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1984
Harvey JT, Mate B.  1984.  Dive characteristics and movements of radio-tagged gray whales in San Ignacio Lagoon, Baja California Sur, Mexico. The Gray Whale. :561-575.
Herzing DL, Mate B.  1984.  Gray whale migrations along the Oregon coast, 1978-1981. The Gray Whale. :289-307.
Herzing DL, Mate B.  1984.  Ocean movements of radio tagged gray whales. The Gray Whale. :577-589.
1990
Scott MD, Wells RS, Irvine AB, Mate B.  1990.  Tagging and marking studies on small cetaceans. The Bottlenose Dolphin. :489-514.
Baker CS, Palumbi SR, Lambertsen RH, Weinrich MT, Calambokidis J, O'Brien SJ.  1990.  Influence of seasonal migration on geographic distribution of mitochondrial DNA haplotypes in humpback whales. Nature. 344(6263):238-40. Abstract
1993
Baker CS, Gilbert DA, Weinrich MT, Lambertsen RH, Calambokidis J, McArdle B, Chambers GK, O'Brien SJ.  1993.  Population characteristics of DNA fingerprints in humpback whales (Megaptera novaeangliae). The Journal of heredity. 84(4):281-90. Abstract
1994
Baker CS, Slade RW, Bannister JL, Abernethy RB, Weinrich MT, Lien J, Urbán-Ramirez J, Corkeron P, Calambokidis J, Vasquez O et al..  1994.  Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide. Molecular Ecology. 3(4):313-327.
1999
Mate B, Lagerquist BA, Calambokidis J.  1999.  Movements of North Pacific blue whales during the feeding season off southern California and their southern fall migration. Marine Mammal Science. 15:1246-1257.
2000
Lagerquist BA, Stafford KM, Mate B.  2000.  Dive characteristics of satellite-monitored blue whales (Balaenoptera musculus) off the central California coast. Marine Mammal Science. 16:375-391.
Le Boeuf BJ, Pérea-Cortés HM, Urbán-Ramirez J, Mate B, Ollervides UF.  2000.  High gray whale mortality and low recruitment in 1999: potential causes and implications. Journal of Cetacean Research Management. 2:85-99.
Baker CS, Lento GM, Cipriano F, Palumbi SR.  2000.  Predicted decline of protected whales based on molecular genetic monitoring of Japanese and Korean markets. Proceedings of the Royal Society B: Biological Sciences. 267(1449):1191-1199.
Williams TM, Davis RW, Fuiman LA, Francis J, Le Boeuf BJ, Horning M, Calambokidis J, Croll D.  2000.  Sink or swim: strategies for cost-efficient diving by marine mammals. Science (New York, N.Y.). 288(5463):133-6. Abstract
2002
Raum-Suryan KL, Pitcher KW, Calkins D, Sease J, Loughlin T.  2002.  Dispersal, rookery fidelity, and metapopulations structure of Steller sea lions (Eumetopias jubatus) in an increasing and decreasing population in Alaska. Marine Mammal Science. 18(3):746-764.
Baker CS, Dalebout ML, Lento GM, Funahashi N.  2002.  Gray whale products sold in commercial markets along the Pacific coast of Japan. Marine Mammal Science. 18(1):295-300.
2003
Mate B, Lagerquist BA, Urbán-Ramirez J.  2003.  A note on using satellite telemetry to document the use of San Ignacio Lagoon by gray whales (Eschrichtius robustus) during their reproductive season. Journal of Cetacean Research and Management. 5:148-154.
2004
Norman SA, Bowlby CE, Brancato MS, Calambokidis J, Duffield D, Gearin PJ, Gornall TA, Gosho ME, Hanson B, Hod H et al..  2004.  Cetacean strandings in Oregon and Washington between 1930 and 2002. Journal of Cetacean Research and Management. 6:87-99.
2005
Mate B, Lagerquist BA, Winsor M, Geraci J, Prescott JH.  2005.  Movements and dive habits of a satellite-monitored long-finned pilot whale (Globicephala melas) in the Northwest Atlantic. Marine Mammal Science. 21:136-144.
Mate B, Duley P, Lagerquist BA, Wenzel F, Stimpert A, Clapham P.  2005.  Observations of a female North Atlantic right whale (Eubalaena glacialis) in simultaneous copulation with two males: supporting evidence for sperm competition. Aquatic Mammals. 31:157-160. Abstract
Raum-Suryan KL, Pitcher KW, Lamy R.  2005.  Sea otter (Enhydra lutris) sightings off Haida Gwaii/Queen Charlotte Islands, Canada during the past tree decades. The Canadian Field-Naturalist. 118:270-272.
2006
Baker CS, Vant MD, Dalebout ML, Lento GM, O'Brien SJ, Yuhki N.  2006.  Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (Suborder: Mysticeti). Immunogenetics. 58:283-296.
Baker CS, Lukoschek V, Lavery S, Dalebout ML, Ma Y-un, Endo T, Funahashi N.  2006.  Incomplete reporting of whale, dolphin and porpoise ‘bycatch' revealed by molecular monitoring of Korean markets. Animal Conservation. 9:474-482.
Pendleton GW, Pitcher KW, Fritz L, Raum-Suryan KL, Loughlin T, Calkins D, York AE, Hastings K, Gelatt TS.  2006.  Survival of Steller sea lions in Alaska: a comparison of increasing and decreasing populations. Canadian Journal of Zoology. 84:1162-1172.
2007
Baker CS, Cooke J, Lavery S, Dalebout ML, Ma Y-un, Funahashi N, Carraher C, Brownell, Jr. RL.  2007.  Estimating the number of whales entering trade using DNA profiling and capture-recapture analysis of market products. Molecular Ecology. 13:2617-2626.
Mate B, Mesecar R, Lagerquist BA.  2007.  The evolution of satellite-monitored radio tags for large whales: One laboratory's experience. Deep Sea Research II. 54:224-247. Abstract
Campbell R, Gales NJ, Lento GM, Baker CS.  2007.  Islands in the sea: extreme female natal site fidelity in the Australian sea lion, Neophoca cinerea. Biology Letters. 4(1):139-142.