Nestler JM, Goodwin RA, Smith DL, Anderson JJ. Mathematical & Conceptual Framework for the New Discipline of Ecohydraulics. In: Wood P, Hannah D, Sadler J Hydroecology and Ecohydrology: Past, Present and Future. Hydroecology and Ecohydrology: Past, Present and Future. New York: Wiley; 2008. pp. 205-224.

Anderson JJ, Gildea MC, Williams DW, Li T. Linking growth, survival and heterogeneity through vitality. American Naturalist [Internet]. 2008 ;171:E20-E43. Available from: http://dx.doi.org/10.1086/524199

Steele-Feldman AM. Learning and animal behavior: exploring the dynamics of simple models. [Internet]. 2006 . Available from: sites/default/files/papers/steele-feldman_thesis.pdf

Bracis C, Anderson JJ. An investigation of the geomagnetic imprinting hypothesis for salmon. Fisheries Oceanography [Internet]. 2012 ;21:170-181. Available from: http://dx.doi.org/10.1111/j.1365-2419.2012.00617.x

Steel AE. In-stream factors affecting juvenile salmonid migration, DRAFT. [Internet]. 1999 . Available from: sites/default/files/papers/diss824.pdf

Shaw P. Inseason Forecasts Temperature Predictions. [Internet]. 1996 . Available from: inseason/methods

Hyun S-Y. Inseason Forecasts of Sockeye Salmon Returns to the Bristol Bay Districts of Alaska. [Internet]. 2002 . Available from: sites/default/files/papers/hyun_diss.pdf

Helu LS, Anderson JJ, Sampson DB. An individual-based fishery model and assessing fishery stability. Natural Resource Modeling [Internet]. 1999 ;12. Available from: http://dx.doi.org/10.1111/j.1939-7445.1999.tb00011.x

Anderson JJ. History of the Flow Survival Relationship and Flow Augmentation Policy in the Columbia River Basin. [Internet]. 2001 . Available from: sites/default/files/papers/anderson/flow_survival_history.pdf

Lindley ST, Schick RS, Agrawal A, Goslin M, Pearson TE, Mora E, Anderson JJ, May BP, Greene S, Hanson C, et al. Historical population structure of Central Valley steelhead and its alteration by dams. San Francisco Estuary and Watershed Science [Internet]. 2006 ;4. Available from: http://escholarship.org/uc/item/1ss794fc

Anderson JJ. Heat Budget of Water Flowing through Hells Canyon and the Effect of Flow Augmentation on Snake River Water Temperature DRAFT. [Internet]. 2000 . Available from: sites/default/files/papers/anderson/SRheatbudget.pdf

Peven C, Giorgi AE, Skalski JR, Langeslay M, Grassell A, Smith SG, Counihan T, Perry R, Bickford S. Guidelines and Suggested Protocols for Conducting, Analyzing, and Reporting Juvenile Salmonid Survival Studies in the Columbia River Basin. [Internet]. 2005 . Available from: sites/default/files/papers/Guidelines_and_Protocols_FINAL_DRAFT.pdf

Beer WN. Growth of Snake River chinook salmon, DRAFT. [Internet]. 1998 . Available from: sites/default/files/papers/growth/fishgrow4.pdf

Beer WN. A growth model for larval salmon with application to field and laboratory observations of chinook salmon. 1996 .

Shaw P. Gas Saturation and Sensitivity Analysis Using CRiSP. [Internet]. 1997 . Available from: sites/default/files/papers/shawpath.pdf

Lindley ST, Schick RS, Mora E, Adams PB, Anderson JJ, Greene S, Hanson C, May BP, McEwan D, MacFarlane B, et al. Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin. San Francisco Estuary and Watershed Science [Internet]. 2007 ;5. Available from: http://escholarship.org/uc/item/3653x9xc

Goodwin RA, Nestler JM, Anderson JJ, Weber LJ, Loucks DP. Forecasting 3-D fish movement behavior using a Eulerian-Lagrangian-agent method (ELAM). Ecological Modelling [Internet]. 2006 ;192:197-223. Available from: http://dx.doi.org/10.1016/j.ecolmodel.2005.08.004

Anderson JJ. The Flow Survival Relationship and Flow Augmentation Policy in the Columbia River Basin. [Internet]. 2002 . Available from: sites/default/files/papers/anderson/flowsurvivalhistory2002.pdf

Gast CM. Fixed and random effects models and multistate estimation procedures for statistical population reconstructions. Quantitative Ecology and Resource Management. 2011 ;Ph.D.

Smith SG, Muir WD, Williams JG, Skalski JR. 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 [Internet]. 2002 ;22:385-405. Available from: http://dx.doi.org/10.1577/1548-8675(2002)022<0385:FAWTTA>2.0.CO;2

Li T. Extension of the Vitality Model and Its Application. [Internet]. 2008 . Available from: sites/default/files/papers/li_ting_thesis.pdf

Beer WN, Iltis S, Anderson JJ. Exposure of migrating salmon populations in the Columbia/Snake River basins to environmental factors. [Internet]. 2003 . Available from: sites/default/files/papers/temp.exposure.6.pdf

Goodwin RA, Nestler JM, Anderson JJ, Kim J, Toney T. Evaluation of Wanapum Dam Bypass Configurations for Outmigrating Juvenile Salmon Using Virtual Fish: Numerical Fish Surrogate (NFS) Analysis. [Internet]. 2005 . Available from: http://el.erdc.usace.army.mil/elpubs/pdf/trel05-7.pdf

Skalski JR, Ngouenet RF. Evaluation of the compliance testing framework for RPA improvement as stated in the 2000 Federal Columbia River Power System (FCRPS) Biological Opinion. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2001 ;VII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00004134-2

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2014 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2015 . Available from: https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P148588

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2014 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon [Oncorhynchus tshawytscha] Returning to the Columbia and Snake Rivers. [Internet]. 2015 . Available from: https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P148589

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2013 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2014 . Available from: https://pisces.bpa.gov/release/documents/DocumentViewer.aspx?doc=P137742

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2013 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon [Oncorhynchus tschawytscha] Returning to the Columbia and Snake Rivers. [Internet]. 2014 . Available from: https://pisces.bpa.gov/release/documents/DocumentViewer.aspx?doc=P137743

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2012 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2013 . Available from: https://pisces.bpa.gov/release/documents/DocumentViewer.aspx?doc=P132683

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2012 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon [Oncorhynchus tschawytscha] Returning to the Columbia and Snake Rivers. [Internet]. 2013 . Available from: https://pisces.bpa.gov/release/documents/DocumentViewer.aspx?doc=P132681

Townsend RL, Westhagen P, Skalski JR. Evaluation of the 2011 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime. [Internet]. 2011 . Available from: sites/default/files/papers/Skalski/M&E Volume XXI (2011 RealTime Report).pdf

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2011 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2012 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P126069

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2011 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. [Internet]. 2012 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P127362

Townsend RL, Westhagen P, Skalski JR. Evaluation of the 2010 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime. [Internet]. 2011 . Available from: sites/default/files/papers/Skalski/M&E Volume XX (2010 RealTime Report).pdf

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2010 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2011 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P121107

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2010 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. [Internet]. 2011 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P121108

Townsend RL, Westhagen P, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2010 ;XIX. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P115115

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2009 Predictions of Run-Timing and Survival of Wild Migrant Yearling Chinook and Steelhead on the Columbia and Snake Rivers. [Internet]. 2010 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P116013

Beer WN, Iltis S, Anderson JJ. Evaluation of the 2009 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) Returning to the Columbia and Snake Rivers. [Internet]. 2010 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P116012

Townsend RL, Westhagen P, Skalski JR. Evaluation of the 2008 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime. [Internet]. 2008 . Available from: sites/default/files/papers/Skalski/M&E Volume XVII (2008 RealTime Report).pdf