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A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate.

Messmer AM, Leong JS, Rondeau EB, Mueller A, Despins CA, Minkley DR, Kent MP, Lien S, Boyce B, Morrison D, Fast MD, Norman JD, Danzmann RG, Koop BF.

Mar Genomics. 2018 Apr 16. pii: S1874-7787(17)30254-4. doi: 10.1016/j.margen.2018.03.005. [Epub ahead of print]


High level efficacy of lufenuron against sea lice (Lepeophtheirus salmonis) linked to rapid impact on moulting processes.

Poley JD, Braden LM, Messmer AM, Igboeli OO, Whyte SK, Macdonald A, Rodriguez J, Gameiro M, Rufener L, Bouvier J, Wadowska DW, Koop BF, Hosking BC, Fast MD.

Int J Parasitol Drugs Drug Resist. 2018 Aug;8(2):174-188. doi: 10.1016/j.ijpddr.2018.02.007. Epub 2018 Mar 13.


Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome.

Christensen KA, Leong JS, Sakhrani D, Biagi CA, Minkley DR, Withler RE, Rondeau EB, Koop BF, Devlin RH.

PLoS One. 2018 Apr 5;13(4):e0195461. doi: 10.1371/journal.pone.0195461. eCollection 2018.


Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon.

Le Luyer J, Laporte M, Beacham TD, Kaukinen KH, Withler RE, Leong JS, Rondeau EB, Koop BF, Bernatchez L.

Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):12964-12969. doi: 10.1073/pnas.1711229114. Epub 2017 Nov 21.


Subcellular localization and characterization of estrogenic pathway regulators and mediators in Atlantic salmon spermatozoal cells.

von Schalburg KR, Gowen BE, Leong JS, Rondeau EB, Davidson WS, Koop BF.

Histochem Cell Biol. 2018 Jan;149(1):75-96. doi: 10.1007/s00418-017-1611-3. Epub 2017 Oct 5.


Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis).

Poley JD, Sutherland BJG, Fast MD, Koop BF, Jones SRM.

BMC Genomics. 2017 Aug 17;18(1):630. doi: 10.1186/s12864-017-4040-8.


Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE Rd, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM; FAASG Consortium.

BMC Genomics. 2017 Jun 27;18(1):484. doi: 10.1186/s12864-017-3862-8.


Cypermethrin exposure induces metabolic and stress-related gene expression in copepodid salmon lice (Lepeophtheirus salmonis).

Poley JD, Braden LM, Messmer AM, Whyte SK, Koop BF, Fast MD.

Comp Biochem Physiol Part D Genomics Proteomics. 2016 Dec;20:74-84. doi: 10.1016/j.cbd.2016.08.004. Epub 2016 Aug 31.


Sex-biased gene expression and sequence conservation in Atlantic and Pacific salmon lice (Lepeophtheirus salmonis).

Poley JD, Sutherland BJ, Jones SR, Koop BF, Fast MD.

BMC Genomics. 2016 Jul 4;17:483. doi: 10.1186/s12864-016-2835-7.


A PCR assay detects a male-specific duplicated copy of Anti-Müllerian hormone (amh) in the lingcod (Ophiodon elongatus).

Rondeau EB, Laurie CV, Johnson SC, Koop BF.

BMC Res Notes. 2016 Apr 22;9:230. doi: 10.1186/s13104-016-2030-6.


The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.


Multi-tissue transcriptome profiles for coho salmon (Oncorhynchus kisutch), a species undergoing rediploidization following whole-genome duplication.

Kim JH, Leong JS, Koop BF, Devlin RH.

Mar Genomics. 2016 Feb;25:33-37. doi: 10.1016/j.margen.2015.11.008. Epub 2015 Nov 21.


Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C).

Müller A, Sutherland BJ, Koop BF, Johnson SC, Garver KA.

BMC Genomics. 2015 Aug 26;16:634. doi: 10.1186/s12864-015-1759-y.


Differential modulation of resistance biomarkers in skin of juvenile and mature pink salmon, Oncorhynchus gorbuscha by the salmon louse, Lepeophtheirus salmonis.

Braden LM, Barker DE, Koop BF, Jones SR.

Fish Shellfish Immunol. 2015 Nov;47(1):7-14. doi: 10.1016/j.fsi.2015.08.008. Epub 2015 Aug 10.


A comprehensive analysis of teleost MHC class I sequences.

Grimholt U, Tsukamoto K, Azuma T, Leong J, Koop BF, Dijkstra JM.

BMC Evol Biol. 2015 Mar 6;15:32. doi: 10.1186/s12862-015-0309-1.


Transcriptomic responses to emamectin benzoate in Pacific and Atlantic Canada salmon lice Lepeophtheirus salmonis with differing levels of drug resistance.

Sutherland BJ, Poley JD, Igboeli OO, Jantzen JR, Fast MD, Koop BF, Jones SR.

Evol Appl. 2015 Feb;8(2):133-48. doi: 10.1111/eva.12237. Epub 2014 Dec 22.


Signatures of resistance to Lepeophtheirus salmonis include a TH2-type response at the louse-salmon interface.

Braden LM, Koop BF, Jones SR.

Dev Comp Immunol. 2015 Jan;48(1):178-91. doi: 10.1016/j.dci.2014.09.015. Epub 2014 Oct 16.


Chemokine receptors in Atlantic salmon.

Grimholt U, Hauge H, Hauge AG, Leong J, Koop BF.

Dev Comp Immunol. 2015 Mar;49(1):79-95. doi: 10.1016/j.dci.2014.11.009. Epub 2014 Nov 15.


Atlantic salmon possesses two clusters of type I interferon receptor genes on different chromosomes, which allows for a larger repertoire of interferon receptors than in zebrafish and mammals.

Sun B, Greiner-Tollersrud L, Koop BF, Robertsen B.

Dev Comp Immunol. 2014 Dec;47(2):275-86. doi: 10.1016/j.dci.2014.08.007. Epub 2014 Aug 19.


The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei.

Rondeau EB, Minkley DR, Leong JS, Messmer AM, Jantzen JR, von Schalburg KR, Lemon C, Bird NH, Koop BF.

PLoS One. 2014 Jul 28;9(7):e102089. doi: 10.1371/journal.pone.0102089. eCollection 2014.


Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis.

Sutherland BJ, Koczka KW, Yasuike M, Jantzen SG, Yazawa R, Koop BF, Jones SR.

BMC Genomics. 2014 Mar 15;15:200. doi: 10.1186/1471-2164-15-200.


Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss.

Sutherland BJ, Hanson KC, Jantzen JR, Koop BF, Smith CT.

Mol Ecol. 2014 Apr;23(8):1952-64. doi: 10.1111/mec.12713. Epub 2014 Apr 5.


Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates.

Dijkstra JM, Grimholt U, Leong J, Koop BF, Hashimoto K.

BMC Evol Biol. 2013 Nov 26;13:260. doi: 10.1186/1471-2148-13-260.


Transcriptional responses in a Drosophila defensive symbiosis.

Hamilton PT, Leong JS, Koop BF, Perlman SJ.

Mol Ecol. 2014 Mar;23(6):1558-70. doi: 10.1111/mec.12603. Epub 2013 Dec 28.


Sex-specific expression and localization of aromatase and its regulators during embryonic and larval development of Atlantic salmon.

von Schalburg KR, Gowen BE, Messmer AM, Davidson WS, Koop BF.

Comp Biochem Physiol B Biochem Mol Biol. 2014 Feb;168:33-44. doi: 10.1016/j.cbpb.2013.11.004. Epub 2013 Nov 13.


Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene.

Rondeau EB, Messmer AM, Sanderson DS, Jantzen SG, von Schalburg KR, Minkley DR, Leong JS, Macdonald GM, Davidsen AE, Parker WA, Mazzola RS, Campbell B, Koop BF.

BMC Genomics. 2013 Jul 6;14:452. doi: 10.1186/1471-2164-14-452.


Sex-specific expression, synthesis and localization of aromatase regulators in one-year-old Atlantic salmon ovaries and testes.

von Schalburg KR, Gowen BE, Rondeau EB, Johnson NW, Minkley DR, Leong JS, Davidson WS, Koop BF.

Comp Biochem Physiol B Biochem Mol Biol. 2013 Apr;164(4):236-46. doi: 10.1016/j.cbpb.2013.01.004. Epub 2013 Feb 4.


Early response of gene expression in the distal intestine of Atlantic salmon (Salmo salar L.) during the development of soybean meal induced enteritis.

Sahlmann C, Sutherland BJ, Kortner TM, Koop BF, Krogdahl A, Bakke AM.

Fish Shellfish Immunol. 2013 Feb;34(2):599-609. doi: 10.1016/j.fsi.2012.11.031. Epub 2012 Dec 11.


Transcriptomics of coping strategies in free-swimming Lepeophtheirus salmonis (Copepoda) larvae responding to abiotic stress.

Sutherland BJ, Jantzen SG, Yasuike M, Sanderson DS, Koop BF, Jones SR.

Mol Ecol. 2012 Dec;21(24):6000-14. doi: 10.1111/mec.12072. Epub 2012 Oct 25.


Identification of surrogates of protection against yersiniosis in immersion vaccinated Atlantic salmon.

Bridle AR, Koop BF, Nowak BF.

PLoS One. 2012;7(7):e40841. doi: 10.1371/journal.pone.0040841. Epub 2012 Jul 12.


Identification of olfactory receptor genes in Atlantic salmon Salmo salar.

Johnstone KA, Lubieniecki KP, Koop BF, Davidson WS.

J Fish Biol. 2012 Jul;81(2):559-75. doi: 10.1111/j.1095-8649.2012.03368.x. Review.


Characterization of the Atlantic salmon (Salmo salar) brain-type fatty acid binding protein (fabp7) genes reveals the fates of teleost fabp7 genes following whole genome duplications.

Lai YY, Lubieniecki KP, Koop BF, Davidson WS.

Gene. 2012 Aug 10;504(2):253-61. doi: 10.1016/j.gene.2012.04.089. Epub 2012 May 8.


Comparative defense-associated responses in salmon skin elicited by the ectoparasite Lepeophtheirus salmonis.

Braden LM, Barker DE, Koop BF, Jones SR.

Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):100-9. doi: 10.1016/j.cbd.2011.12.002. Epub 2011 Dec 29.


Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka).

Pavey SA, Sutherland BJ, Leong J, Robb A, von Schalburg K, Hamon TR, Koop BF, Nielsen JL.

BMC Ecol. 2011 Dec 2;11:31. doi: 10.1186/1472-6785-11-31.


Expression of olfactory receptors in different life stages and life histories of wild Atlantic salmon (Salmo salar).

Johnstone KA, Lubieniecki KP, Koop BF, Davidson WS.

Mol Ecol. 2011 Oct;20(19):4059-69. doi: 10.1111/j.1365-294X.2011.05251.x. Epub 2011 Aug 29.


GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets.

Jantzen SG, Sutherland BJ, Minkley DR, Koop BF.

BMC Res Notes. 2011 Jul 28;4:267. doi: 10.1186/1756-0500-4-267.


Ribosomal genes and heat shock proteins as putative markers for chronic, sublethal heat stress in Arctic charr: applications for aquaculture and wild fish.

Quinn NL, McGowan CR, Cooper GA, Koop BF, Davidson WS.

Physiol Genomics. 2011 Sep 22;43(18):1056-64. doi: 10.1152/physiolgenomics.00090.2011. Epub 2011 Jul 12.


Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes.

Yasuike M, Leong J, Jantzen SG, von Schalburg KR, Nilsen F, Jones SR, Koop BF.

Mar Biotechnol (NY). 2012 Apr;14(2):155-66. doi: 10.1007/s10126-011-9398-z. Epub 2011 Jul 12.


A transcriptomic scan for positively selected genes in two closely related marine fishes: Sebastes caurinus and S. rastrelliger.

Heras J, Koop BF, Aguilar A.

Mar Genomics. 2011 Jun;4(2):93-8. doi: 10.1016/j.margen.2011.02.001. Epub 2011 Mar 9.


Differentiating size-dependent responses of juvenile pink salmon (Oncorhynchus gorbuscha) to sea lice (Lepeophtheirus salmonis) infections.

Sutherland BJ, Jantzen SG, Sanderson DS, Koop BF, Jones SR.

Comp Biochem Physiol Part D Genomics Proteomics. 2011 Jun;6(2):213-23. doi: 10.1016/j.cbd.2011.04.001. Epub 2011 Apr 15.


Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress.

Quinn NL, McGowan CR, Cooper GA, Koop BF, Davidson WS.

Physiol Genomics. 2011 Jun 15;43(11):685-96. doi: 10.1152/physiolgenomics.00008.2011. Epub 2011 Apr 5.


A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.).

Jantzen SG, Sanderson DS, von Schalburg KR, Yasuike M, Marass F, Koop BF.

BMC Res Notes. 2011 Mar 29;4:88. doi: 10.1186/1756-0500-4-88.


Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010.

Molecular Ecology Resources Primer Development Consortium, Aggarwal RK, Allainguillaume J, Bajay MM, Barthwal S, Bertolino P, Chauhan P, Consuegra S, Croxford A, Dalton DL, den Belder E, Díaz-Ferguson E, Douglas MR, Drees M, Elderson J, Esselink GD, Fernández-Manjarrés JF, Frascaria-Lacoste N, Gäbler-Schwarz S, Garcia de Leaniz C, Ginwal HS, Goodisman MA, Guo B, Hamilton MB, Hayes PK, Hong Y, Kajita T, Kalinowski ST, Keller L, Koop BF, Kotzé A, Lalremruata A, Leese F, Li C, Liew WY, Martinelli S, Matthews EA, Medlin LK, Messmer AM, Meyer EI, Monteiro M, Moyer GR, Nelson RJ, Nguyen TT, Omoto C, Ono J, Pavinato VA, Pearcy M, Pinheiro JB, Power LD, Rawat A, Reusch TB, Sanderson D, Sannier J, Sathe S, Sheridan CK, Smulders MJ, Sukganah A, Takayama K, Tamura M, Tateishi Y, Vanhaecke D, Vu NV, Wickneswari R, Williams AS, Wimp GM, Witte V, Zucchi MI.

Mol Ecol Resour. 2011 Jan;11(1):219-22. doi: 10.1111/j.1755-0998.2010.02944.x.


General and family-specific gene expression responses to viral hemorrhagic septicaemia virus infection in rainbow trout (Oncorhynchus mykiss).

Jørgensen HB, Sørensen P, Cooper GA, Lorenzen E, Lorenzen N, Hansen MH, Koop BF, Henryon M.

Mol Immunol. 2011 Apr;48(8):1046-58. doi: 10.1016/j.molimm.2011.01.014. Epub 2011 Feb 22.


Identification of the sex chromosomes of brown trout (Salmo trutta) and their comparison with the corresponding chromosomes in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss).

Li J, Phillips RB, Harwood AS, Koop BF, Davidson WS.

Cytogenet Genome Res. 2011;133(1):25-33. doi: 10.1159/000323410. Epub 2011 Jan 20.


Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon.

von Schalburg KR, Yasuike M, Yazawa R, de Boer JG, Reid L, So S, Robb A, Rondeau EB, Phillips RB, Davidson WS, Koop BF.

BMC Genomics. 2011 Jan 13;12:31. doi: 10.1186/1471-2164-12-31.


Comparative genomic analysis of Atlantic salmon, Salmo salar, from Europe and North America.

Lubieniecki KP, Jones SL, Davidson EA, Park J, Koop BF, Walker S, Davidson WS.

BMC Genet. 2010 Nov 23;11:105. doi: 10.1186/1471-2156-11-105.


Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire.

Quinn NL, Boroevich KA, Lubieniecki KP, Chow W, Davidson EA, Phillips RB, Koop BF, Davidson WS.

BMC Genomics. 2010 Oct 5;11:539. doi: 10.1186/1471-2164-11-539.


Sequencing the genome of the Atlantic salmon (Salmo salar).

Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW.

Genome Biol. 2010;11(9):403. doi: 10.1186/gb-2010-11-9-403. Epub 2010 Sep 30.

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