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A
Witteveen BH, Straley JM, von Ziegesar O, Steel DJ, Baker CS.  2004.  Abundance and mtDNA differentiation of humpback whales (Megaptera novaeangliae) in the Shumagin Islands, Alaska. Canadian Journal of Zoology. 82:1352-1359.
Constantine R, Jackson JA, Steel DJ, Baker CS, Brooks L, Burns D, Clapham P, Hauser N, Madon B, Mattila D et al..  2012.  Abundance of humpback whales in Oceania using photo-identification and microsatellite genotyping. Marine Ecology Progress Series. 453:249-261.
Carroll EL, Patenaude NJ, Childerhouse SJ, Kraus SD, Fewster RM, Baker CS.  2011.  Abundance of the New Zealand subantarctic southern right whale population estimated from photo-identification and genotype mark-recapture. Marine Biology. 158(11):2565-2575. Abstract
Hollatz C, VILAÇA SIBELLETORRES, REDONDO RODRIGOAF, MARMONTEL MÍRIAM, Baker CS, Santos FR.  2011.  The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 102(4):812-827. Abstract
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.
B
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
C
Caballero S, Baker CS.  2009.  Captive-born intergeneric hybrid of a Guiana and bottlenose dolphin: Sotalia guianensis x Tursiops truncatus. Zoo Biology. Abstract
Sremba AL, Hancock-Hanser B, Branch TA, LeDuc RL, Baker CS.  2012.  Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia). PLoS ONE. 7(3):e32579.
Heimeier D, Baker CS, Duignan PJ, Russell K, Hutt A, Stone GS.  2009.  Confirmed expression of MHC class I and class II genes in the New Zealand endemic Hector's dolphin (Cephalorhynchus hectori). Marine Mammal Science. 25:68-90. Abstract
Baker CS, Chilvers BL, Constantine R, DuFresne S, Mattlin RH, van Helden A, Hitchmough R.  2010.  Conservation status of New Zealand marine mammals (suborders Cetacea and Pinnipedia), 2009. New Zealand Journal of Marine and Freshwater Research. 44(2):101-115. Abstract
Endo T, Hisamichi Y, Kimura O, Haraguchi K, Baker CS.  2008.  Contamination levels of mercury and cadmium in melon-headed whales (Peponocephala electra) from a mass stranding on the Japanese coast. The Science of the Total Environment. 401(1-3):73-80. Abstract
D
Tezanos-Pinto G, CONSTANTINE ROCHELLE, Brooks L, Jackson JA, Mourão F, Wells S, Baker CS.  2013.  Decline in local abundance of bottlenose dolphins (Tursiops truncatus) in the Bay of Islands, New Zealand. Marine Mammal Science. :n/a-n/a.
Robineau D, Goodall RNP, Pichler FB, Baker CS.  2007.  Description of a new subspecies of Commerson's dolphin, Cephalorhynchus commersonii (Lacépède, 1804), inhabiting the coastal waters of the Kerguelen Islands. Mammalia. 71:172-180.
Oremus M, Hamner RM, Stanley M, Brown P, Baker CS, Constantine R.  2012.  Distribution, group characteristics and movements of the Critically Endangered Maui’s dolphin Cephalorhynchus hectori maui. Endangered Species Research. 19(1):1-10.
Dalebout ML, Baker CS, Steel DJ, Robertson KM, Chivers SJ, Perrin WF, Mead JG, Grace RV, Schofield TD.  2007.  A divergent mtDNA lineage among Mesoplodon beaked whales: Molecular evidence for a new species in the tropical pacific? Marine Mammal Science. 23:954-966.
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.
E
Jackson J, Pinsky ML, Baker CS.  2009.  Erratum. How few whales were there after whaling? Inference from contemporary mtDNA diversity. Molecular Ecology. 18(19):4134-5.
Hamner RM, Oremus M, Stanley M, Brown P, Constantine R, Baker CS.  2012.  Estimating the abundance and effective population size of Maui’s dolphins using microsatellite genotypes in 2010–11, with retrospective matching to 2001–07.
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.
F
Garrigue C, Franklin T, Constantine R, Russell K, Burns D, Poole MM, Paton D, Hauser N, Oremus M, Childerhouse S et al..  2011.  First assessment of interchange of humpback whales between Oceania and the east coast of Australia. Journal of Cetacean Research and Management. (Special Issue 3):269-74.
G
Hamner RM, Pichler FB, Heimeier D, CONSTANTINE ROCHELLE, Baker CS.  2012.  Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins. Conservation Genetics. 13(4):987-1002.
Baker CS, Steel DJ, Choi Y, Lee H, Kim KS, Choi SK, Ma Y-un, Hambleton C, Psihoyos L, Brownell RL et al..  2010.  Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea. Biology Letters. Abstract
Oremus M, Gales R, Kettles H, Baker CS.  2013.  Genetic Evidence of Multiple Matrilines and Spatial Disruption of Kinship Bonds in Mass Strandings of Long-finned Pilot Whales, Globicephala melas. Journal of Heredity.
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.
Jackson JA, Laikre L, Baker CS, Kendall KC.  2012.  Guidelines for collecting and maintaining archives for genetic monitoring. Conservation Genetics Resources. 4(2):527-536.