Student and Post-doc Publications



Adams, GD, Holsman, KK, Barbeaux, SJ, Dorn, MW, Ianelli, JN, Spies, I, Stewart, IJ, Punt, AE. 2022. An ensemble approach to understand predation mortality for groundfish in the Gulf of Alaska. Fish. Res. 251:106303. doi:10.1016/j.fishres.2022.106303.

Cronin-Fine, L, Punt, AE. 2022. Factors influencing size-structured models’ ability to estimate natural mortality. Fish Res. 250:106292. doi:10.1016/j.fishres.2022.106292.

Priviteria-Johnson, KM, Methot, RD, Punt, AE. 2022. Towards best practice for specifying selectivity in age-structured integrated stock assessments. Fish Res. 249: 106247. doi:10.1016/j.fishres.2022.106247.

Romero, M.A., Coscarella, M.A., Adams, G.D., Pedraza, J.C., González, R.A., 2022. Historical reconstruction of the population dynamics of southern right whales in the southwestern Atlantic Ocean. Sci. Rep. 1–17. doi:10.1038/s41598-022-07370-6

Siple, MC, Punt, AE, Francis, TB, Hammond, PS, Heinemann, D, Long, KJ, Moore, J, Sepulveda, M, Reeves, RR, Sigurdsson, GM, Vikingsson, G, Wade, PA, Williams, R, Zerbini, AN. 2022. mmrefpoints: Projecting long-term marine mammal abundance with bycatch. JOSS. 7(1): 13888.

Free, CM, Vargas Poulsen, C, Bellquist, LF, Wassermann, SN, Oken, KL. 2022. The CALFISH database: A century of California’s non-confidential fisheries
landings and participation data. Ecol. Inform. 69:101599.


Cronin-Fine, L., Punt, A.E., 2021. Modeling time-varying selectivity in size-structured assessment models. Fish. Res. 239, 105927.

Carvalho, F., Winker, H., Courtney, D., Kapur, M., Kell, L., Cardinale, M., Schirripag, M., Kitakado, T., Yemane, D., Piner, K.R., Maunder, M.N., Taylor, I., Wetzel, C.R., Doering, K., Johnson, K.F., Methot, R.D., 2021. A Cookbook for Using Model Diagnostics in Integrated Stock Assessments. Fish. Res. 240, 105959.

Kapur, M., Siple, M., Olmos, M., Privitera-Johnson, K., Adams, G., Best, J., Castillo-Jordán, C., Cronin-Fine, L., Havron, A. M., Lee, Q., Methot, R., Punt, A.E. Equilibrium reference point calculations for the next generation of spatial assessments. Res. 244, 106132.


Hurley, K.K.C., Kapur, M., Siple, M., Kotubetey, K., Kawelo, H., Toonen, R., J. A co-developed management tool to determine harvest limits of introduced mud crabs (Scylla serrata, Forskål 1775) within a Native Hawaiian Fishpond. Pac. Bios. 

Kapur, M., Haltuch, M., Connors, B., Rogers, L., Berger, A., Koontz, E., Cope, J., Echave, K., Fenske, K., Hanselman, D., Punt, A.E., 2020. Oceanographic features delineate growth zonation in Northeast Pacific sablefish. Fish. Res. 222.

Winker, H., Carvalho, F., Thorson, J.T., Kell, L.T., Parker, D., Kapur, M., Sharma, R., Booth, A.J., Kerwath, S.E., 2020. JABBA-Select: Incorporating life history and fisheries’ selectivity into surplus production models. Fish. Res.

Dippold, D., G. D. Adams, & S. Ludsin. 2020. Spatial patterning of walleye recreational harvest in Lake Erie: role of density-dependent and –independent factors. Fisheries Research. 230: 105676.

Nifong, R., J. M. Taylor, G. Adams, M. T. Moore, & J. Farris. 2020. Recognizing both denitrification and nitrogen consumption improves performance of stream diel N2 flux models. Limnology and Oceanography: Methods.


Wood, C.L., Sokolow, S.H., Jones, I.J., Chamberlin, A.J., Lafferty, K.D., Kuris, A.M., Jocque, M., Hopkins, S., Adams, G., Buck, J.C. and Lund, A.J., 2019. Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission. Proceedings of the National Academy of Sciences, 116(46), 23182 – 23191.

Zerbini, A., G. Adams, J. Best, P. Clapham, J. Jackson, & A. Punt. 2019. Assessing the recovery of an Antarctic predator from historical exploitation. Royal Society Open Science. 6: 190368.

Thorson, J., G. Adams, & K Holsman. 2019. Spatio-Temporal Models of Intermediate Complexity for Ecosystem Assessments:  a new tool for spatial fisheries management. Fish and Fisheries. 00:1-17.


Carvalho, F., Piner, K., Lee, H., Kapur, M., Clarke, S. 2018. Can the status of pelagic shark populations be determined using simple fishery indicators? Biol. Conserv. 228, 195-204.

Adams, GD, Leaf, RT, Ballenger, JA, Arnot, McDonough, SA. 2018. Spatial variability in the individual growth of Sheepshead (Archosargus probatocephalus) in the Southeast US: Implications for assessment and management. Fisheries Research 206: 35-43. doi:10.1016/j.fishres.2018.04.023.

Adams, G.D., R.T. Leaf, W. Wu & F.J. Hernandez. 2018. Environmentally-driven fluctuations in condition factor of adult Gulf Menhaden (Brevoortia patronus) in the northern Gulf of Mexico. ICES Journal of Marine Science 75: 1269-1279.

Quiñones, J., L. Chiaverano, P. Ayón, G. Adams, H. Mianzan & M. Acha. 2018. Spatial patterns of large jellyfish Chrysaora plocamia blooms in the Northern Humboldt Upwelling System in relation to biological drivers and climate. ICES Journal of Marine Science 75: 1405-1415.


Boyd, C, Barlow, J, Becker, EA, Forney, KA, Gerrodette, T, Moore, JE, Punt, AE. 2017. Estimation of population size and trends for highly mobile species with dynamic spatial distributions. Divers. Distributions 00:00-00. doi:10.1111/ddi.12663.

Lee, Q, Thorson, JT, Gertseva, VV, and Punt, AE. 2017. The benefits and risks of incorporating climate-driven growth variation into stock assessment models, with application to Splitnose Rockfish (Sebastes diploproa). ICES J. Mar. Sci. 00:00-00. doi:10.1093/icesjms/fsx147.

Ono, K, Haynie, AC, Hollowed, AB, Ianelli, JN, McGilliard, CR, Punt, AE. 2017. Management strategy analysis for multispecies fisheries including technical interactions and human behavior in modeling management decisions and fishing. Can. J. Fish. Aquat. Sci. 00:00-00, doi:10.1139/cjfas-2017-0135.

Ono, K, Ianelli, JN, McGilliard, CR, Punt, AE. 2017. Integrating data from multiple surveys and accounting for spatio-temporal correlation to index the abundance of juvenile Pacific halibut in Alaska. ICES J. Mar. Sci. 00:00-00. doi:10.1093/icesjms/fsx174.

Punt, AE, Akselrud, CA, Cronin-Fine, L. 2017. The effects of applying mis-specified age- and size-structured models. Fish. Res. 188:58-73. doi:10.1016/j.fishres.2016.11.017.

Sampson, DB, Hamel, OS, Bosley, K, Budrick, J, Cronin-Fine, L, Hillier, LK, Hinton, KE, Krigbaum, MJ, Miller, S, Privitera-Johnson, KM, Ramey, K, Rodomsky, BT, Solinger, LK, Whitman, AD. 2017. 2017 Assessment Update for the US West Coast Stock of Arrowtooth Flounder. Pacific Fishery Management Council, Portland, OR.

Thorson, JT, Johnson, KF, Methot, RD, and Taylor, IG. 2017. Model-based estimates of effective sample size in stock assessment models using the Dirichlet-multinomial distribution. Fish. Res. 192:84-93. doi:10.1016/j.fishres.2016.06.005.

Wetzel, CR and Cronin-Fine, L 2017. Status of Pacific ocean perch (Sebastes alutus) along the US west coast in 2017. Pacific Fishery Management Council, Portland, OR.


Johnson, KF, Councill, E, Thorson, JT, Brooks, E, Methot, RD, and Punt, AE. 2016. Can autocorrelated recruitment be estimated using integrated assessment models and how does it affect population forecasts?. Fish. Res. 183:222-232. doi:10.1016/j.fishres.2016.06.004.

Johnson, KF, and Punt, AE. 2016. Summary statistics for the comparison between the currently implemented Catch Limit Algorithm (CLA) and the variant proposed by Norway. J. Cetacean Res. Manage. 17(Suppl.):123-127.

Kuriyama, PT, Ono, K, Hurtado-Ferro, F, Hicks, AC, Taylor, IG, Licandeo, RR, Johnson, KF, Anderson, SC, Monnahan, CC, Rudd, MB, Stawitz, CC, Valero, JL. 2016. An empirical weight-at-age approach reduces estimation bias compared to modeling parametric growth in integrated, statistical stock assessment models when growth is time varying. Fish Res. 180:119-127. doi:10.1016/j.fishres.2015.09.007.

Monnahan, CC, Ono, K, Anderson, SC, Rudd, MB, Hicks, AC, Hurtado-Ferro, F, Johnson, KF, Kuriyama, PT, Licandeo, RR, Stawitz, CC, Taylor, IG, Valero, JL. 2016. The effect of length bin width on growth estimation in integrated age-structured stock assessments. Fish. Res. 180:103-112. doi:10.1016/j.fishres.2015.11.002.

Ortiz, I, Aydin, K, Hermann, AJ, Gibson, GA, Punt, AE, Wiese, FK, Eisner, LB, Ferm, N, Buckley, TW, Moffitt, EA, Ianelli, JN, Murphy, J, Dalton, M, Cheng, W, Wang, M, Hedstrom, K, Bond, NA, Curchitser, EN, Boyd, C. 2016. Climate to fish: Synthesizing field work, data and models in a 39-year retrospective analysis of seasonal processes on the eastern Bering Sea shelf and slope. Deep-Sea Res. Pt. II 134:390-412. doi: 10.1016/j.dsr2.2016.07.009.

Punt, AE, MacCall, AD, Essington, TE, Francis, TB, Hurtado-Ferro, F, Johnson, KF, Kaplan, IC, Koehn, LE, Levin, PS, Sydeman, WJ. 2016. Exploring the implications of the harvest control rule for Pacific sardine, accounting for predator dynamics: A MICE model. Ecol. Model. 337:79-95. doi: 10.1016/j.ecolmodel.2016.06.004.

Stawitz, CC, Siple, MC, Munsch, SH, Lee, Q and Derby, SR. 2017. Financial and Ecological Implications of Global Seafood Mislabeling. Conservation Letters. 00:00-00. doi:10.1111/conl.12328.

Wetzel, CR, and Punt, AE. 2016. The impact of alternative rebuilding strategies to rebuild overfished stocks. ICES J. Mar. Sci. 73:2190–2207. doi:10.1093/icesjms/fsw073.


Brieuc, MSO, Ono, K, Drinan, DP, Naish, KA. 2015. Integration of Random Forest with population‐based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecol. 24: 2729-2746. doi: 10.1111/mec.13211.

Hurtado-Ferro, F, Szuwalski, CS, Valero, JL, Anderson, SC, Cunningham, CJ, Johnson, KF, Licandeo, R, McGilliard, CR, Monnahan, CC, Muradian, ML, Ono, K, Vert-Pre, KA, Whitten, AR, and Punt, AE. 2015. Looking in the rear-view mirror: bias and retrospective patterns in integrated, age-structured stock assessment models. ICES J. Mar. Sci. 72:99-110. doi:10.1093/icesjms/fsu198.

Johnson, KF, Monnahan, CC, McGilliard, CR, Vert-pre, KA, Anderson, SC, Cunningham, CJ, Hurtado-Ferro, F, Licandeo, RR, Muradian, ML, Ono, K, Szuwalski, CS, Valero, JL, Whitten, AR, Punt, AE. 2015. Time-varying natural mortality in fisheries stock assessment models: identifying a default approach. ICES J. Mar. Sci. 72:137-150. doi:10.1093/icesjms/fsu055.

Johnson, KF, Rudd, MB, Pons, M, Allen, C, Lee, Q, Hurtado-Ferro, F, Haltuch, MA, Hamel, OS. 2015. Status of the US sablefish resource in 2015. Pacific Fisheries Management Council. Portland, OR.

Ono, K, Licandeo, R, Muradian, ML, Cunningham, CJ, Anderson, SC, Hurtado-Ferro, F, Johnson, KF, McGilliard, CR, Monnahan, CC, Szuwalski, CS, Valero, JL, Vert-pre, KA, Whitten, AR, Punt, AE. 2015. The importance of length and age composition data in statistical age-structured models for marine species. ICES J. Mar. Sci. 72:31-43. doi:10.1093/icesjms/fsu007.

Ono, K, Punt, AE, and Hilborn, R. 2015. How do marine closures affect the analysis of catch and effort data? Can. J. Fish. Aquat. Sci. 72:1-14. doi: 10.1139/cjfas-2014-0146.

Ono, K, Punt, AE, and Hilborn, R. 2015. Think outside the grids: An objective approach to define spatial strata for catch and effort analysis. Fisheries Res. 170: 89-101. doi: 10.1016/j.fishres.2015.05.021.

Ono, K, Shelton, AO, Ward, EJ, Thorson, JT, Feist, BE, Hilborn, R. 2015. Space-time investigation of the effects of fishing on fish populations. Eco. App. doi: 10.1890/14-1874.1.

Stawitz, CC, Hurtado-Ferro, F, Kuriyama, P, Trochta, JT, Johnson, KF, Haltuch, MA, Hamel, OS. 2015. Stock assessment update: status of the US petrale sole resource in 2014. Pacific Fisheries Management Council. Portland, OR.

Szuwalski, CS, Vert-Pre, KA, Punt, AE, Branch, TA, Hilborn, R. 2015. Examining common assumptions about recruitment: a meta-analysis of recruitment dynamics for worldwide marine fisheries. Fish and Fish. 16:633–648. doi: 10.1111/faf.12083.

Thorson, JT, Ianelli, JN, Munch, SB, Ono, K, Spencer, PD. 2015. Spatial delay-difference models for estimating spatiotemporal variation in juvenile production and population abundance. Can. J. Fish. Aquat. Sci. doi: 10.1139/cjfas-2014-0543.

Ward, EJ, Jannot, JE, Lee, YW, Ono, K, Shelton, AO, Thorson, JT. 2015. Using spatiotemporal species distribution models to identify temporally evolving hotspots of species co-occurrence. Eco. App. doi: 10.1890/15-0051.1.


Anderson, SC, Monnahan, CC, Johnson, KF, Ono, K, Valero, JL. 2014. ss3sim: An R Package for fisheries stock assessment simulation with Stock Synthesis. PLoS ONE 9(4):e92725. doi:10.1371/journal.pone.0092725.

Boyd, C, Punt, AE, Weimerskirch H, Betrand, S. 2014. Movement models provide insights into variation in the foraging effort of central place foragers. Ecol. Model. 286:13-25.  doi:10.1016/j.ecolmodel.2014.03.015.

Hurtado-Ferro, F, Punt, AE, Hill, KT. 2014. Use of multiple selectivity patterns as a proxy for spatial structure. Fish. Res. 158:102-115. doi: 10.1016/j.fishres.2013.10.001.

Kotwicki, S, Ianelli, JN, Punt, AE. 2014. Correcting density-dependent effects in abundance estimates from bottom trawl surveys. ICES J. Mar. Sci. 71:1107-1116. doi:10.1093/icesjms/fst208.

Plaganyi, EE, Punt, AE, Hillary, R, Morello, EB, Thébaud, O, Hutton, T, Pillans, RD, Thorson, JT, Fulton, EA, Smith, ADM, Smith, F, Bayliss, P, Haywood, M, Lyne, V,  Rothlisberg, PV. 2014. Models of intermediate complexity for ecosystem assessment to support tactical management decisions in fisheries and conservation. Fish and Fish. 15:1-22. doi:10.1111/j.1467-2979.2012.00488.x

Punt, AE, Hurtado-Ferro, F, Whitten, AR. 2014. Model selection for selectivity in fisheries stock assessments. Fish. Res. 158:124-134. doi:10.1016/j.fishres.2013.06.003.

Punt, AE, Poljak, D, Dalton, MG,  Foy, RJ. 2014. Evaluating the impact of Ocean Acidification on fishery yields and profits: The example of red king crab in Bristol Bay. Ecol. Model. 285:39-53. doi:10.1016/j.ecolmodel.2014.04.017.


Brandon, JR, Punt, AE. 2013. Testing the Gray Whale Strike Limit Algorithm (SLA): allowing environmental variability to influence population dynamics. J Cetacean Res. Manage. 13:81-88.

Fay, G, Punt, AE. 2013. Methods for estimating spatial trends in Steller sea lion pup production using the Kalman filter. Ecol Appl 23:1455-1474. doi:10.1890/12-1645.1.

Foy, RJ, Carls, M, Dalton, M, Hurst, T, Long, CW, Poljak, D, Punt, AE, Sigler, MF, Stillman, J, Stone, RP, Swiney, KM. 2013. CO2, pH, and Anticipating a Future under Ocean Acidification. Oncorhynchus 33: 1-5

Kotwicki, S, De Robertis, A, Ianelli, JN, Punt, AE, Horne, JK. 2013. Combining bottom trawl and acoustic data to model acoustic dead zone correction and bottom trawl efficiency parameters for semi-pelagic species. Can. J. Fish. Aquat. Sci. 70: 208-219. doi:10.1139/cjfas-2012-0321.

Methot, RD, Wetzel, CR. 2013. Stock synthesis: a biological and statistical framework for fish stock assessment and fishery management. Fish. Res. 142:86-99. doi:10.1016/j.fishres.2012.10.012.

Szuwalski, C. 2013. Production is a poor metric for identifying regime-like behavior in marine stocks. Proc. Nat. Acad. Sci. 110: E1436. doi: 10.1073/pnas.1301759110.

Szuwalski, CS, Punt, AE. 2013. Fisheries management for regime-based ecosystems: A management strategy evaluation for the snow crab fishery in the eastern Bering Sea. ICES J. Mar. Sci. 70:955-967. doi:10.1093/icesjms/fss182.

Szuwalski, CS, Punt, AE. 2013.  Regime shifts and recruitment dynamics of snow crab, Chionoecetes opilio, in the eastern Bering Sea. Fish. Ocean. 22:345-354. doi:10.1111/fog.12026.

Thorson, JT, Clarke, ME, Stewart, IJ, Punt, AE. 2013. The implications of spatially varying catchability on bottom trawl surveys of fish abundance, and a proposed solution involving underwater vehicles. Can. J. Fish. Aquat. Sci. 70:294-306.doi:10.1139/cjfas-2012-0330.

Thorson, JT, Stewart, IJ, Taylor, IG, Punt, AE. 2013. Using a recruitment-linked multispecies model to estimate common trends in recruitment for U.S. West Coast groundfishes. Mar. Ecol. Prog. Ser. 483:245-256. doi:10.3354/meps10295.

Thorson, JT, Zhou, S, Punt, AE, Smith, ADM. 2013. A stepwise-spline approximation to time-varying effects in population dynamics models, with application to occupancy modelling. Meth. Ecol. Evol. 4:123-132. doi:10.1111/j.2041-210x.2012.00260.x.

Stewart, IJ, Hicks, AC, Taylor, IG, Thorson, JT, Wetzel, C, Kupschus, S. 2013. A comparison of stock assessment uncertainty estimates using maximum likelihood and Bayesian methods implemented with the same model framework. Fish. Res. 142:37-46. doi:10.1016/j.fishres.2012.07.003.


Cope, JM, Haltuch, MA. 2012. Temporal and spatial summer groundfish assemblages in trawlable habitat off the west coast of the USA, 1977 to 2009. Mar. Ecol. Prog. Ser. 451: 187-200. doi:10.3354/meps09595.

Gutierrez, NL, Valencia, SR, Branch, TA, Agnew, DJ, Baum, JK, Bianchi, PL, Cornejo-Donoso, J, Costello, C, Defeo, O, Essington, TE, Hoggarth, D, Larsen, A, Ninnes, C, Selden, RL, Sistla, S, Smith, ADM, Stern-Pirlot, A, Teck, SJ, Thorson, JT, Williams, NE. 2012. Eco-label conveys reliable information on fish stock health to seafood consumers. PLoS One 7(8): e43765. doi:10.1371/journal.pone.0043765.

Keller, AA, Molton, KJ, Hicks, AC, Haltuch, M, Wetzel, CR. 2012. Variation in age and growth of greenstriped rockfish (Sebasted elongatus) along the US west coast (Washington to California). Fish. Res. 119:80-88. doi:10.1016/j.fishres.2011.12.012.

Punt, AE, Szuwalski, C. 2012. How well can FMSY and BMSY be estimated using empirical measures of surplus production? Fish. Res. 134-136:113-124. doi:10.1016/j.fishres.2012.08.014.

Szuwalski, C, Punt, AE. 2012. Identifying research priorities for management under uncertainty: The estimation ability of the stock assessment method used for eastern Bering Sea snow crab (Chionoecetes opilio). Fish. Res. 134-136:82-94. doi:10.1016/j.fishres.2012.08.007.

Thorson, JT, Branch, TA, Jensen, OP. 2012. Using model-based inference to evaluate global fisheries status from landings, location, and life history data. Can. J. Fish. Aquat. Sci.  69:645-655. doi:10.1139/f2012-016.

Thorson, JT, Cope, JM, Branch, TA, Jensen, OP. 2012. Spawning biomass reference points for exploited marine fishes, incorporating taxonomic and body size information. Can. J. Fish. Aquct. Sci. 69:1556-1568. doi:10.1139/f2012-077.

Thorson, JT, Punt, AE, Nel, R. 2012. Evaluating population recovery for sea turtles under nesting beach protection while accounting for nesting behaviours and changes in availability. J. Appl. Ecology 49:601-610. doi:10.1111/j.1365-2664.2012.02143.x.

Thorson, JT, Stewart, IJ, Punt, AE. 2012. Development and application of an agent based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.). ICES J. Mar. Sci. 69:635-647. doi:10.1093/icesjms/fss003.

Zhou, S, Yin, S, Thorson, JT, Smith, ADM, Fuller, M. 2012. Linking fishing mortality reference points to life history traits: an empirical study. Can. J. Fish. Aquat. Sci. 69:1292-301. doi:10.1139/f2012-060.


Cope, JM, Punt, AE. 2011. Reconciling stock assessment and management scales under conditions of spatially varying catch histories. Fish. Res. 107:22–38. doi: 10.1016/j.fishres.2010.10.002.

Fay, G, Punt, AE, Smith, ADM. 2011. Impacts of spatial uncertainty on performance of age structure-based harvest strategies for blue eye trevalla (Hyperoglyphe antarctica). Fish. Res. 110:391-407doi: 10.1016/j.fishres.2011.04.015.

Garrison, TM, Hamel, OS, Punt, AE. 2011. Can data collected from marine protected areas improve estimates of life-history parameters? Can. J. Fish. Aquat. Sci. 68:1761-1771. doi: 10.1139/F2011-073.

Haltuch, MA, Punt, AE. 2011. The promises and pitfalls of including decadal-scale climate forcing of recruitment in groundfish stock assessment. Can. J. Fish. Aquat. Sci. 68:912-926. doi: 10.1139/F2011-030.

Thorson, JT. 2011. Auxiliary and focal assessment models: a proof-of-concept involving time-varying catchability and fishery stock-status evaluation. ICES J. Mar. Sci. 68: 2264-2276. doi: 10.1093/icesjms/fsr160.

Thorson, JT, Prager, MH. 2011. Better catch curves: incorporating age-specific natural mortality and logistic selectivity. Trans Am. Fish. Soc. 140:356-366. doi:10.1080/00028487.2011.557016.

Thorson, JT, Stewart, IJ, Punt, AE. 2011. Accounting for fish shoals in single- and multispecies survey data using mixture distribution models. Can. J. Fish. Aquat. Sci. 68:1681-1693. doi: 10.11.39/F2011-086.

Wetzel, CR, Punt, AE. 2011. Model performance for the determination of appropriate harvest levels in the case of data-poor stocks. Fish. Res. 110:342-355. doi:10.1016/j.fishres.2011.04.024.

Wetzel, CR, Punt, AE. 2011. Performance of a fisheries catch-at-age model (Stock Synthesis) in data-limited situations. Mar and Freshw. Res. 62:927-936. doi:10.1071/MF11006.


A’mar, ZT, Punt, AE, Dorn, MW. 2010. Incorporating ecosystem forcing through predation into a management strategy evaluation for the Gulf of Alaska walleye pollock (Theragra chalcogramma) fishery. Fish. Res. 102:98-114. doi:10.1016/j.fishres.2009.10.014

Lapointe, NWR, Thorson, JT, Angermeier, PJ. 2010. Seasonal meso- and microhabitat selection by the northern snakehead (Channa argus) in the Potomac river system. Ecol. Freshw. Res. 9:566-577. doi:10.1111/j.1600-0633.2010.00437.x.

Thorson, JT, Berkson, J. 2010. Multispecies estimation of Bayesian priors for catchability trends and density dependence in the US Gulf of Mexico. Can. J. Fish. Aquat. Sci. 67: 936-954. doi:10.1139/F10-040.

Hurtado-Ferro, F, Hiramatsu, K, Shirakihara, K. 2010. Allowing for environmental effects in a management strategy evaluation for Japanese sardine. ICES J. Mar. Sci. 67:2012-2017. doi:10.1093/icesjms/fsq126.


A’mar, ZT, Punt, AE, Dorn, MW. 2009. The evaluation of two management strategies for the Gulf of Alaska walleye pollock fishery under climate change. ICES J. Mar. Sci. 66:1614-1632. doi:10.1093/icesjms/fsp044.

A’mar, ZT, Punt, AE, Dorn, MW. 2009. The impact of regime shifts on the performance of management strategies for the Gulf of Alaska walleye pollock (Theragra chalcogramma) fishery. Can. J. Fish. Aquat. Sci. 66:2222-2242.doi:10.1139/F09-142.

Cope, JM, Punt, AE. 2009. Length-based reference points for data-limited situations: applications and restrictions. Mar. Coast. Fish. Dyn. Mgmt. Ecosys. Sci. 1:169-186. doi: 10.1577/C08-025.1.

Cope, JM, AE Punt. 2009. Drawing the lines: resolving fishery management units with simple fisheries data. Can. J. Fish. Aquat. Sci. 66:1256-1273. doi:10.1139/F09-084.

Haltuch, MA, Punt, AE, Dorn, MW. 2009. Evaluating the estimation of fishery management reference points in a variable environment. Fish. Res. 100:42-56. doi:10.1016/j.fishres.2009.03.001.

Hollowed, AB, Bond, NA, Wilderbauer, TK, Stochhausen, WT, A’mar, ZT, Beamish, RJ, Overland, JE, Schirripa, MJ. 2009. A framework for modelling fish and shellfish responses to future climate change. ICES J. Mar. Sci. 66:1584-1594. doi: 10.1093/icesjms/fsp057.

Holt, CA, Punt, AE. 2009. Incorporating climate information into rebuilding plans for overfished groundfish species of the U.S. west coast. Fish. Res. 100:57-67. doi:10.1016/j.fishres.2009.03.002.

Kinzey, D, Punt, AE. 2009. Multispecies and single-species models of fish population dynamics: comparing parameter estimates. Nat. Res. Model. 22:67-104. doi:10.1111/j.1939-7445.2008.00030.x.

Zador, SG, Parrish, JK, Punt, AE. 2009. Factors influencing subcolony colonization and persistence in a colonial seabird, the common murre Uria aalgeMar. Ecol. Prog. Ser. 376:283-293. doi:10.3354/meps07797.


A’Mar, ZT, Punt, AE, Dorn, MW. 2008. The management strategy evaluation approach and the fishery for walleye pollock in the Gulf of Alaska. p. 317-346. In: G.H. Kruse, K. Drinkwater, J.N. Ianelli, J.S. Link, D.L. Stram, V. Wespestad, and D. Woodby [Ed.] Resiliency of Gadid Stocks to Fishing and Climate Change. Alaska Sea Grant College Program, University of Alaska Fairbanks.

Boyd, C, Brooks, TM, Butchart, SHM, Edgar, GJ, da Fonseca, GAB, Hawkins, F, Hoffmann, M, Sechrest, W, Stuart, SN, van Dijk, PP. 2008. Spatial scale and the conservation of threatened species. Cons. Let. 1: 37-43. doi:10.1111/j.1755-263X.2008.00002.x.

Gunderson, DR, Parma, AM, Hilborn, R, Cope, JM, Fluharty, DL, Miller, ML, Vetter, RD, Heppell, SH, Greene, HG. 2008. The challenge of managing rocky reef resources. Fisheries 33:172-179.

Haltuch, MA, Punt, AE, Dorn, MW. 2008. Evaluating alternative estimators of fishery management reference points. Fish. Res. 94:290-303. doi:10.1016/j.fishres.2008.01.008.

Punt, AE, Cope, JM, Haltuch, MA. 2008. Reference points and decision rules in U.S. Federal fisheries: West coast groundfish experiences. p. 1343-1356. In: Nielsen, JL, Doson, K, Friedland, TR, Hamon, J, Musick, J, Verspoor, E [Ed.] Reconciling Fisheries with Conservation: Proceedings of the Fourth World Fisheries CongressAmerican Fisheries Society Symposium  49.

Punt, AE, Dorn, MW, Haltuch, MA, 2008. Evaluation of threshold management strategies for groundfish off the U.S.West Coast. Fish. Res. 94:251-266. doi:10.1016/j.fishres.2007.12.008.

Smith, ADM,  Smith, DC, Tuck, GN, Klaer, N, Punt, AE, Knuckey, I, Prince, J, Morison, A, Kloser, R, Haddon, M, Wayte, S, Day, J, Fay, G, Pribac, F, Fuller, M, Taylor, B, Little, LR. 2008. Experience in implementing harvest strategies in Australia’s south-eastern fisheries. Fish. Res. 94:373-379. doi:10.1016/j.fishres.2008.06.006.

Waples, RS, Punt, AE, Cope, JM. 2008. Integrating genetic data into management of marine resources: how can we do it better? Fish and Fisheries 9:423-449.doi:10.1111/j.1467-2979.2008.00303.x.

Zador, SG, Punt,AE, Parrish, JK. 2008. Population impacts of endangered short-tailed albatross bycatch in the Alaskan trawl fishery. Biol. Cons. 141:872-882. doi:10.1016/j.biocon.2008.01.001.

Zador, SG, Parrish, JK, Punt, AE, Burke, BL, Fitzgerald, SM. 2008. Determining spatial and temporal overlap of an endangered seabird with a large commercial trawl fishery. End. Spec. Res. 5:103-115. doi:10.3354/esr00152.


Brandon, JR, Breiwick, JM, Punt, AE, Wade, PR. 2007. Constructing a coherent joint prior while respecting biological realism: application to marine mammal stock assessments. ICES J. Mar. Sci. 64:1085-1100. doi:10.1093/icesjms/fsm102.

Cope, JM, Punt, AE. 2007. Admitting ageing error when fitting growth curves: An example using the von Bertalanffy growth function with random effects. Can. J. Fish. Aquat. Sci. 64: 205-218. doi:10.1139/F06-179.

Turvey, ST, Pitman, RL, Taylor, BL, Barlow, J, Tomonari, A, Barret, LA, Zhao, X, Reeves, RR, Stewart, BS, Wang, K, Wei, Z, Zhang, X, Pusser, LT, Richlen, M, Brandon, JR,  Wang, D. 2007. First human-caused extinction of a cetacean? Biol. Lett. 3: 537-540 doi:10.1098/rsbl.2007.0292.


Branch, TA, Hilborn, T, Haynie, AC, Fay, G, Flynn, L, Griffiths, J, Marshall, KN, Randall, JK, Scheuerell, JM, Ward, EJ, Young, M. 2006. Fleet dynamics and fishermen behavior: lessons for fisheries managers. Can. J. Fish. Aquat. Sci. 63:1647-1668. doi:10.1139/f06-072.

Brandon, J, Wade, PR. 2006. Assessment of the Bering-Chukchi-Beaufort Seas stock of bowhead whales using Bayesian model averaging. J. Cetacean Res. Manage.  8:225-239.

Cope, JM. 2006. Exploring intraspecific life history patterns in sharks. Fish. Bull. 104:311-320.

Fay, G, Punt, AE. 2006.  Modeling the spatial dynamics of Steller sea lions (Eumetopias jubatus) using maximum likelihood and Bayesian methods: evaluating causes for population decline. p. 205-433. In: Trites AW,  Atkinson, SK, DeMaster, DP, Fritz,LW, Gelatt, TS, Rea, LD,  Wynne, K [Ed.]. Sea lions of the world. Alaska Sea Grant College Program, University of Alaska Fairbanks.

Punt, AE, Fay, G. 2006. Can experimental manipulation be used to determine the cause of the decline of western stock of Steller sea lions (Eumetopias jubatus)? p. 435-454. In: Trites AW,  Atkinson, SK, DeMaster, DP, Fritz,LW, Gelatt, TS, Rea, LD,  Wynne, K [Ed.]. Sea lions of the world. Alaska Sea Grant College Program, University of Alaska Fairbanks.

Towell, RG, Ream, RR, York, AE. 2006. Decline in northern fur seal (callorhinus ursinus) pup production on the Pribilof Islands. Mar. Mamm. Sci. 22:486-491. do:10.1111/j.1748-7692.2006.00026.x.


A’mar, ZT, Punt, AE. 2005. Minimum Stock Size Thresholds: How well can we detect whether stocks are below them? p 487-508. In: Kruse, G, Gallucci, VF, Hay, DE, Perry, RI, Peterman, RM, Shirley, TC, Spencer, PD, Wilson, B,  Woodby, D [ed.] Assessment and management of new and developed fisheries in data-limited situations. Alaska Sea Grant College Program, University of Alaska Fairbanks.

Piner, KR, Haltuch, MA, Wallace, J. 2005. Preliminary use of oxygen stable isotopes and the 1983 El Nino to assess the accuracy of aging black rockfish (Sebastes melanops). Fish Bull. 103:553-558.


Cope, JM. 2004. Population genetics and phylogeography of the blue rockfish (Sebastes mystinus) from Washington to California. Can. J. Fish. Aquat. Sci. 61:332-342.  doi:10.1139/F04-008.

Punt, AE,  Allison, C, Fay, G. 2004. An examination of assessment models for the Eastern North Pacific Gray whale based on inertial dynamics.  J. Cetacean. Res. Manage. 6:121-132


Kinzey, D, Gerrodette, T. 2003. Distance measurements using binoculars from ships at sea: accuracy, precision and effects of refraction. J. Cetacean Res. Manage. 5: 159-171.

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