Skalski JR. Statistical Sampling Plan for the 1999 Lower Granite Dam Hydroacoustic Studies. [Internet]. 1999 . Available from: sites/default/files/papers/Skalski/Skalski 1999 - Stat Sampling Plan for LGR in 1999.pdf

Skalski JR. Statistical Framework for Monitoring Basal Area Coverage of Eelgrass in Puget Sound. [Internet]. 2003 . Available from: sites/default/files/papers/Skalski/Skalski 2003 - Stat Framework for Basal Area Coverage of Eelgrass.pdf

Parsons AL, Skalski JR. A Statistical Critique of Estimating Salmon Escapement in the Pacific Northwest. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2009 ;XXIV. Available from: sites/default/files/papers/Skalski/D&A Volume 24 (Salmon Escapement).pdf

Perry R, Skalski JR. Effects of Array Configuration on Statistical Independence of Replicated Telemetry Arrays used in Smolt Survival Studies. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2008 ;XXIII. Available from: sites/default/files/papers/Skalski/D&A Volume 23 (Independence of Replicated Arrays).pdf

Skalski JR, Griswold J. A Summary of Methods for Conducting Salmonid Fry Mark-Recapture Studies for Estimating Survival in Tributaries. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2006 ;XXI. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00025091-2

Lowther AB, Skalski JR. 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. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 1997 ;VIII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=02341-6

Lowther AB, Skalski JR. Monte-Carlo Comparison of Confidence Interval Procedures for Estimating Survival in a Release-Recapture Study, with Applications to Snake River Salmonids. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 1996 ;VII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=02341-5

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

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

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

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

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

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

Townsend RL, Westhagen P, Skalski JR. Evaluation of the 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2007 ;XIV. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00025093-2

Griswold J, Townsend RL, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2006 ;XIII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00013690-5

Griswold J, Townsend RL, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2005 ;XII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00013690-4

Burgess C, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2003 ;XI. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00004134-6

Burgess C, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2002 ;X. Available from: sites/default/files/papers/Skalski/ser2vol10FINAL.pdf

Burgess C, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2001 ;IX. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00004134-1

Burgess C, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2001 ;VI. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-5

Burgess C, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2000 ;V. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-4

Burgess C, Townsend RL, Skalski JR. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 1999 ;IV. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-7

Townsend RL, Skalski JR, Yasuda D. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 1999 ;III. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-6

Townsend RL, Skalski JR, Yasuda D. Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Subyearling Chinook in the Snake River Basin using Program RealTime. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 1997 ;II. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-2

Townsend RL, Skalski JR, Yasuda D. Evaluation of the 1996 Predictions of the Run-Timing of Wild Migrant Spring/Summer Yearling Chinook in the Snake River Basin using Program RealTime. [Internet]. 1997 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=91572-1

Townsend RL, Skalski JR, Yasuda D. Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Subyearling Fall Chinook in the Snake River Basin using Program RealTime. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 1996 ;I. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=35885-12

Townsend RL, Westhagen P, Yasuda D, Skalski JR, Ryding KE. Evaluation of the 1995 Predictions of the Run-Timing of Wild Migrant Yearling Chinook in the Snake River Basin using Program RealTime. [Internet]. 1996 . Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=35885-9

Skalski JR. Evaluation and Recommendations on Alternative Hydroacoustic Array Deployments for the Mouth of the Columbia River to Provide Estimates of Salmonid Smolt Survival and Movements. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2006 ;XX. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00025091-1

Perry R, Skalski JR. Evaluating Wetland Restoration Projects in the Columbia River Estuary using Hydroacoustic Telemetry Arrays to Estimate Movement, Survival, and Residence Times of Juvenile Salmonids. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2008 ;XXII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P107849

Skalski JR, Ngouenet RF. 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. Monitoring and Evaluation of Smolt Migration in the Columbia Basin [Internet]. 2002 ;VIII. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00004134-3

Townsend RL, Skalski JR. A Comparison of Statistical Methods of Estimating Treatment-Control Ratios (Transportation Benefit Ratios) Based on Spring Chinook Salmon on the Columbia River, 1986-1988. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 1997 ;IX. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=02341-11

Parsons AL, Skalski JR. A Bibliography of Literature on Estimating Salmon Escapement with Focus on the Pacific Northwest. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin [Internet]. 2009 ;XXV. Available from: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P112588

Skalski JR, Whitlock SL. Vitality models found useful in modeling tag-failure times in acoustic-tag survival studies. [Internet]. 2020 ;8(1):26. Available from: https://doi.org/10.1186/s40317-020-00213-z

Buchanan RA, Skalski JR. Using multistate mark-recapture methods to model adult salmonid migration in an industrialized river. Ecological Modelling [Internet]. 2010 ;221:582-589. Available from: http://dx.doi.org/10.1016/j.ecolmodel.2009.11.014

Skalski JR, Smith SG, Iwamoto RN, Williams JG, Hoffmann A. 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 [Internet]. 1998 ;55:1484-1493. Available from: http://dx.doi.org/10.1139/cjfas-55-6-1484

Buchanan RA, Brandes PL, Skalski JR. Survival of Juvenile Fall‐Run Chinook Salmon through the San Joaquin River Delta, California, 2010–2015. North American Journal of Fisheries Management. 2018 ;38(3):663-679.

McMichael GA, Skalski JR, Deters KA. Survival of Juvenile Chinook Salmon during Barge Transport. North American Journal of Fisheries Management [Internet]. 2011 ;31:1187-1196. Available from: http://dx.doi.org/10.1080/02755947.2011.646455

Perry R, Brandes PL, Burau JR, Klimley PA, MacFarlane B, Michel C, Skalski JR. Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta. Environmental Biology of Fishes. 2013 ;96(2-3):381 - 392.

Skalski JR, Buchanan RA, Griswold J. 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 [Internet]. 2009 ;17:391-401. Available from: http://dx.doi.org/10.1080/10641260902752199

Buchanan RA, Skalski JR. Relating survival of fall-run Chinook Salmon through the San Joaquin delta to river flow. Environmental Biology of Fishes. 2020 ;103:389-410.