Ruggerone, G. T. and J. L. Nielsen. 2008. Growth and survival of salmon at sea in response to competition and climate change. (accepted) Sea Grant Publication AYK Sustainable Salmon Initiative.
Nielsen, J. L., A. Byrne, S. L. Graziano and C. C. Kozfay. 2008. Steelhead genetic diversity at multiple scales in a managed basin – Snake River, Idaho. (Accepted with revision) North American Journal Fisheries Management.
Nielsen, J. L., C. E. Zimmerman, R. Phillips, D. Noakes, J. Holmes and S. Crawford. Biology, life history and systematics of salmonid and osmerid fishes. In R. Mayden (ed.) Freshwater Fishes of North America. Academic Press (in press).
Nielsen, J. L., J. Dodson, K. Friedland, T. Hammon J. Musick, and E. Verspoor, (Eds.) 2008. Reconciling Fisheries with Conservation: Proceedings of the Fourth World Fisheries Congress. American Fisheries Society. Volumes I and II. 1946pp.
Nielsen, J. L. and G. Ruggerone. 2008. Climate change and a dynamic ocean carrying capacity: Growth and survival of Pacific salmon at sea. Proceedings Pacific Salmon Environment and Life History Models: Advancing Science for Sustainable Salmon. AFS Symposium Publication (in press).
Nielsen, J. L. 2007. AFS President’s Hook. The Last Hook. Fisheries 32(8):368.
Nielsen, J. L. 2007. AFS President’s Hook. Talent du jour: what’s in a name? Fisheries 32(7): 316 & 352.
Ruggerone, G. T., J. L. Nielsen and J. Bumgarner. 2007. Linkages between climate, growth at sea, and sockeye abundance in Bristol Bay, Alaska 1955-2002. Deep Sea Research II 54:2776-2793; doi:10.1016/j.dsr2.2007.08.016.
Ramey, A., S. L. Graziano, and J. L. Nielsen. 2007. Isolation and characterization of microsatellite loci from the Arctic cisco Coregonus autumnalis. Molecular Ecology Notes doi:10.1111/j.1471-8286.2007.1955.
Nielsen, J. L. 2007. AFS President’s Hook. Member-centric IT at AFS. Fisheries 32(6):264 & 304.
Nielsen, J. L. 2007. AFS President’s Hook. Savoring the Concept. Fisheries 32(5):212 & 250.
Pavey, S. A., T. R. Hamon and J. L. Nielsen. 2007. Revisiting the “evolutionary dead-end” hypothesis in sockeye salmon life history. Canadian Journal Fisheries and Aquatic Sciences 64:1199-1208.
Nielsen, J. L. 2007. AFS President’s Hook. Exploitation and conservation of nourishing males – Project Seahorse. Fisheries 32(4):160 & 196.
Nielsen, J. L. 2007. AFS President’s Hook. On the changing art of science. Fisheries 32(3):108 & 147.
Verspoor, E., L. Stradmeyer and J. Nielsen (Eds.) 2007. The Atlantic Salmon: Genetics, Conservation and Management. Blackwell Publishing pp 514.
Farley, E. V., J. M. Murphy, M. D. Adkison, J. J. Helle, J. H. Moss and J. L. Nielsen. 2007. Early marine growth in relation to marine-stage survival rates for Alaska sockeye salmon (Oncorhynchus nerka). Fisheries Bulletin 105: 121-130.
Williams, I., G. H. Reeves, S. Graziano and J. L. Nielsen. 2007. Genetic investigation of natural hybridization between rainbow and coastal cutthroat trout in the Copper River Delta, Alaska. Transactions AFS 136:926-942.
Nielsen, J. L. 2007. AFS President’s Hook. Fish Ecology and Economics: Complementary or transdisciplinary? Fisheries 32(2):56 & 95.
Nielsen, J. L. 2007. AFS President’s Hook. Sharing the Table and the Source. Fisheries 32(1): 4 & 46.
Nielsen, J. L. 2007. Atlantic Salmon Genetics: Past, Present and What’s in the Future? Chapter 15. In E. Vespoor, J. Nielsen, and L. Stradmeyer (eds.) The Atlantic Salmon: Genetics, Conservation and Management. Blackwell Scientific pp 483-494.
Hendrickson, D., D. Neely, R. Mayden, K. Anderson, J. Brooks, F. Camarena-Rosales, R. Cutted, L. Cutter, A. de Los Santos, G. Ernsting, H. Espinosa-Perez, L. Findley, F. Garcia de Leon, A. George, J. Hatch, B. Kuhajda, K. Mayden, K. McNyset, J. L. Nielsen, F. Pfeiffer, D. Propst, G. Ruiz-Campos, E. St. Clair, J. Tomelleri and A. Varela-Romero. 2006. Conservation of Mexican native trout and the discovery, status, protection and recovery of the Conchos trout, the first native Oncorhynchus of the Atlantic drainage in Mexico. Pages 162-201 in M. De Lourdes Lozano-Vilano and A. Contreras-Balderas (eds.) Studies of North American Desert Fishes. In Honor of E. P. (Phil) Pister, Conservationist. Universidad Autonoma de Nuevo, Leon, Mexico.
Nielsen, J. L. 2006. AFS President’s Hook. The nuances of grey and open access publishing at AFS. Fisheries 31(12):584.
Nielsen, J. L. 2006. AFS President’s Hook. Fair and Good Governance in AFS. Fisheries 31(11): 532.
Nielsen, J. L. 2006. AFS President’s Hook. Thoughts from Kansas. Fisheries 31(10): 480-514.
Nielsen, J. L. 2006. AFS President’s Hook. Looking downstream and downcurrent: Addressing complexity and unintended consequences in fish and fisheries. Fisheries 31(9):428-429.
Seitz, A. C., B. L. Norcross, D. Wilson and J. L. Nielsen. 2006. An evaluation of light-based geolocation for Pacific halibut (Hippoglossus stenolepis) in the northern Gulf of Alaska. Fisheries Research 104:571-578.
Graziano, S. L., K. Brown and J. L. Nielsen. 2005. Comment: Nomenclature of mitochondrial DNA haplotypes in Oncorhynchus mykiss. Transactions of the American Fisheries Society 14:1271-1273.
Nielsen, J. L., S. A. Pavey, T. Wiacek and I. Williams. 2005. Genetic analyses of Central Valley O. mykiss populations: Drainage and watershed scale analyses. San Francisco Estuary & Watershed Science.
Ruggerone, G. T., E. Farley, J. L. Nielsen and P. Hagen. 2005. Seasonal marine growth of Bristol Bay sockeye salmon (Oncorhynchus nerka) in relation to competition with Asian pink salmon (O. gorbuscha) and the 1997 ocean regime shift. Fisheries Bulletin 103:355-370.
Ruggerone G. and J. L. Nielsen. 2005. Evidence for competitive dominance of pink salmon (Oncorhynchus gorbuscha) over other salmonids in the North Pacific Ocean. Reviews in Fish Biology and Fisheries.
Seitz, A. C., B. L. Norcross, D. Wilson and J. L. Nielsen. 2005. Identifying spawning behavior in Pacific halibut, Hippogolssus stenolepis, using electronic tags. Environmental Biology of Fishes.
Nielsen, J. L. and G. Ruggerone. 2005. Non-linearity in Bristol Bay sockeye salmon growth: implication of Asian hatchery pink salmon production. In Burkett, V., D. A. Wilcox, R. Stottlemyer, W. Barrow, D. Fagre, J. Barton, J. Price, J. L. Nielsen, C. Allen, D. L. Peterson, G. Ruggerone, and T. Doyle. Nonlinear Dynamics in Ecosystem Response to Climatic Change: Case Studies and Policy Implications. Ecological Complexity.
Zimmerman, C. E. and J. L. Nielsen. 2005. Introduction to Special Issue: Interactions of Hatchery and Wild Salmonids in Marine and Estuarine Environments. Reviews in Fish Biology and Fisheries 14:301-303.
Nielsen, J. L. and H. Regier. 2004. Sustaining salmonid populations: a caring understanding of the naturalness of taxa. In D. MacDonald and E. Knudsen (eds.) Fish in Our Future? Perspectives on Fisheries Sustainability. American Fisheries Society Symposium 43: 203-211.
Thrower, F., C. Guthrie III, J. L. Nielsen, and J. Joyce. 2004. A comparison of genetic variation between an anadromous steelhead (Oncorhynchus mykiss) population and seven derived populations sequestered in freshwater for 70 years. Environmental Biology of Fishes 69: 111-125.
Nielsen, J. L., I. Williams, G. K. Sage and C. E. Zimmerman. 2003. The importance of genetic verification of identification of Atlantic salmon in Pacific waters. Journal of Fish Biology 62: 871-878.
Ruggerone, G. T., M. Zimmermann, K. W. Meyers, J. L. Nielsen and D. E. Rogers. 2003. Competition between Asian pink salmon and North American sockeye salmon in the North Pacific Ocean. Fisheries and Oceanography 12(3): 209-219.
Nielsen, J. L. and G. K. Sage. 2002. Population genetic structure in Lahontan cutthroat trout. Transactions American Fisheries Society. 131: 376-388.
Nielsen, J. L. and K. Sage. 2001. Microsatellite analyses of the trout of Northwest Mexico. Genetica 111(No.1-3): 269-278.