Koop:Publications

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Koop lab publications (partial list)

2008 Yazawa R, Cooper GA, Hunt P, Beetz-Sargent M, Robb A, Conrad M, McKinnel L, So S, Jantzen S, Phillips RB, Davidson WS, and Koop BF. Striking antigen recognition diversity in the Atlantic salmon T-cell receptor alpha/delta locus. Dev Comp Immunol. 2008;32(3):204-12. DOI:10.1016/j.dci.2007.05.002 |

2007 Wilson MD, Wang D, Wagner R, Breyssens H, Gertsenstein M, Lobe C, Lu X, Nagy A, Burke RD, Koop BF, and Howard PL. ARS2 is a conserved eukaryotic gene essential for early mammalian development. Mol Cell Biol. 2008 Mar;28(5):1503-14. DOI:10.1128/MCB.01565-07 | de Boer JG, Yazawa R, Davidson WS, and Koop BF. Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics. 2007 Nov 16;8:422. DOI:10.1186/1471-2164-8-422 | Wright JJ, Lubieniecki KP, Park JW, Ng SH, Devlin RH, Leong J, Koop BF, and Davidson WS. Sixteen type 1 polymorphic microsatellite markers from Chinook salmon (Oncorhynchus tshawytscha) expressed sequence tags. Anim Genet. 2008 Feb;39(1):84-5. DOI:10.1111/j.1365-2052.2007.01666.x | Conrad ML, Davis WC, and Koop BF. TCR and CD3 antibody cross-reactivity in 44 species. Cytometry A. 2007 Nov;71(11):925-33. DOI:10.1002/cyto.a.20435 | Lukacs MF, Harstad H, Grimholt U, Beetz-Sargent M, Cooper GA, Reid L, Bakke HG, Phillips RB, Miller KM, Davidson WS, and Koop BF. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics. 2007 Jul 25;8:251. DOI:10.1186/1471-2164-8-251 | Mos L, Tabuchi M, Dangerfield N, Jeffries SJ, Koop BF, and Ross PS. Contaminant-associated disruption of vitamin A and its receptor (retinoic acid receptor alpha) in free-ranging harbour seals (Phoca vitulina). Aquat Toxicol. 2007 Mar 10;81(3):319-28. DOI:10.1016/j.aquatox.2006.12.017 | Finne EF, Cooper GA, Koop BF, Hylland K, and Tollefsen KE. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture. Aquat Toxicol. 2007 Mar 10;81(3):293-303. DOI:10.1016/j.aquatox.2006.12.010 | Conrad ML, Mawer MA, Lefranc MP, McKinnell L, Whitehead J, Davis SK, Pettman R, and Koop BF. The genomic sequence of the bovine T cell receptor gamma TRG loci and localization of the TRGC5 cassette. Vet Immunol Immunopathol. 2007 Feb 15;115(3-4):346-56. DOI:10.1016/j.vetimm.2006.10.019 |

2006 Rise ML, Douglas SE, Sakhrani D, Williams J, Ewart KV, Rise M, Davidson WS, Koop BF, and Devlin RH. Multiple microarray platforms utilized for hepatic gene expression profiling of GH transgenic coho salmon with and without ration restriction. J Mol Endocrinol. 2006 Oct;37(2):259-82. DOI:10.1677/jme.1.02031 | Wilson MD, Cheung J, Martindale DW, Scherer SW, and Koop BF. Comparative analysis of the paired immunoglobulin-like receptor (PILR) locus in six mammalian genomes: duplication, conversion, and the birth of new genes. Physiol Genomics. 2006 Nov 27;27(3):201-18. DOI:10.1152/physiolgenomics.00284.2005 | Duffy SP, Young AM, Morin B, Lucarotti CJ, Koop BF, and Levin DB. Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome. J Virol. 2006 Jul;80(14):6952-63. DOI:10.1128/JVI.00187-06 | Morrison RN, Cooper GA, Koop BF, Rise ML, Bridle AR, Adams MB, and Nowak BF. Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.): a role for tumor suppressor p53 in AGD pathogenesis?. Physiol Genomics. 2006 Jun 16;26(1):15-34. DOI:10.1152/physiolgenomics.00320.2005 | Artieri CG, Mitchell LA, Ng SH, Parisotto SE, Danzmann RG, Hoyheim B, Phillips RB, Morasch M, Koop BF, and Davidson WS. Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2. Cytogenet Genome Res. 2006;112(1-2):152-9. DOI:10.1159/000087528 | von Schalburg KR, McCarthy SP, Rise ML, Hutson JC, Davidson WS, and Koop BF. Expression of morphogenic genes in mature ovarian and testicular tissues: potential stem-cell niche markers and patterning factors. Mol Reprod Dev. 2006 Feb;73(2):142-52. DOI:10.1002/mrd.20359 |

2005 Hunt PN, Wilson MD, von Schalburg KR, Davidson WS, and Koop BF. Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein. BMC Genomics. 2005 Nov 22;6:165. DOI:10.1186/1471-2164-6-165 | von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson CC, Davidson WS, and Koop BF. Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics. 2005 Sep 15;6:126. DOI:10.1186/1471-2164-6-126 | Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, and Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005 Oct;86(4):396-404. DOI:10.1016/j.ygeno.2005.06.001 | Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, and Høyheim B. A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics. 2005 Apr 4;6:50. DOI:10.1186/1471-2164-6-50 | von Schalburg KR, Rise ML, Brown GD, Davidson WS, and Koop BF. A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biol Reprod. 2005 Mar;72(3):687-99. DOI:10.1095/biolreprod.104.034967 |

2004 Rise ML, Jones SR, Brown GD, von Schalburg KR, Davidson WS, and Koop BF. Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiol Genomics. 2004 Dec 15;20(1):21-35. DOI:10.1152/physiolgenomics.00036.2004 | McKay SJ, Trautner J, Smith MJ, Koop BF, and Devlin RH. Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. Genome. 2004 Aug;47(4):714-23. DOI:10.1139/g04-018 | Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, and Koop BF. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 2004 Mar;14(3):478-90. DOI:10.1101/gr.1687304 |

2003 Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HH, Koop BF, and Scherer SW. Recent segmental and gene duplications in the mouse genome. Genome Biol. 2003;4(8):R47. DOI:10.1186/gb-2003-4-8-r47 | Montpetit A, Wilson MD, Chevrette M, Koop BF, and Sinnett D. Analysis of the conservation of synteny between Fugu and human chromosome 12. BMC Genomics. 2003 Jul 23;4(1):30. DOI:10.1186/1471-2164-4-30 | Wen XY, Hegele RA, Wang J, Wang DY, Cheung J, Wilson M, Yahyapour M, Bai Y, Zhuang L, Skaug J, Young TK, Connelly PW, Koop BF, Tsui LC, and Stewart AK. Identification of a novel lipase gene mutated in lpd mice with hypertriglyceridemia and associated with dyslipidemia in humans. Hum Mol Genet. 2003 May 15;12(10):1131-43. DOI:10.1093/hmg/ddg124 | Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HH, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GA, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJ, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, and Tsui LC. Human chromosome 7: DNA sequence and biology. Science. 2003 May 2;300(5620):767-72. DOI:10.1126/science.1083423 | Rexroad CE 3rd, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, and Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res. 2003;102(1-4):347-54. DOI:10.1159/000075773 | R. J. Nelson , C. C. Wood, G. Cooper, C. Smith and B. Koop. 2003. Population structure of sockeye salmon of the central coast of British Columbia: Implications for recovery planning. North American Journal of Fisheries Management 23, 703-720.

2002 Dunn HG, Stoessl AJ, Ho HH, MacLeod PM, Poskitt KJ, Doudet DJ, Schulzer M, Blackstock D, Dobko T, Koop B, and de Amorim GV. Rett syndrome: investigation of nine patients, including PET scan. Can J Neurol Sci. 2002 Nov;29(4):345-57. DOI:10.1017/s0317167100002213 | Shuttleworth TL, Wilson MD, Wicklow BA, Wilkins JA, and Triggs-Raine BL. Characterization of the murine hyaluronidase gene region reveals complex organization and cotranscription of Hyal1 with downstream genes, Fus2 and Hyal3. J Biol Chem. 2002 Jun 21;277(25):23008-18. DOI:10.1074/jbc.M108991200 | Conrad ML, Pettman R, Whitehead J, McKinnel L, Davis SK, and Koop BF. Genomic sequencing of the bovine T cell receptor beta locus. Vet Immunol Immunopathol. 2002 Sep 10;87(3-4):439-41. DOI:10.1016/s0165-2427(02)00093-4 | C. T. Smith, R. J. Nelson , S. Pollard, E. Rubidge, S. McKay, J. Rodzen, B. May, B. Koop. 2002. Population genetic analysis of white sturgeon. Journal of Applied Ichthyology 18, 307-312. T. W. J. Garner, P. T. Gregory, G. F. McCracken, G. M. Burghardt, B. F. Koop, S. E. Houts and R. J. Nelson . 2002. Geographic variation of multiple paternity in the common garter snake ( Thamnophis sirtalis ). Copeia 1 , 15-23.

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