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1990
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.
1996
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.
1998
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.
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
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
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.
2010
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