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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
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Baker CS, Medrano-Gonzalez L, Calambokidis J, Perry A, Pichler FB, Rosenbaum H, Straley JM, Urbán-Ramirez J, Yamaguchi M, von Ziegesar O.  1998.  Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific. Molecular Ecology. 7(6):695-707.
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
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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.
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Calambokidis J, Steiger GH, Evenson JR, Flynn KR, Balcomb KC, Claridge DE, Bloedel P, Straley JM, Baker CS, von Ziegesar O et al..  1996.  INTERCHANGE AND ISOLATION OF HUMPBACK WHALES OFF CALIFORNIA AND OTHER NORTH PACIFIC FEEDING GROUNDS. Marine Mammal Science. 12(2):215-226.
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
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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.
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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.
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Berman-Kowalewski M, Gulland F, Wilkin S, Calambokidis J, Mate B, Cordaro J, Rotstein D, St. Leger J, Collins P, Fahy K et al..  2010.  Association between blue whale mortality and ship strikes along the California coast. Aquatic Mammal. 36(1):59-66. Abstract