Beer WN, Salinger DH, Iltis S, Anderson JJ. Evaluation of the 2004 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon (Oncorhynchus tschawytscha) returning to the Columbia and Snake Rivers. [Internet]. 2006 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00020638-2

Beer WN, Iltis S, VanHolmes C, Anderson JJ. 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. [Internet]. 2004 . Available from: sites/default/files/papers/PO.2003.pdf

Beer WN, Salinger DH, Iltis S, Anderson JJ. Evaluation of the 2003 Predictions of Run-size and Passage Distributions of Adult Chinook Salmon returning to the Columbia and Snake Rivers. [Internet]. 2004 . Available from: sites/default/files/papers/PO.Adult.2003.pdf

Beer WN, Iltis S, VanHolmes C, Anderson JJ. 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. [Internet]. 2003 . Available from: sites/default/files/papers/PO.2002.pdf

Beer WN, Iltis S, VanHolmes C, Anderson JJ. 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. [Internet]. 2002 . Available from: sites/default/files/papers/PO.2001.pdf

Beer WN, Iltis S, VanHolmes C, Anderson JJ. 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. [Internet]. 2001 . Available from: sites/default/files/papers/PO.2000.pdf

Beer WN, Iltis S, VanHolmes C, Anderson JJ. 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. [Internet]. 2000 . Available from: sites/default/files/papers/PO.99.pdf

Beer WN, Hayes JA, Shaw P, Zabel RW, Anderson JJ. 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. [Internet]. 1999 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=02347-1

Hayes JA, Zabel RW, Shaw P, Anderson JJ. 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. [Internet]. 1996 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P104650

Salinger DH, Anderson JJ. Effects of Water Temperature and Flow on Adult Salmon Migration Swim Speed and Delay. Transactions of the American Fisheries Society [Internet]. 2006 ;135:188-199. Available from: http://dx.doi.org/10.1577/T04-181.1

Hinrichsen RA, Anderson JJ, Matthews GM, Ebbesmeyer CC. Effects of the ocean and river environments on the survival of Snake River stream-type chinook salmon. In: Marmorek DR, Peters CN, Parnell I Plan for Analyzing and Testing Hypotheses (PATH): Retrospective and prospective analyses of spring/summer chinook reviewed in fiscal year 1997. Plan for Analyzing and Testing Hypotheses (PATH): Retrospective and prospective analyses of spring/summer chinook reviewed in fiscal year 1997. Vancouver, B.C.: ESSA Technologies Ltd; 1997. Available from: sites/default/files/papers/effectsofocean.pdf

Anderson JJ, Hinrichsen RA, VanHolmes C. Effects of Flow Augmentation on Snake River Fall Chinook. [Internet]. 2000 . Available from: sites/default/files/papers/anderson/flowaug_fch.pdf

Enders EC, Gessel MH, Anderson JJ, Williams JG. Effects of Decelerating and Accelerating Flows on Juvenile Salmonid Behavior. Transactions of the American Fisheries Society [Internet]. 2012 ;141(2):357-364. Available from: http://dx.doi.org/10.1080/00028487.2012.664604

Beer WN, Anderson JJ. Effect of spill on adult salmon passage delay at Columbia River and Snake River dams. [Internet]. 2012 . Available from: sites/default/files/papers/Spill.and.Passage.whitepaper.2012.pdf

Beer WN, Anderson JJ. Effect of spawning day and temperature on salmon emergence: interpretations of a growth model for Methow River chinook. Canadian Journal of Fisheries and Aquatic Sciences [Internet]. 2001 ;58:943-949. Available from: http://dx.doi.org/10.1139/f01-049

Ham KD, Anderson JJ, Vucelick JA. Effect of Multiple Turbine Passage on Juvenile Snake River Salmonid Survival. [Internet]. 2005 . Available from: http://www.pnl.gov/main/publications/external/technical_reports/PNNL-15450.pdf

Goodwin RA, Anderson JJ, Nestler JM, Liong S-Y, Phoon K-K, Babovic V. Decoding 3-D movement patterns of fish in response to hydrodynamics and water quality for forecast simulation. Hydroinformatics [Internet]. 2004 ;1:254-261. Available from: http://dx.doi.org/10.1142/9789812702838_0031

Anderson JJ. Decline and Recovery of Snake River Salmon. [Internet]. 1995 . Available from: sites/default/files/papers/snake.recovery.pdf

Anderson JJ, Emmett RL, Schiewe MH. Decadal Scale Climate Pattern and Salmon Survival: Indicators, Interactions and Implications. Estuarine and Ocean Survival of Northeastern Pacific Salmon [Internet]. 1996 . Available from: sites/default/files/papers/anderson/newport.pdf

Anderson JJ, Knudsen EE. Decadal climate cycles and declining Columbia River salmon. In: Sustainable Fisheries Management: Pacific Salmon. Sustainable Fisheries Management: Pacific Salmon. New York: CRC Press LLC; 2000. pp. 467-484. Available from: sites/default/files/papers/anderson/victoria.pdf

Springman KR, Kurath G, Anderson JJ, Emlen JM. Contaminants as viral cofactors: assessing indirect population effects. Aquatic Toxicology [Internet]. 2005 ;71:13-23. Available from: http://dx.doi.org/10.1016/j.aquatox.2004.10.006

Gosselin JL. Conservation planning for freshwater-marine carryover effects on Chinook salmon survival Zabel RW, Anderson JJ, Faulkner JR, Baptista AM, Sandford BP. Ecology and Evolution. 2018 ;3:319-332.

Zabel RW, Faulkner J, Smith SG, Anderson JJ, VanHolmes C, Beer WN, Iltis S, Krinke J, Fredicks G, Bellerud B, et al. Comprehensive Passage (COMPASS) Model: a model of downstream migration and survival of juvenile salmonids through a hydropower system. Hydrobiologia [Internet]. 2008 ;609:289-300. Available from: http://dx.doi.org/10.1007/s10750-008-9407-z

Anderson JJ. Comparison of Mainstem Recovery Options Recover-1 and DFOP. [Internet]. 1994 . Available from: sites/default/files/papers/anderson/recover1.pdf

Gosselin JL, Anderson JJ. Combining Migration History, River Conditions, and Fish Condition to Examine Cross-Life-Stage Effects on Marine Survival in Chinook Salmon. Transactions of the American Fisheries Society. 2017 ;146(3):408-421.

Anderson JJ. Columbia River World Wide Web Group. [Internet]. 1995 . Available from: papers/anderson/webgrp

Anderson JJ, Beer WN, Frever T, Hayes JA, Iltis S, Moore MP, Salinger DH, Shaw P, VanHolmes C, Zabel RW. Columbia River Salmon Passage Model CRiSP.1.6 Theory and Calibration. [Internet]. 2000 . Available from: sites/default/files/manuals/crisp16_tc.pdf

Anderson JJ, Hayes JA, Zabel RW. Columbia River Salmon Passage Model CRiSP.1.5 User manual for SUNOS. [Internet]. 1996 . Available from: sites/default/files/manuals/crisp15_user.pdf

Anderson JJ, Hayes JA, Shaw P, Zabel RW. Columbia River Salmon Passage Model CRiSP.1.5 Theory, Calibration and Validation for SUNOS. [Internet]. 1996 . Available from: sites/default/files/manuals/crisp15_theory.pdf

Anderson JJ, Hinrichsen RA. Climate Indicators of Salmon Survival. [Internet]. 1996 . Available from: sites/default/files/papers/anderson/draft.pdf

Anderson JJ. Characterizing System Failure Curves with Vitality. Army Science Conference, 26th [Internet]. 2008 . Available from: sites/default/files/papers/anderson/2008_army26thscienceconf.pdf

Beer WN, Anderson JJ. Characteristics of annual water temperature profiles in snowmelt-influenced and rain-dominated watersheds. [Internet]. 2007 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P102771

Anderson JJ. Assessment of the risk of pile driving to juvenile fish. [Internet]. 1990 . Available from: sites/default/files/papers/anderson/deep.foundations.pdf

Gosselin JL, Anderson JJ, Sanderson BL, Middleton MA, Sandford BP, Weitkamp LA. Assessing seasonal and biological indices of juvenile Chinook Salmon for freshwater decision triggers that increase ocean survival. Freshwater Science [Internet]. 2022 . Available from: https://www.journals.uchicago.edu/doi/10.1086/720007

Beer WN, Anderson JJ. Application of the Out-Migrant Survival Simulator (OMSS) using the SWARM modeling environment to study smolt-predator interactions. [Internet]. 2000 . Available from: sites/default/files/papers/swarmfest.pdf

Weber LJ, Goodwin RA, Li S, Nestler JM, Anderson JJ. Application of an Eulerian-Lagrangian-Agent method (ELAM) to rank alternative designs of a juvenile fish passage facility. J. Hydroinformatics [Internet]. 2006 ;8:271-295. Available from: http://dx.doi.org/10.2166/hydro.2006.006

Anderson JJ. 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. [Internet]. 1995 . Available from: sites/default/files/papers/anderson/testimonies/senate.june.95.pdf

Anderson JJ, VanHolmes C. An analysis of smolt survival with implications to flow management. [Internet]. 2003 . Available from: sites/default/files/papers/anderson/FlowSurvivalAnalysisNRC.pdf

Anderson JJ. Analysis of Fish Response to Flows in the 1991 Pasco Flume Experiments. [Internet]. 1991 . Available from: sites/default/files/papers/anderson/acoe92.pdf

Anderson JJ. An agent-based event driven foraging model. Natural Resource Modeling [Internet]. 2002 ;15:55-82. Available from: http://dx.doi.org/10.1111/j.1939-7445.2002.tb00080.x