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Cooke, S.J., Raby, G.D., Bett, N.N., *Teffer, A.K., Burnett, N.J., Jeffries, K.M., Eliason, E.J., Martins, E.G., Miller, K.M., Patterson, D.A. Nguyen, V.M. 2021. On conducting management-relevant mechanistic science for upriver migrating adult Pacific salmon. Chapter 3 in Conservation Physiology: Applications for Wildlife Conservation and Management (eds. Madliger, C.L., Franklin, C.E., Love, O.P., Cooke, S.J.) Oxford University Press, UK. DOI: 10.1093/oso/9780198843610.003.0003 Furey, N.B., Bass, A.L., Miller, K.M., Li, S., Lotto, A.G., Healy, S.J., Drenner, S.M. Hinch, S.G. 2021. Infected juvenile salmon can experience increased predation during freshwater migration. Royal Society open science, 8(3), p.201522. DOI: 10.1098/rsos.201522 *Chapman, JM, Kelly, L, *Teffer, AK, Miller, KM, Cooke, SJ. 2021. Disease ecology of wild fish: Opportunities and challenges for linking infection metrics with behaviour, condition, and survival . Canadian Journal of Fisheries and Aquatic Sciences. DOI: 10.1139/cjfas-2020-0315 Mordecai, G.J., Miller, K.M., Bass, A.L., Bateman, A.W., Teffer, A.K., Caleta, J.M., Di Cicco, E., Schulze, A.D., Kaukinen, K.H., Li, S. Tabata, A., 2021. Aquaculture mediates global transmission of a viral pathogen to wild salmon . Science Advances, 7(22), p.eabe2592. DOI: 10.1126/sciadv.abe2592 Jeffries, K.M., Teffer, A., Michaleski, S., Bernier, N.J., Heath, D.D., Miller, K.M. 2021. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes . Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, p.110629. DOI: 10.1016/j.cbpb.2021.110629 He, X., Gilmore, S.R., Sutherland, T.F., Hajibabaei, M., Miller, K.M., Westfall, K.M., Pawlowski, J., Abbott, C.L. 2021. Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments . Molecular Ecology, 30(13), pp.3158-3174. DOI: 10.1111/mec.15814 *Chapman, JM, Lennox, RJ , *Twardek, WM, *Teffer, AK, Robertson, MJ, Miller, KM, Cooke, SJ. 2021. Serial sampling reveals temperature associated response in transcription profiles and shifts in condition and infectious agent communities in wild Atlantic salmon . Freshwater Biology, 66(11) p.2086-2104 DOI: 10.1111/fwb.13817 *Mordecai, GJ, *Di Cicco, Gunther, OP, *Schulze, AD, *Kaukinen, KH, *Li, S, *Tabata, A, *Ming, TJ, Ferguson, HW, Suttle, CA, Miller, KM. 2021. Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR . Virus Evolution 7(1). DOI: 10.1093/ve/veaa069 *Bateman, AW, *Schulze, AD, *Kaukinen, KH, *Tabata, A, *Mordecai, G,* Flynn, K, *Di Cicco, E, Miller, KM. 2021. Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean . Scientific Reports 11, 3466. DOI: 10.1038/s41598-020-78978-9. 2020
*Teffer A.K., Carr, J., *Tabata, A.,* Schulze, A., Bradbury, I., Deschamps, D., Gillis, C-A., Brunsdon, E.B., *Mordecai, G., Miller, K.M. 2020. A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks . Facets 5(1), 234-263. DOI: 10.1139/facets-2019-0048 *Chapman, J.M., *Teffer, A.K., *Bass, A.L., Patterson, D.A., Hinch, S.G., Miller, K.M., Cooke, S.J. 2020. Handling, infectious agents, and physiological condition influence survival and post-release behaviour in migratory adult coho salmon after experimental displacement . Conservation Physiology 8(1). DOI:10.1093/conphys/coaa033 Lennox, R.J., Eldøy, S.H., Vollset, K.W., Miller, K.M., Li, S., *Kaukinen, K.H., Isaksen, T.E., Davidsen, J.G. 2020. How pathogens affect the marine habitat use and migration of sea trout (Salmo trutta) in two Norwegian fjord systems . Journal of Fish Diseases 43: 729-746. DOI: 10.1111/jfd.13170 Akbarzadeh, A., Houde, A.L.S., Sutherland, B.J., Günther, O.P., Miller, K.M. 2020. Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR . G3: Genes, Genomes, Genetics, 10(9), p.3321-3336. DOI:10.1534/g3.120.401487 Shea, D., Bateman, A., Li, S., Tabata, A., Schulze, A., Mordecai, G., Ogston, L., Volpe, J.P., Neil Frazer, L., Connors, B. Miller, K.M., Short, S., Krkosek, M. 2020. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms . Proceedings of the Royal Society B, 287(1937), p.20202010. DOI: 10.1098/rspb.2020.2010 Lehman, B, Johnson, R, Foott, S, Som, NA, Burgess, O, Adkison, M, Miller, K, Hallet, S, Purcell, M, Martínez-López, B, Valdes-Donoso, P, Connon, R, Fangu, N, Collins, AL. 2020. Disease in Central Valley salmon: Status and lessons from other systems . San Francisco Estuary and Watershed Science 18(3). DOI: 10.15447//sfews.2020v18iss3art2 2019
*Laurin, E., Jaramillo, D., Vanderstichel, R., Ferguson, H., Kaukinen, K.H., Schulze, A.D., Keith, I.R., Gardner, I.A., Miller, K.M. 2019. Histopathological and novel high-throughput molecular monitoring data from farmed salmon (Salmo salar and Oncorhynchus spp.) in British Columbia, Canada, from 2011-2013 . Aquaculture 499, p. 220-224. DOI: 10.1016/j.aquaculture.2018.08.072 *Thakur, K.K., Vanderstichel, R., Kaukinen, K.H., Nekouei, O., Laurin, E., Miller, K.M. 2019. Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia (1985-1994). Journal of Fish Diseases, 42(4) p. 533-547. DOI: 10.1111/jfd.12951 *Pagowski, V.A., *Mordecai, G.J., Miller, K.M., *Schulze, A., *Kaukinen, K., *Ming, T., *Li, S, *Teffer, A.K., *Tabata, A., Suttle, C.A. 2019. Distribution and phylogeny of erythrocytic necrosis virus (ENV) in salmon suggests marine origin . Viruses 11(4), p.358. DOI: 10.3390/v11040358 *Stevenson, C.F., *Bass, A.L., *Furey, N.C., Miller, K.M., Li, S., Rechisky, E.L., Porter, A,S., Welch, D.W., Hinch S.G. 2019. Infectious agents and gene expression differ between sockeye salmon (Oncorhynchus nerka) smolt age classes but do not predict migration survival . Canadian Journal of Fisheries and Aquatic Sciences: DOI: 10.1139/cjfas-2019-0113. EDITORS CHOICE AWARD *Houde, A.L.S., Schulze, A.D., Kaukinen, K.H., Strohm, J., Patterson, D.A., Beacham, T.D., Farrell, A.P., Hinch, S.G., Miller, K.M. 2019. Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments . Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 29. P. 32-42. DOI: 10.1016/j.cbd.2018.10.002 *Houde, A.L.S., Gunther, O.P., Strohm, J., Ming, T.J., Li, S., Kaukinen, K.H., Patterson, D.A., Farrell, A.P., Hinch, S.G., Miller, K.M. 2019. Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids. Conservation Physiology 7(1), p.coz051 DOI: 10.1093/conphys/coz051 *Houde, A.L.S., Akbarzadeh, A., Gunther, O.P., Li, S., Patterson, D.A., Farrell, A.P., Hinch, S.G., Miller, K.M. 2019. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen. Journal of Experimental Biology p.jeb-198036. DOI: 10.1242/jeb-198036 *Twardek, W.M., *Chapman, J.M., Miller, K.M., Beere, M.C., *Li, S., *Kaukinen, K.H., Danylchuk, A.J., Cooke, S.J. 2019. Evidence of a hydraulically challenging reach serving as a barrier for the upstream migration of infection-burdened adult steelhead. Conservation Physiology 7(1); coz023, DOI: 10.1093/conphys/coz023 *Mordecai, G.J., Miller, K.M., *Di Cicco, E., *Schulze, A.D., *Kaukinen, K.H.,*Ming, T.J.,*Li, S., *Tabata, A., *Teffer, A., Patterson, D.A., Ferguson, H., Suttle, C.A. 2019 Endangered wild salmon infected by newly discovered viruses . eLife, 8. DOI: 10.7554/eLife.47615 Ferguson, H.W., *Di Cicco, E., Sandoval, C., MacPhee, D.D., Miller, K.M. 2019. Haemorrhagic kidney syndrome may not be a variation of Infectious salmon anaemia . Aquaculture, 516 p.734498. DOI: 10.1016/j.aquaculture.2019.734498 *Nekouei, O., Vanderstichel, R., *Kaukinen, K.H., *Thakur, K., *Ming, T., Patterson, D.A., Trudel, M., Neville, C., Miller, K.M. 2019. Comparison of infectious agents detected from hatchery and wild juvenile Coho salmon in British Columbia, 2008-2018. PloS one, 14(9). DOI: 10.1371/journal.pone.0221956 *Teffer, A.K, Hinch, S., Miller, K.M.,*Jeffries, K., Patterson, D., Cooke, S., Farrell, A., *Kaukinen, K.H., *Li, S., Juanes, F. 2019. Cumulative Effects of Thermal and Fisheries Stressors Reveal Sex-Specific Effects on Infection Development and Early Mortality of Adult Coho Salmon (Oncorhynchus kisutch) . Physiological and Biochemical Zoology, 92(5), pp.505-529. DOI: 10.1086/705125 2018
Welch, D.W., Futia, M.H., Rinchard, J., *Teffer, A.K., Miller, K.M., Hinch, S.G. Honeyfield, D.C. 2018. Thiamine Levels in Muscle and Eggs of Adult Pacific Salmon from the Fraser River, British Columbia . Journal of Aquatic Animal Health, 30(3), p.191-200. DOI: 10.1002/aah.10024 *Healy, S., Hinch, S.G., *Bass, A.L., Porter, A.D., Rechisky, E.L., Welch, D.W., *Lotto, A.G., *Furey, N.B., Miller, K.M. 2018. Transcriptome profiles relate to migration fate in hatchery Steelhead (Oncorhynchus mykiss ) smolts . Canadian Journal of Fisheries and Aquatic Sciences. DOI: 10.1139/cjfas-2017-0424 *Teffer AK, *Bass AL, Miller KM, Patterson, DM, Juanes, F, Hinch, SG. 2018. Infections, fisheries capture, temperature and host responses: multi-stressor influences on survival and behaviour of adult Chinook salmon . Canadian Journal of Fisheries and Aquatic Sciences. DOI: 10.1139/cjfas-2017-0491 *Thakur, K.K., Vanderstichel, R., *Li, S., *Laurin, E., *Tucker, S., Neville, C., *Tabata, A., Miller, K.M. 2018. A comparison of infectious agents between hatchery-enhanced and wild out-migrating juvenile Chinook salmon (Oncorhynchus tshawytscha ) from Cowichan River, British Columbia . FACETS 3(1): 695-721. DOI: 10.1139/facets-2017-0113 *Di Cicco, E., Ferguson, H.W., Kaukinen, K.H., Schulze, A.D., Li, S., Tabata, A., Gunther, O.P., Mordecai, G., Suttle, C.A., Miller, K.M. 2018. The same strain of Piscine orthoreovirus (PRV) is involved with the development of different, but related, diseases in Atlantic and Pacific Salmon in British Columbia . FACETS 3(1): 599-641. DOI: 10.1139/facets-2018-0008. *Nekouei, O., Vanderstichel, R., Ming, T. Kaukinen, K.H., Thakur, K.K., Tabata, A., Laurin, E., Tucker, S., Beacham, T.D., Miller, K.M. 2018. Detection and assessment of the distribution of infectious agents in juvenile Fraser River Sockeye salmon , Canada, in 2012 and 2013. Frontiers in Microbiology 9: 3221. DOI: 10.3389/fmicb.2018.03221 *Akbarzadeh, Gunther, O.P., Houde, A.L., Li, S. Ming, T.J., Jeffries, K.M., Hinch, S.G., Miller, K.M. 2018. Developing specific molecular biomarkers for thermal stress in salmonids . BMC Genomics, 19(1): 749. DOI: 10.1186/s12864-018-5108-9. 2017
*Drenner, S.M., Hinch, S.G.,* Furey, N.B., Clark, T.D., *Li, S.,*Ming, T., *Jeffries, K.M., Patterson, D.A., Cooke, S.J., Robichaud, D., Welch, D.W., Farrell, A.P., Miller, K.M. 2017. Transcriptome patterns and blood physiology associated with homing success of sockeye salmon during their final stage of marine migration . Canadian Journal of Fisheries and Aquatic. Sciences. 75(9) p. 1511-1524. DOI: 10.1139/cjfas-2017-0391. *Di Cicco, E., Ferguson, H.W., *Schulze, A.D., *Kaukinen, K.H., *Li, S., Vanderstichel, R., Wessel, Ø., Rimstad, E., Gardner, I.A., Hammell, K.L., Miller, K.M. 2017. Heart and skeletal muscle inflammation (HSMI) disease diagnosed on a British Columbia salmon farm through a longitudinal farm study . PLOS ONE 12 (2017) e0171471. DOI: 10.1371/journal.pone.0171471. *Teffer A.K., Hinch, S.G., Miller, K.M., Patterson, D.A., Farrell, A.P., Cooke, S.J., Bass, A.L., Szekeres, P., Juanes, F. 2017. Capture severity, infectious disease processes, and sex influence post-release mortality of sockeye salmon bycatch . Conservation Physiology 5(1). DOI: 10.1093/conphys/cox017. Miller, K.M., *Li, S., *Ming, T., *Kaukinen, K., *Ginther, N., Patterson, D.A., Trudel, M. 2017. Survey of infectious agents detected in juvenile chinook and sockeye salmon from British Columbia and Washington. NPAFC doc1718. Bernatchez, L., Wellenreuther, M., Araneda, C., Ashton, D.T., Barth, J.M.I., Beacham, T.D., Maes, G.E., Martinsohn, J.T., Miller, K.M., Naish, K.A., Ovenden, J.R. Primmer, C.R., Suk, H.Y., Therkildsen, N.O., Withler, R.E. 2017. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends in Ecology & Evolution . 32(9) p.665-680. DOI: 10.1016/j.tree.2017.06.010. 2016
Miller, K.M., Gardner, I.A., Vanderstichel, R., Burnley, T., *Schulze, A.D., *Li, S., *Kaukinen, K.H., *Ming, T.J.,*Ginther, N.G. 2016. Report on the performance evaluation of the Fluidigm BioMarkTM platform for high-throughput microbe monitoring in salmon. Canadian Science Advisory Secretariat. Research Document 2016/038. Groner, M.L., Maynard, J., Breyta, R., Carnegie, R.B., Dobson, A., Friedman, C.S, Forelich, B., Garren, M., Gulland, F.M.D., Heron, S.F., Nobel, R.T., Revie, C.W., Shields, J.D., Vanderstchel, R., Weil, E., Wyllie-Echeverria, S. Harvell C.D. 2016. Managing marine disease emergencies in an era of rapid change . Philosophical Transactions of the Royal Society B, 371: 20150364. DOI: 10.1098/rstb.2015.0364 Garner, B.A., Hand, B.K., Amish, S.J., Bernatchez, L., Foster, J.T., Miller, K.M., Morin, P.A., Naurum, S.R., O’Brian, S.J., Roffler, G., Templin, W.D., Sunnucks, P., Strait, J., Warheit, K.I., Seamons, T.R., Wenburg, J., Olsen, J., Luikart, G. 2016. Genomics in conservation: case studies and bridging the gap between data and application . Trends in Ecology and Evolution. 31(2) p. 81-83. DOI: 10.1016/j.tree.2015.10.009 Patterson, D.A, Cooke, S.J., Hinch, S.G., Robinson, K.A., Young, N., Farrell, A.P., Miller, K.M. 2016. A perspective on physiological studies supporting the provision of scientific advice for the management of Fraser River sockeye salmon (Oncorhynchus nerka) . Conservation Physiology 4(1) cow026. DOI: 10.1093/conphys/cow026 2015
Raby, G.D., Donaldson, M.R., Hinch, S.G., Clark, T.D., Eliason, E.J., *Jeffries, K.M., Cook, K.V., *Teffer, A., *Bass, A.L, Miller, K.M, Patterson, D.A, Farrell, A.P, Cooke, S.J. 2015. Fishing for Effective Conservation: Context and Biotic Variation are Keys to Understanding the Survival of Pacific Salmon after Catch-and-Release . Integrative and Comparative Biology, 55(4) p. 554-576. DOI: 10.1093/icb/icv088 2014
*Jeffries, K.M., Hinch, S.G., Gale, M.K., Clark, T.D., *Lotto, A.G., Casselman, M.T., Miller, K.M. 2014. Immune response genes and pathogen presence predict migration survival in wild salmon smolts . Molecular Ecology. 23 p. 5803-5815. DOI: 10.1111/mec.12980 Miller, K.M., *Teffer, A., *Tucker, S., Li, S., *Schulze, A.D., Trudel, M., Juanes, F., *Tabata, A., *Kaukinen, K.H., *Ginther, N.G., *Ming, T.J., Cooke, S.J., Hipfner, J.M., Patterson, D.A., Hinch, S.G. 2014. Infectious disease, shifting climates and opportunistic predators: cumulative factors potentially impacting wild salmon declines . Evolutionary Applications 7(7) p. 812-855. DOI:10.1111/eva.12164
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