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Thompson K, Baker CS, van Helden A, Patel S, Millar C, CONSTANTINE ROCHELLE.  2012.  The world’s rarest whale. Current Biology. 22(21):R905-R906.
Tezanos-Pinto G, Baker CS, Russell K, Martien KK, Baird RW, Hutt A, Stone GS, Mignucci-Giannoni AA, Caballero S, Endo T et al..  2009.  A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand. The Journal of Heredity. 100(1):11-24. Abstract
Oremus M, Gales R, Dalebout ML, Funahashi N, Endo T, Kage T, Steel DJ, Baker CS.  2009.  Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.). Biological Journal of the Linnean Society. 98(4):729-744.
Rosenbaum H, Brownell RL, Brown MW, Schaeff C, Portway V, White BN, Malik S, Pastene LA, Patenaude NJ, Baker CS et al..  2000.  World-wide genetic differentiation of Eubalaena: questioning the number of right whale species. Molecular Ecology. 9(11):1793-1802.
Costello MJ, Baker CS.  2011.  Who eats sea meat? Expanding human consumption of marine mammals Biological Conservation. 144(12):2745-2746.
Baker CS, Palumbi SR.  1994.  Which Whales Are Hunted? A Molecular Genetic Approach to Monitoring Whaling Science. 265(5178):1538-1539.
Tallmon DA, Gregovich DP, Waples RS, Baker CS, Jackson J, Taylor BL, Archer E, Martien KK, Allendorf FW, Schwartz MK.  2010.  When are genetic methods useful for estimating contemporary abundance and detecting population trends? Molecular Ecology Resources. 10(4):684-692. Abstract
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Witteveen BH, Straley JM, Chenoweth E, Baker CS, Barlow J, Matkin C, Gabriele CM, Neilson J, Steel DJ, von Ziegesar O et al..  2011.  Using movements, genetics and trophic ecology to differentiate inshore from offshore aggregations of humpback whales in the Gulf of Alaska. Endangered Species Research. 14(3):217-225.
Tiedemann R, Cipriano F, Morin PA, Hoelzel AR, Palsbøll P, Waples RS, Natoli L, Bachmann L, Postma L, Double MC et al..  2012.  Updated guidelines for DNA data quality control and error rate estimation, for genetic studies relevant to IWC management advice. Report to the Scientific Committee of the International Whaling Commission.
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Baker CS.  2008.  A truer measure of the market: the molecular ecology of fisheries and wildlife trade. Molecular Ecology. 17(18):3985-98. Abstract
Caballero S, Trujillo F, Vianna JA, Barrios-Garrido H, Montiel MG, Beltrán-Pedreros S, Marmontel M, Santos MC, Rossi M, Santo FR et al..  2007.  Taxonomic status of the genus Sotalia: species level ranking for “tucuxi” (Sotalia fluviatilis) and “costero” (Sotalia guianensis) dolphins. Marine Mammal Science. 23:358-386.
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Endo T, Hisamichi Y, Kimura O, Haraguchi K, Lavery S, Dalebout ML, Funahashi N, Baker CS.  2010.  Stable isotope ratios of carbon and nitrogen and mercury concentrations in 13 toothed whale species taken from the western Pacific Ocean off Japan. Environmental Science & Technology. 44(7):2675-81. Abstract
Endo T, Hotta Y, Hisamichi Y, Kimura O, Sato R, Haraguchi K, Funahashi N, Baker CS.  2012.  Stable isotope ratios and mercury levels in red meat products from baleen whales sold in Japanese markets. Ecotoxicology and Environmental Safety. 79:35-41.
Baker CS, Hutt A, Thompson K, Dalebout ML, Robins J, Stone GS.  2012.  Species identity and local use of cetaceans in the Gilbert Islands, Republic of Kiribati. Report to the Scientific Committee of the International Whaling Commission.
Baker CS, Hutt A, Thompson K, Dalebout ML, Robins J, Brownell RL, Stone GS.  2013.  Species identity and human consumption of beaked whales in the Gilbert Islands, Republic of Kiribati. Animal Conservation. :n/a-n/a.
Tezanos-Pinto G, Baker CS.  2011.  Short-term reactions and long-term responses of bottlenose dolphins (Tursiops truncatus) to remote biopsy sampling. New Zealand Journal of Marine and Freshwater Research. :1-17. Abstract
Wiseman N, Parsons S, Stockin KA, Baker CS.  2011.  Seasonal occurrence and distribution of Bryde's whales in the Hauraki Gulf, New Zealand. Marine Mammal Science. 27(4):E253-E267. Abstract
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Baker CS, Galletti B, Childerhouse S, Brownell, Jr. RL, Friedlaender A, Gales N, Hall A, Jackson J, Leaper R, Perryman W et al..  2012.  Report of the Symposium and Workshop on Living Whales in the Southern Ocean: Puerto Varas, Chile 27–29 March 2012. Report to the Scientific Committee of the International Whaling Commission.
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Slikas B, Baker CS, Clapham P, Frasier TR, Seger J, Valenzuela L, Wade P.  2012.  Proposal to the Scientific Committee: Worldwide genetic diversity and phylogenetic relationships among right whales based on next-generation sequencing of complete mitochondrial geneomes and multiple nuclear loci. Report to the Scientific Committee of the International Whaling Commission.
Baker CS, Sremba AL, Martin AR.  2012.  Proposal to the Scientific Committee: Single nuclear polymorphism (SNP) discovery and diversity in bones from South Georgia Island and contemporary Antarctic blue whales: a request for access to IDCR-SOWER biopsy samples (1990-2009). Report to the Scientific Committee of the International Whaling Commission.
Oremus M, Legata J, Hurutarau J, Taei S, Donoghue M, Baker CS.  2012.  Progress report on the genetic and demographic assessment of dolphin taken in live-capture and traditional drive-hunt in the Solomon Islands. Report to the Scientific Committee of the International Whaling Commission.
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.
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.
Olavarria C, Baker CS, Garrigue C, Poole MM, Hauser N, Caballero S, Flórez-González L, Brasseur M, Bannister JL, Capella J et al..  2007.  Population structure of humpback whales throughout the South Pacific and the origins of the eastern Polynesian breeding grounds. Marine Ecology Progress Series. 330:257-268.
Carroll E, Patenaude N, Alexander A, Steel DJ, Harcourt R, Childerhouse S, Smith S, Bannister JL, Constantine R, Baker CS.  2011.  Population structure and individual movement of southern right whales around New Zealand and Australia. Marine Ecology Progress Series. 432:257-268. Abstract