon & Steelhead Trout, & Hatchery Sockeye Salmon in the Snake River Basin, & Combined Wild & Hatchery Salmonids migrating to Rock Island & McNary Dams Using Program RealTime. Technical Report DOE/BP-91572-5. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VII: Evaluation of the compliance testing framework for RPA improvement as stated in the 2000 Federal Columbia River Power System (FCRPS) Biological Opinion. 2001. Skalski, John R. and Roger F. Ngouenet.

Final Publication: Skalski, J.R and R.F. Ngouenet. 2001. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VII: Evaluation of the compliance testing framework for RPA improvement as stated in the 2000 Federal Columbia River Power System (FCRPS) Biological Opinion. Technical Report DOE/BP-00004134-2. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VIII: Comparison of the RPA testing rules provided in the 2000 Federal Columbia River Power System (FCRPS) Biological Opinion with new test criteria designed to improve the statistical power of the biological assessments. 2002. Skalski, John R. and Roger F. Ngouenet.

Final Publication: Skalski, J.R and R.F. Ngouenet. 2002. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume VIII: Comparison of the RPA testing rules provided in the 2000 Federal Columbia River Power System (FCRPS) Biological Opinion with new test criteria designed to improve the statistical power of the biological assessments. Technical Report DOE/BP-00004134-3. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume X: Evaluation of the 2002 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolt to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. 2002. Burgess, Caitlin and John R. Skalski.

Final Publication: Burgess, C. and J.R. Skalski. 2002. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume X: Evaluation of the 2002 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolt to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. Technical Report DOE/BP-00004134-5. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XI: Evaluation of the 2003 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. 2003. Burgess, Caitlin and John R. Skalski.

Final Publication: Burgess, C. and J.R. Skalski. 2003. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XI: Evaluation of the 2003 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, and John Day Dams using Program RealTime. Technical Report DOE/BP-00004134-6. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XII: Evaluation of the 2004 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, John Day, and Bonneville Dams using Program RealTime. 2005. Griswold, Jim, Richard L. Townsend and John R. Skalski.

Final Publication: Griswold, J., R.L. Townsend and J.R. Skalski. 2005. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XII: Evaluation of the 2004 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, John Day, and Bonneville Dams using Program RealTime. Technical Report DOE/BP-00013690-4. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIII: Evaluation of the 2005 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, John Day, and Bonneville Dams using Program RealTime. 2006. Griswold, Jim, Richard L. Townsend and John R. Skalski.

Final Publication: Griswold, J., R.L. Townsend and J.R. Skalski. 2006. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIII: Evaluation of the 2005 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Trout migrating to Lower Granite, Rock Island, McNary, John Day, and Bonneville Dams using Program RealTime. Technical Report DOE/BP-00013690-5. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIV; Evaluation of 2006 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolt at Rock Island, Lower Granite, McNary, John Day and Bonneville Dams using Program Real Time. 2007. Townsend, Richard L., Peter Westhagen, and John R. Skalski.

Final Publication: Griswold, J., R.L. Townsend and J.R. Skalski. 2007. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIV; Evaluation of 2006 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolt at Rock Island, Lower Granite, McNary, John Day and Bonneville Dams using Program Real Time. Technical Report DOE/BP-00025093-2. Portland, OR : Bonneville Power Administration.

Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIX: Evaluation of the 2009 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime. 2010. Townsend, Richard L., Peter Westhagen, and John R. Skalski.

Final Publication: Townsend, R.L., P. Westhagen and J.R. Skalski. 2010. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIX: Evaluation of the 2009 Predictions of the Run-Timing of Wild and Hatchery-Reared Migrant Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime. Technical Report P115115. Portland, OR : Bonneville Power Administration.

Monitoring and evaluation of smolt migration in the Columbia River Basin, Volume I: Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Subyearling Fall Chinook in the Snake River Basin using Program RealTime. 1996. Townsend, Richard L., John R. Skalski, and Dean Yasuda.

Final Publication: Townsend, R.L., J.R. Skalski, and D. Yasuda. 1997. Monitoring and evaluation of smolt migration in the Columbia River Basin, Volume I: Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Subyearling Fall Chinook in the Snake River Basin using Program RealTime. Technical Report DOE/BP-35885-12. Portland, OR : Bonneville Power Administration.

A multiple reach model to describe the migratory behavior of Snake River yearling chinook salmon (Oncorhynchus tshawytscha). 1998. Zabel, Richard W., James J. Anderson and Pamela Shaw.

Final Publication: Zabel, R.W., J.J. Anderson, and P. Shaw. A multiple reach model to describe the migratory behavior of Snake River yearling chinook salmon (Oncorhynchus tshawytscha). Can. J. Fish. Aquat. Sci. 55(3): 658-667.

A Multiple-Release Model to Estimate Route-Specific and Dam Passage Survival at a Hydroelectric Project. 2009. John R. Skalski, Rebecca A. Buchanan, Richard L. Townsend, Tracey W. Steig, Steven Hemstrom. .

Final Publication: Skalski, J.R., R.A. Buchanan, R.L. Townsend, T.W. Steig, and S. Hemstrom. 2009. A Multiple-Release Model to Estimate Route-Specific and Dam Passage Survival at a Hydroelectric Project. North American Journal of Fisheries Management 29(3):670-679.

Multivariate regression relationships between ocean conditions and early marine survival of coho salmon (Oncorhynchus kisutch). 1999. Kristen E. Ryding, John R. Skalski. .

Final Publication: Ryding, K.E. and J.R. Skalski. 1999. Multivariate regression relationships between ocean conditions and early marine survival of coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences 56(12): 2374-2384.

A New Tool to Forecast Fish Movement and Passage. 2007. Goodwin, R. A., J. M. Nestler, J. J. Anderson, L. J. Weber. JJAnderson.

Final Publication: Goodwin, R. A., J. M. Nestler, J. J. Anderson, L. J. Weber. 2007. A New Tool to Forecast Fish Movement and Passage. Hydro Review 26(4):58-71.

Notes on Snake River Recovery Plan. 1995. Anderson, James J. Public Power Tour.

Oceanic, riverine, and genetic influences on spring chinook salmon migration timing. 2009. James J. Anderson, W. Nicholas Beer. .

Final Publication: Anderson, J.J. and W.N. Beer. 2009. Oceanic, riverine, and genetic influences on spring chinook salmon migration timing. Ecological Applications 19(8):1989-2003.

Optimization Models For Understanding Migration Patterns of Juvenile Chinook Salmon. 1994. Hinrichsen, Richard A. Dissertation.

Final Publication: Hinrichsen, R.A. 1994. Optimization Models For Understanding Migration Patterns of Juvenile Chinook Salmon. Ph.D. diss., University of Washington, Seattle.

Optimization of Spill for Reduction of Dam and Reservoir Mortality in CRiSP: Modeling Support to Army Corps of Engineers Columbia River Fisheries Programs, DRAFT. 1999. Kropp, Stephen.

Optimum fish passage and guidance designs are based in the hydrogeomorphology of natural rivers. 2008. J. M. Nestler, R. A. Goodwin, D. L. Smith, J. J. Anderson, and S. Li. JJAnderson.

Final Publication: Nestler, J. M., R. A. Goodwin, D. L. Smith, J. J. Anderson, and S. Li. 2008. Optimum fish passage and guidance designs are based in the hydrogeomorphology of natural rivers. River Research and Applications 24(2):148-168.

A parameter estimation routine for the vitality-based survival model. 2003. Salinger, David H., James J. Anderson and Owen S. Hamel. Abstract.

Final Publication: Salinger, D.H., J.J. Anderson, and O.S. Hamel. 2003. A parameter estimation routine for the vitality-based survival model. Ecological Modelling 166(3): 287-294.

Performance of Three Alternative Estimators of Stream Residence Time Based on Live and Dead Counts of Salmonids. 2010. John R. Skalski, Shiquan Liao, Rebecca A. Buchanan. .

Final Publication: Skalski, J.R., S. Liao and R.A. Buchanan. 2010. Performance of Three Alternative Estimators of Stream Residence Time Based on Live and Dead Counts of Salmonids. North American Journal of Fisheries Management 30(1):191-208.

A Personal In-side Review of PATH. 1999. Anderson, James J. Presented at the Idaho State House in Boise, Jan 20, 1999.

Potential Impacts of Pile Driving on Juvenile Pink (Oncorhynchus gorbuscha) and Chum (O. keta) Salmon Behavior and Distribution. 1991. Feist, Blake E. Thesis.

Final Publication: Feist, B.E. 1991. Potential Impacts of Pile Driving on Juvenile Pink (Oncorhynchus gorbuscha) and Chum (O. keta) Salmon Behavior and Distribution. Master of Science Thesis. University of Washington. Seattle, Washington.

Potential Impacts of Pile Driving on Juvenile Pink (Oncorhynchus gorbuscha) and Chum (O. keta) Salmon Behavior and Distribution. 1992. Feist, Blake E., James J. Anderson, and Robert Miyamoto.

Final Publication: Feist, B.E., J.J. Anderson, and R. Miyamoto. 1996. Potential Impacts of Pile Driving on Juvenile Pink (Oncorhynchus gorbuscha) and Chum (O. keta) Salmon Behavior and Distribution. FRI-UW-9603. Seattle, WA : Fisheries Research Institute, School of Fisheries, University of Washington.

Predicted Fall Chinook Survival and Passage Timing Under BiOp and Alternative Summer Spill Programs Using CRiSP. 2003. Van Holmes, Chris and James J. Anderson. white paper.

Predicted Fall Chinook Survival and Passage Timing Under BiOp and Alternative Summer Spill Programs Using the Columbia River Salmon Passage Model. 2004. Van Holmes, Chris, and James J. Anderson. white paper.

Predicting and Monitoring Adult Spring Chinook Salmon Migration on the Columbia River in 2009. 2010. Beer, W. Nicholas, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Predicting and Monitoring Adult Spring Chinook Salmon Migration on the Columbia River in 2010. 2011. Beer, W. Nicholas, and James J. Anderson. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Predicting and Monitoring Spring Chinook Salmon Migrations on the Columbia River. 2009. Beer, W. Nicholas. Report to Bonneville Power Administration, Division of Fish and Wildlife.

Preliminary analysis of hydroacoustically tagged salmon smolt survival and migration rates in the mid-Columbia River. 2006. Gurarie, Eli.

Quantitative Assessment of Salmonid Escapement Techniques in the Pacific Northwest. . Amber L. Parsons, John R. Skalski. accepted Reviews in Fisheries Sciences.

Realtime Temperature Predictions. 1996. Shaw, Pamela.

Relationship between antigen concentration and bacterial load in Pacific salmon with bacterial kidney disease. 2002. Hamel, Owen S. and James J. Anderson.

Final Publication: Hamel, O.S. and J.J. Anderson. 2002. Relationship between antigen concentration and bacterial load in Pacific salmon with bacterial kidney disease. Diseases of Aquatic Organisms 51(2): 85-92.

Review of Marking Methods and Release-Recapture Designs for Estimating the Survival of Very Small Fish: Examples from the Assessment of Salmonid Fry Survival. 2009. John R. Skalski, Rebecca A. Buchanan, Jim Griswold. .

Final Publication: Skalski, J.R., R.A. Buchanan, and J. Griswold. 2009. Review of Marking Methods and Release-Recapture Designs for Estimating the Survival of Very Small Fish: Examples from the Assessment of Salmonid Fry Survival. Reviews in Fisheries Science 17(3):391-401.

Review of Salmon Management Model Migration Algorithms DRAFT. 1997. Norris, James G.

Review of the Influence of Climate on Salmon. 1996. Anderson, James J.

Final Publication: Anderson, J.J. 1996. Review of the influence of climate on salmon. In Plan for Analyzing and Testing Hypotheses (PATH): Final report on retrospective analyses for fiscal year 1996, ed. D.R. Marmorek. Vancouver, B.C. : ESSA Technologies Ltd.

Run timing of adult Chinook salmon passing Bonneville dam on the Columbia River. 2007. Beer, W. Nicholas. white paper.

Sensitivity of juvenile salmonid growth to future climate trends. 2010. Beer, W. Nicholas and James J. Anderson. Early view, article online in advance of print.

Final Publication: Beer, W.N. and J.J. Anderson. 2010. Sensitivity of juvenile salmonid growth to future climate trends. River Research and Applications.

Sensitivity of salmon survival to temperature in the mainstem Snake and Columbia Rivers. 2004. Beer, W. Nicholas and James J. Anderson. white paper.

A Simple Spreadsheet Model For Evaluating Recovery Strategies For Snake River Fall Chinook Salmon. NA. Norris, James G.

Snake River yearling chinook travel time estimation. 1996. Zabel, Richard W. Memo to William Stelle, NMFS.

Spatial and Temporal Models of Migrating Juvenile Salmon with Applications. 1994. Zabel, Richard W. Dissertation.

Final Publication: Zabel, R.W. 1994. Spatial and Temporal Models of Migrating Juvenile Salmon with Applications. Ph.D. diss., University of Washington, Seattle.

A Splitting Algorithm for Multistage Stochastic Programming with Application to Hydropower Scheduling. 1997. Salinger, David H. Dissertation.

Final Publication: Salinger, D.H. 1997. A Splitting Algorithm for Multistage Stochastic Programming with Application to Hydropower Scheduling. Ph.D. diss., University of Washington, Seattle.

Statistical Framework for Monitoring Basal Area Coverage of Eelgrass in Puget Sound. 2003. John R. Skalski. To: Nearshore Habitat Program, Aquatic Resources Division, Department of Natural Resources, State of Washington.

A statistical model for in-season forecasts of sockeye salmon (Oncorhynchus nerka) returns to the Bristol Bay districts of Alaska. 2005. Hyun, S., R. Hilborn, J.J. Anderson, and B. Ernst. Abstract.

Final Publication: Hyun, S., R. Hilborn, J.J. Anderson, and B. Ernst. 2005. A statistical model for in-season forecasts of sockeye salmon (Oncorhynchus nerka) returns to the Bristol Bay districts of Alaska. Canadian Journal of Fisheries and Aquatic Sciences 62(7): 1665-1680.

Statistical Sampling Plan for the 1999 Lower Granite Dam Hydroacoustic Studies. 1999. John R. Skalski. To: U.S. Army Corps of Engineers and Battelle Pacific Northwest Laboratories, 3110 Port of Benton Boulevard, Richland, WA 99352.

Stock Separation of Chinook salmon at Bonneville Dam for Adult Upstream Migration Model (2008). 2008. Beer, W. Nicholas. white paper.

Stress, Growth and Survival of Juvenile Chinook Salmon. 2003. Cobleigh, Molly M. Thesis.

Final Publication: Cobleigh, M.M. 2003. Stress, Growth and Survival of Juvenile Chinook Salmon. Master of Science Thesis. University of Washington. Seattle, Washington.

Survival of Juvenile Chinook Salmon during Barge Transport. 2011. Geoffrey A. McMichael, John R. Skalski & Katherine A. Deters. .

Final Publication: McMichael, G.A., J.R. Skalski and K.A. Deters. 2011. Survival of Juvenile Chinook Salmon during Barge Transport. North American Journal of Fisheries Management 31(6):1187-1196.

Testimony of James J Anderson before the Subcommittee on Water and Power of the U.S. House of Representatives Committee on Resources Held May 19, 2001 in Tacoma, Washington. 2001. Anderson, James J.

Testimony of James J. Anderson Associate Professor, School of Fisheries, University of Washington, Before The U.S. House of Representatives Committee on Resources, September 2, 1998 Pasco, Washington. 1998. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, before the Subcommittee on Fisheries, Wildlife and Water of the Senate Committee on Environment and Public Works held in Boise, Idaho, November 20, 2000. 2000. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Fisheries, University of Washington, Seattle, Washington, before the Subcommittee on Water and Power of the Senate Energy and Natural Resources Committee held in Cascade Locks, Oregon, April 18, 2000. 2000. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Fisheries, University of Washington, Seattle, Washington, before the U.S. House of Representatives Committee on Resources Subcommittee on Water and Power and Subcommittee on Fisheries, Conservation, Wildlife and Oceans held in the Longworth House Office Building Washington D.C. May 27, 1999. 1999. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Fisheries, University of Washington, Seattle, Washington, before the U.S. House of Representatives Subcommittee on Water and Power in Lewiston, Idaho, May 31, 1997. 1997. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Fisheries, University of Washington, Seattle, Washington, before the U.S. Senate Subcommittee on Water and Power in Hood River, Oregon, April 6, 1999. 1999. Anderson, James J.

Testimony of James J. Anderson, Associate Professor, School of Fisheries, University of Washington, Seattle, Washington, before the U.S. Senate Subcommittee on Water and Power in Vancouver, Washington, February 17, 1998. 1998. Anderson, James J.

Testimony presented before the Subcommittee on Water and Power of the US House of Representatives Committee on Resources. June 1995 Washington D.C. 1995. Anderson, James J.

Total Dissolved Gas submodel parameter calibration for use with CRiSP. 2003. Beer, W. Nicholas.

Toward a Resolution of the Flow/Survival Debate and the Impacts of Flow Augmentation and Water Withdrawal in the Columbia/Snake River System. 2003. Anderson, James J. white paper.

Use of passive integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and Columbia rivers. 1998. John R. Skalski, Steven G. Smith, Robert N. Iwamoto, John G. Williams, and Annette Hoffmann. .

Final Publication: Skalski, J.R., S.G. Smith, R.N. Iwamoto, J.G. Williams, and A. Hoffmann. 1998. Use of passive integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and Columbia rivers. Canadian Journal of Fisheries and Aquatic Sciences 55(6): 1484-1493.

Using multistate mark-recapture methods to model adult salmonid migration in an industrialized river. 2010. Rebecca A. Buchanan, John R. Skalski. .

Final Publication: Buchanan, R.A. and J.R. Skalski. 2010. Using multistate mark-recapture methods to model adult salmonid migration in an industrialized river. Ecological Modelling 221:582-589.

Visualize the Intrinsic and Extrinsic Processes that Determine the Patterns of Human Mortality. 2011. Li, Ting. Dissertation.

Final Publication: Li, T. 2011. Visualize the Intrinsic and Extrinsic Processes that Determine the Patterns of Human Mortality. Ph.D. diss., Quantitative Ecology and Resource Management, University of Washington, Seattle.

A vitality based model relating stressors and environmental properties to organism survival - DRAFT. 2000. Anderson, James J.

Final Publication: Anderson, J.J. 2000. Ecological Monographs 70(3): 445-470.


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