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2013
Ruegg K, Rosenbaum HC, Anderson EC, Engel M, Rothschild A, Baker CS, Palumbi SR.  2013.  Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure. Conservation Genetics. 14(1):103-114.
2010
Ruegg KC, Anderson EC, Baker CS, Vant MD, Jackson J, Palumbi SR.  2010.  Are Antarctic minke whales unusually abundant because of 20th century whaling? Molecular Ecology. 19(2):281-291.
2009
Jackson J, Baker CS, Vant MD, Steel DJ, Medrano-Gonzalez L, Palumbi SR.  2009.  Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti). Molecular Biology and Evolution. 26(11):2427-40. Abstract
2000
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.
1996
Baker CS, Cipriano F, Palumbi SR.  1996.  Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan. Molecular Ecology. 5(5):671-685.
1994
Baker CS, Palumbi SR.  1994.  Which Whales Are Hunted? A Molecular Genetic Approach to Monitoring Whaling Science. 265(5178):1538-1539.
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.
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