Koop:Publications

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Koop lab publications (partial list)

2007 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.

== [publications] == 2001 Smith CT, Nelson RJ, Wood CC, and Koop BF. Glacial biogeography of North American coho salmon (Oncorhynchus kisutch). Mol Ecol. 2001 Dec;10(12):2775-85. DOI:10.1046/j.1365-294x.2001.t01-1-01405.x | Wilson MD, Ruttan CC, Koop BF, and Glickman BW. ERCC1: a comparative genomic perspective. Environ Mol Mutagen. 2001;38(2-3):209-15. DOI:10.1002/em.1073 | Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, and Koop BF. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res. 2001 Mar 15;29(6):1352-65. DOI:10.1093/nar/29.6.1352 | Friedman JS, Koop BF, Raymond V, and Walter MA. Isolation of a ubiquitin-like (UBL5) gene from a screen identifying highly expressed and conserved iris genes. Genomics. 2001 Jan 15;71(2):252-5. DOI:10.1006/geno.2000.6439 | Hadano S, Yanagisawa Y, Skaug J, Fichter K, Nasir J, Martindale D, Koop BF, Scherer SW, Nicholson DW, Rouleau GA, Ikeda J, and Hayden MR. Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2. Genomics. 2001 Jan 15;71(2):200-13. DOI:10.1006/geno.2000.6392 | C. T. Smith, R. J. Nelson , C. C. Wood and B. Koop. 2001. Glacial biogeography of North American coho salmon ( Oncorhynchus kisutch ). Molecular Ecology 10, 2775-2785.

2000 Martindale DW, Wilson MD, Wang D, Burke RD, Chen X, Duronio V, and Koop BF. Comparative genomic sequence analysis of the Williams syndrome region (LIMK1-RFC2) of human chromosome 7q11.23. Mamm Genome. 2000 Oct;11(10):890-8. DOI:10.1007/s003350010166 | Bech-Hansen NT, Naylor MJ, Maybaum TA, Sparkes RL, Koop B, Birch DG, Bergen AA, Prinsen CF, Polomeno RC, Gal A, Drack AV, Musarella MA, Jacobson SG, Young RS, and Weleber RG. Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness. Nat Genet. 2000 Nov;26(3):319-23. DOI:10.1038/81619 | Edwards SV, Gasper J, Garrigan D, Martindale D, and Koop BF. A 39-kb sequence around a blackbird Mhc class II gene: ghost of selection past and songbird genome architecture. Mol Biol Evol. 2000 Sep;17(9):1384-95. DOI:10.1093/oxfordjournals.molbev.a026421 | Brown G, Martindale D, Wilson MD, Koop BF. Mouse and human DNA sequence comparisons: further evidence for a mosaic model of genomic evolution. In Sankoff D, Nadeau JH, eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families. Volume 1 of Series in Computational Biology. Dordrecht, NL: Kluwer Academic Press; 2000.

1999 McArthur AG and Koop BF. Partial 28S rDNA sequences and the antiquity of hydrothermal vent endemic gastropods. Mol Phylogenet Evol. 1999 Nov;13(2):255-74. DOI:10.1006/mpev.1999.0645 | Nelson CC, Hendy SC, Shukin RJ, Cheng H, Bruchovsky N, Koop BF, and Rennie PS. Determinants of DNA sequence specificity of the androgen, progesterone, and glucocorticoid receptors: evidence for differential steroid receptor response elements. Mol Endocrinol. 1999 Dec;13(12):2090-107. DOI:10.1210/mend.13.12.0396 | Moreau EJ, Langerak AW, van Gastel-Mol EJ, Wolvers-Tettero IL, Zhan M, Zhou Q, Koop BF, and van Dongen JJ. Easy detection of all T cell receptor gamma (TCRG) gene rearrangements by Southern blot analysis: recommendations for optimal results. Leukemia. 1999 Oct;13(10):1620-6. DOI:10.1038/sj.leu.2401540 | Brooks-Wilson A, Marcil M, Clee SM, Zhang LH, Roomp K, van Dam M, Yu L, Brewer C, Collins JA, Molhuizen HO, Loubser O, Ouelette BF, Fichter K, Ashbourne-Excoffon KJ, Sensen CW, Scherer S, Mott S, Denis M, Martindale D, Frohlich J, Morgan K, Koop B, Pimstone S, Kastelein JJ, Genest J Jr, and Hayden MR. Mutations in ABC1 in Tangier disease and familial high-density lipoprotein deficiency. Nat Genet. 1999 Aug;22(4):336-45. DOI:10.1038/11905 | Yang D, Kusser I, Köpke AK, Koop BF, and Matheson AT. The structure and evolution of the ribosomal proteins encoded in the spc operon of the archaeon (Crenarchaeota) Sulfolobus acidocaldarius. Mol Phylogenet Evol. 1999 Jul;12(2):177-85. DOI:10.1006/mpev.1998.0607 | Brickner AG, Koop BF, Aronow BJ, and Wiginton DA. Genomic sequence comparison of the human and mouse adenosine deaminase gene regions. Mamm Genome. 1999 Feb;10(2):95-101. DOI:10.1007/s003359900951 | Hadano S, Nichol K, Brinkman RR, Nasir J, Martindale D, Koop BF, Nicholson DW, Scherer SW, Ikeda JE, and Hayden MR. A yeast artificial chromosome-based physical map of the juvenile amyotrophic lateral sclerosis (ALS2) critical region on human chromosome 2q33-q34. Genomics. 1999 Jan 1;55(1):106-12. DOI:10.1006/geno.1998.5637 |

1998 Rasper DM, Vaillancourt JP, Hadano S, Houtzager VM, Seiden I, Keen SL, Tawa P, Xanthoudakis S, Nasir J, Martindale D, Koop BF, Peterson EP, Thornberry NA, Huang J, MacPherson DP, Black SC, Hornung F, Lenardo MJ, Hayden MR, Roy S, and Nicholson DW. Cell death attenuation by 'Usurpin', a mammalian DED-caspase homologue that precludes caspase-8 recruitment and activation by the CD-95 (Fas, APO-1) receptor complex. Cell Death Differ. 1998 Apr;5(4):271-88. DOI:10.1038/sj.cdd.4400370 | Smith CT, Koop BF, and Nelson RJ. Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Mol Ecol. 1998 Nov;7(11):1614-6. Mears AJ, Jordan T, Mirzayans F, Dubois S, Kume T, Parlee M, Ritch R, Koop B, Kuo WL, Collins C, Marshall J, Gould DB, Pearce W, Carlsson P, Enerbäck S, Morissette J, Bhattacharya S, Hogan B, Raymond V, and Walter MA. Mutations of the forkhead/winged-helix gene, FKHL7, in patients with Axenfeld-Rieger anomaly. Am J Hum Genet. 1998 Nov;63(5):1316-28. DOI:10.1086/302109 | Kotturi G, de Boer JG, Koop BF, and Glickman BW. Correlation of UV-induced mutational spectra and the in vitro damage distribution at the human hprt gene. Mutat Res. 1998 Jul 17;403(1-2):237-48. DOI:10.1016/s0027-5107(98)00085-2 | Bech-Hansen NT, Naylor MJ, Maybaum TA, Pearce WG, Koop B, Fishman GA, Mets M, Musarella MA, and Boycott KM. Loss-of-function mutations in a calcium-channel alpha1-subunit gene in Xp11.23 cause incomplete X-linked congenital stationary night blindness. Nat Genet. 1998 Jul;19(3):264-7. DOI:10.1038/947 | Kuo CL, Chen ML, Wang K, Chou CK, Vernooij B, Seto D, Koop BF, and Hood L. A conserved sequence block in murine and human T cell receptor (TCR) Jalpha region is a composite element that enhances TCR alpha enhancer activity and binds multiple nuclear factors. Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3839-44. DOI:10.1073/pnas.95.7.3839 | Bridge MA, Zhou Q, Koop BF, and Pearson TW. Cloning and characterization of the kinetoplastid membrane protein-11 gene locus of Trypanosoma brucei. Mol Biochem Parasitol. 1998 Mar 15;91(2):359-63. DOI:10.1016/s0166-6851(97)00229-6 | C. T. Smith, B. F. Koop, and R. J. Nelson . 1998. Isolation and characterization of coho salmon ( Oncorhynchus kisutch ) microsatellites and their use in other salmonids. Molecular Ecology 7, 1614-1615.

1997 Funkhouser W, Koop BF, Charmley P, Martindale D, Slightom J, and Hood L. Evolution and selection of primate T cell antigen receptor BV8 gene subfamily. Mol Phylogenet Evol. 1997 Aug;8(1):51-64. DOI:10.1006/mpev.1997.0406 | Cao JX, Koop BF, and Upton C. A human homolog of the vaccinia virus HindIII K4L gene is a member of the phospholipase D superfamily. Virus Res. 1997 Apr;48(1):11-8. DOI:10.1016/s0168-1702(96)01422-0 | Byun, S. A., B. Koop, T. E. Reimchen. 1997. North American black bear mtDNA phylogeography: implications for morphology and the Haida Gwaii refugium controversy. Evolution 51: 1647-1653. PDF file from Reimchen lab page

1996 Osborne LR, Martindale D, Scherer SW, Shi XM, Huizenga J, Heng HH, Costa T, Pober B, Lew L, Brinkman J, Rommens J, Koop B, and Tsui LC. Identification of genes from a 500-kb region at 7q11.23 that is commonly deleted in Williams syndrome patients. Genomics. 1996 Sep 1;36(2):328-36. DOI:10.1006/geno.1996.0469 | Belloni E, Muenke M, Roessler E, Traverso G, Siegel-Bartelt J, Frumkin A, Mitchell HF, Donis-Keller H, Helms C, Hing AV, Heng HH, Koop B, Martindale D, Rommens JM, Tsui LC, and Scherer SW. Identification of Sonic hedgehog as a candidate gene responsible for holoprosencephaly. Nat Genet. 1996 Nov;14(3):353-6. DOI:10.1038/ng1196-353 | Cattell K, Koop B, Olafson RS, Fellows M, Bailey I, Olafson RW, and Upton C. Approaches to detection of distantly related proteins by database searches. Biotechniques. 1996 Dec;21(6):1118-22, 1124-5. DOI:10.2144/96216bc03 | Rowen L, Koop BF, and Hood L. The complete 685-kilobase DNA sequence of the human beta T cell receptor locus. Science. 1996 Jun 21;272(5269):1755-62. DOI:10.1126/science.272.5269.1755 | Koop BF and Nadeau JH. Pufferfish and new paradigm for comparative genome analysis. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1363-5. DOI:10.1073/pnas.93.4.1363 | Koop BF, Richards JE, Durfee TD, Bansberg J, Wells J, Gilliam AC, Chen HL, Clausell A, Tucker PW, and Blattner FR. Analysis and comparison of the mouse and human immunoglobulin heavy chain JH-Cmu-Cdelta locus. Mol Phylogenet Evol. 1996 Feb;5(1):33-49. DOI:10.1006/mpev.1996.0005 |

1995 Koop BF. Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. Trends Genet. 1995 Sep;11(9):367-71. DOI:10.1016/s0168-9525(00)89108-8 | Hood L, Rowen L, and Koop BF. Human and mouse T-cell receptor loci: genomics, evolution, diversity, and serendipity. Ann N Y Acad Sci. 1995 Jun 30;758:390-412. DOI:10.1111/j.1749-6632.1995.tb24844.x |