Refereed publications

Eslamloo K, Xue X, Booman M, Smith NC, and Rise ML. 2016. Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages. Developmental and Comparative Immunology 63, 187-205.

Hixson SM, Parrish CC, Xue X, Wells JS, Collins SA, Anderson DM, and Rise ML. 2016. Growth performance, tissue composition, and gene expression responses in Atlantic salmon (Salmo salar) fed varying levels of different lipid sources. Aquaculture (In press. Available online 19 April 2016.

Brown TD, Hori TS, Xue X, Ye CL, Anderson DM, and Rise ML. 2016. Functional genomic analysis of the impact of camelina (Camelina sativa) meal on Atlantic salmon (Salmo salar) distal intestine gene expression and physiology. Marine Biotechnology 18(3), 418-435.

Katan T, Nash GW, Rise ML, Hall JR, Fernandes, JMO, Boyce D, Johnsen CE, and Gamperl AK. 2016. A little goes a long way: Improved growth in Atlantic cod (Gadus morhua) fed small amounts of wild zooplankton. Aquaculture 451, 271-282.

Rise ML, Hall JR, Nash GW, Xue X, Booman M, Katan T, and Gamperl AK. 2015. Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis. BMC Genomics 16, 1016.

Alzaid A, Hori TS, Hall JR, Rise ML, and Gamperl AK. 2015. Cold-induced changes in stress hormone and steroidogenic transcript levels in cunner (Tautogolabrus adspersus), a fish capable of metabolic depression. General and Comparative Endocrinology 224, 126-135.

Inkpen SM, Hori TS, Gamperl AK, Nash GW, and Rise ML. 2015. Characterization and expression analyses of five interferon regulatory factor transcripts (Irf4a, Irf4b, Irf7, Irf8, Irf10) in Atlantic cod (Gadus morhua). Fish and Shellfish Immunology 44(1), 365-381.

Xue X, Hixson SM, Hori TS, Booman M, Parrish CC, Anderson DM, and Rise ML. 2015. Atlantic salmon (Salmo salar) liver transcriptome response to diets containing Camelina sativa products. Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics 14, 1-15.


Hall JR, Clow KA, Rise ML, and Driedzic WR. 2015. Cloning and characterization of aquaglyceroporin genes from rainbow smelt (Osmerus mordax) and transcript expression in response to cold temperature. Comparative Biochemistry and Physiology, Part B: Biochemistry and Molecular Biology 187, 39-54.

McDonald M, Mannion M, Pike D, Lewis K, Flynn A, Brannan AM, Browne MJ, Jackman D, Madera L, Power Coombs MR, Hoskin DW, Rise ML, and Booth V. 2015. Structure-function relationships in histidine-rich antimicrobial peptides from Atlantic cod. Biochimica et Biophysica Acta - Biomembranes 1848(7), 1451-1461.

Evans ML, Hori TS, Rise ML, and Fleming, IA. 2015. Transcriptomic responses of Atlantic salmon (Salmo salar) to environmental enrichment during juvenile rearing. PLoS One 10(3), e0118378.

Zanuzzo FS, Urbinati EC, Rise ML, Hall JR, Nash GW, and Gamperl AK. 2015. Aeromonas salmonicida induced immune gene expression in Aloe vera fed steelhead trout, Oncorhynchus mykiss (Walbaum). Aquaculture 435, 1-9.

Søfteland L, Kurwan JA, Hori TS, Størseth TR, Sommer U, Berntssen MH, Viant MR, Rise ML, Waagbø R, Torstensen BE, Booman M, and Olsvik PA. 2014. Toxicological effect of single contaminants and contaminant mixtures associated with plant ingredients in novel salmon feeds. Food and Chemical Toxicology 73, 157-174.

Tuziak SM, Rise ML, and Volkoff H. 2014. An investigation of appetite-related peptide transcript expression in Atlantic cod (Gadus morhua) brain following a Camelina sativa meal-supplemented feeding trial. Gene 550, 253-263.

Xue X, Feng CY, Hixson SM, Johnstone K, Anderson DM, Parrish CC, and Rise ML. 2014. Characterization of the fatty acyl elongase (elovl) gene family, and hepatic elovl and delta-6 fatty acyl desaturase transcript expression and fatty acid responses to diets containing camelina oil in Atlantic cod (Gadus morhua). Comparative Biochemistry and Physiology, Part B: Biochemistry and Molecular Biology 175, 9-22.

Andrews CD, Payne JF, and Rise ML. 2014. Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar. Journal of Fish Biology 84(6), 1793-1819.

Booman M, Xu Q, and Rise ML. 2014. Evaluation of the impact of camelina oil-containing diets on the expression of genes involved in the innate anti-viral immune response in Atlantic cod (Gadus morhua). Fish and Shellfish Immunology 41(1), 52-63.

Rise ML, Nash GW, Hall JR, Booman M, Hori TS, Trippel EA, and Gamperl AK. 2014. Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) broodstock: a functional genomics study. Marine Genomics 18, 3-20.

Dunham RA, Taylor JF, Rise ML, and Liu Z. 2014. Development of strategies for integrated breeding, genetics and applied genomics for genetic improvement of aquatic organisms. Aquaculture 420-421, S121-S123.

Hori TS, Gamperl AK, Nash GW, Booman M, Barat A, and Rise ML. 2013. The impact of a moderate chronic temperature increase on spleen immune-relevant gene transcription depends on whether Atlantic cod are stimulated with bacterial versus viral antigens. Genome 56, 567-576.

Xu Q, Feng CY, Hori TS, Plouffe DA, Buchanan JT, and Rise ML. 2013. Family-specific differences in growth rate and hepatic gene expression in juvenile triploid growth hormone (GH) transgenic Atlantic salmon (Salmo salar). Comparative Biochemistry and Physiology, Part D, Genomics and Proteomics 8, 317-333.

Liu Q, Rise ML, Spitsbergen JM, Hori TS, Mieritz M, Geis S, McGraw JE, Goetz G, Larson J, Hutz RJ, and Carvan MJ III. 2013. Gene expression and pathologic alterations in juvenile rainbow trout due to chronic dietary TCDD exposure. Aquatic Toxicology 140-141, 356-368.

Rise ML, Hall JR, Alcock BP, and Hori TS. 2012. Dynamic expression profiles of virus-responsive and putative antimicrobial peptide-encoding transcripts during Atlantic cod (Gadus morhua) embryonic and early larval development. Gene 509(2), 232-246.

Hori TS, Gamperl AK, Booman M, Nash GW, and Rise ML. 2012. A moderate increase in ambient temperature modulates the Atlantic cod (Gadus morhua) spleen transcriptome response to intraperitoneal viral mimic injection. BMC Genomics 13, 431.

Hall JR, Short CE, Rise ML, and Driedzic WR. 2012. Expression analysis of glycerol synthesis-related liver transcripts in rainbow smelt (Osmerus mordax) exposed to a controlled decrease in temperature. Physiological and Biochemical Zoology 85(1), 74-84.

Hori TS, Rise ML, Johnson SC, Afonso LO, and Gamperl AK. 2012. The mRNA expression of cortisol axis related genes differs in Atlantic cod (Gadus morhua) categorized as high or low responders. General and Comparative Endocrinology 175(2), 311-320.

Hall JR, Clow KA, Rise ML, and Driedzic WR. 2011. Identification and validation of differentially expressed transcripts in a hepatocyte model of cold-induced glycerol production in rainbow smelt (Osmerus mordax). American Journal of Physiology – Regulatory, Integrative and Comparative Physiology 301(4), R995-R1010.

Feng CY and Rise ML. 2011. Identification and molecular cloning of Atlantic cod (Gadus morhua) activating transcription factor 3 (ATF3) transcript and its induction in spleen following intraperitoneal polyriboinosinic polyribocytidylic acid injection. Fish and Shellfish Immunology 31, 475-481.

Booman M, Borza T, Hori TS, Feng CY, Higgins B, Culf A, Leger D, Chute I, Hall JR, Belkaid A, Rise M, Gamperl AK, Hubert S, Kimball J, Ouelette R, Johnson SC, Bowman S, and Rise ML. 2011. Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs. Marine Biotechnology 13, 733-750.

Bowman S, Hubert S, Higgins B, Stone C, Kimball J, Borza T, Bussey JT, Simpson G, Hall JR, Hori TS, Feng CY, Gamperl AK, Booman M, Rise M, Symonds J, Johnson SC, and Rise ML. 2011. An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua). Marine Biotechnology 13, 242-255.

Browne MJ, Feng CY, Booth V, and Rise ML. 2011. Characterization and expression studies of Gaduscidin-1 and Gaduscidin-2; paralogous antimicrobial peptide-like transcripts from Atlantic cod (Gadus morhua). Developmental and Comparative Immunology 35, 399-408.

Borza T, Stone C, Rise ML, Bowman S, and Johnson SC. 2010. Atlantic cod (Gadus morhua) CC chemokines: diversity and expression analysis. Developmental and Comparative Immunology 34, 904-913.

Callahan AG, Deibel D, McKenzie CH, Hall JR, and Rise ML. 2010. Survey of harbours in Newfoundland for indigenous and non-indigenous ascidians and an analysis of their cytochrome c oxidase I gene sequences. Aquatic Invasions 5, 31-39.

Feng CY and Rise ML. 2010. Characterization and expression analyses of anti-apoptotic Bcl-2-like genes NR-13, Mcl-1, Bcl-X1, and Bcl-X2 in Atlantic cod (Gadus morhua). Molecular Immunology 47, 763-784.

Hori TS, Gamperl AK, Afonso LOB, Johnson SC, Hubert S, Kimball J, Bowman S, and Rise ML. 2010. Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques. BMC Genomics 11, 72.

Lewis JM, Hori TS, Rise ML, Walsh PJ, and Currie S. 2010. Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss). Physiological Genomics 42, 361-373.

Rise ML, Hall JR, Rise M, Hori TS, Browne M, Gamperl AK, Hubert S, Kimball J, Bowman S, and Johnson SC. 2010. Impact of asymptomatic nodavirus carrier state and intraperitoneal viral mimic injection on brain transcript expression in Atlantic cod (Gadus morhua). Physiological Genomics 42, 266-280.

Workenhe ST, Rise ML, Kibenge MJT, and Kibenge FS. 2010. The fight between the teleost fish immune response and aquatic viruses. Molecular Immunology 47, 2525-2536.

Devlin RH, Sakhrani D, Tymchuk WE, Rise ML, and Goh B. 2009. Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch). Proceedings of the National Academy of Sciences USA 106, 3047-3052.

Feng CY, Johnson SC, Hori TS, Rise M, Hall JR, Gamperl AK, Hubert S, Kimball J, Bowman S, and Rise ML. 2009. Identification and analysis of differentially expressed genes in the immune tissues of Atlantic cod stimulated with formalin-killed, atypical Aeromonas salmonicida. Physiological Genomics 37, 149-163.

Goetz FW, Rise ML, Rise M, Goetz GW, Binkowski F, and Shepherd BS. 2009. Stimulation of growth and changes in the hepatic transcriptome by estradiol-17b in the yellow perch (Perca flavescens). Physiological Genomics 38, 261-280.

Lang AS, Rise ML, Culley AI, and Steward GF. 2009. RNA viruses in the sea. FEMS Microbiology Reviews 33, 295-323.

Workenhe ST, Hori TS, Rise ML, Kibenge MJT, and Kibenge FSB. 2009. Infectious salmon aneamia virus (ISAV) isolates induce distinct gene expression responses in the Atlantic salmon (Salmo salar) macrophage/dendritic-like cell line TO, assessed using genomic techniques. Molecular Immunology 46, 2955-2974.

Carvan MJ, Incardona JP, and Rise ML. 2008. Meeting the challenges of aquatic vertebrate ecotoxicology. BioScience 58, 1015-1025.

King Heiden TC, StrubleCA, Rise ML, Hessner MJ, Hutz RJ, and Carvan MJ. 2008. Molecular targets of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: Insights into TCDD-induced endocrine disruption and reproductive toxicity. Reproductive Toxicology 25, 47-57.

Pérez-Casanova JC, Rise ML, Dixon B, Hall JR, Afonso LOB, and Gamperl AK. 2008. Immune and stress responses of juvenile Atlantic cod (Gadus morhua) to a chronic thermal challenge. Fish and Shellfish Immunology 24, 600-609.

Rise ML, Hall J, Rise M, Hori T, Gamperl AK, Kimball J, Hubert S, Bowman S, and Johnson SC. 2008. Functional genomic analysis of the response of Atlantic cod (Gadus morhua) spleen to the viral mimic polyriboinosinic polyribocytidylic acid (pIC). Developmental and Comparative Immunology 32, 916-931.

von Schalburg KR, Cooper GA, Leong J, Robb A, Lieph R, Rise ML, Davidson WS, and Koop BF. 2008. Expansion of the genomics research on Atlantic salmon Salmo salar L. project (GRASP) microarray tools. Journal of Fish Biology 72, 2051-2070.

Gahr SA, Rexroad CE, Rise ML, Hunt P, Koop B. 2007. A survey of expressed sequence tags from the rainbow trout (Oncorhynchus mykiss) pituitary. Animal Biotechnology 18, 213-230.

Morrison RN, Cooper GA, Koop BF, Rise ML, Bridle AR, Adams MB, and Nowak BF. 2006. Transcriptome profiling of the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.): a role for the tumor suppressor protein p52 in AGD-pathogenesis? Physiological Genomics 26, 15-34. Cover Article.

Rise ML, Douglas SE, Sakhrani D, Williams J, Ewart KV, Rise M, Davidson WS, Koop BF, and Devlin RH. 2006. Multiple microarray platforms utilized for hepatic gene expression profiling of growth hormone transgenic coho salmon with and without ration restriction. Journal of Molecular Endocrinology 37, 259-282.

von Schalburg KR, McCarthy SP, Rise ML, Hutson JC, Davidson WS, and Koop BF. 2006. Expression of morphogenic genes in mature ovarian and testicular tissues: potential stem-cell niche markers and patterning factors. Molecular Reproduction and Development 73, 142-152.

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. 2005. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 86, 396-404.

von Schalburg KR, Rise ML, Brown GD, Davidson WS, and Koop BF. 2005. A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biology of Reproduction 72, 687-699.

von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson CC, Davidson WS, and Koop BF. 2005. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6, 126.

Rise ML, Jones SRM, Brown GD, von Schalburg KR, Davidson WS, and Koop BF. 2004. Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiological Genomics 20, 21-35.

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 SRM, Smailus DE, Jones SJM, Schein JE, Marra MA, Butterfield YSN, Stott JM, Ng SHS, Davidson WS, and Koop BF. 2004. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Research 14, 478-490.

Burke RD, Murray GA, Rise M, and Wang D. 2004. Integrins on eggs: the bC integrin subunit is essential for formation of the cortical actin cytoskeleton in sea urchin eggs. Developmental Biology 265, 53-60.

Rise M and Burke RD. 2002. SpADAM, a sea urchin ADAM, has conserved structure and expression. Mechanisms of Development 117, 275-281.

Murray G, Reed C, Marsden M, Rise M, Wang D, and Burke RD. 2000. The alphaBbetaC integrin is expressed on the surface of the sea urchin egg and removed at fertilization. Developmental Biology 227, 633-647.

Seyfried TN, Brigande JV, Flavin HJ, Frankel WN, Rise ML, and Wieraszko A. 1992. Genetic and biochemical correlates of epilepsy in El mouse. Neurosciences 18, 9-20.

Rise ML, Frankel WF, Coffin JM, and Seyfried TN. 1991. Genes for epilepsy mapped in the mouse. Science 253, 669-673.

Non-refereed contributions

Co-editor of book:

Aquaculture Biotechnology (edited by Garth L. Fletcher and Matthew L. Rise). 2012. Wiley-Blackwell, Ames, IA. 379 pages.

Book chapters (Rise trainees underlined):

Torresen OK, Rise ML, Jin X, Star B, MacKenzie S, Jakobsen KS, Nederbragt AJ, and Jentoft S. 2016. An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming. In Genomics in Aquaculture (eds. S. MacKenzie and S. Jentoft), Academic Press (Elsevier, London, UK). pp. 45-72.

Rise ML. 2012. Functional genomics research of Atlantic cod (Gadus morhua). In Functional Genomics in Aquaculture (eds. M. Saroglia and Z. Liu), John Wiley & Sons, Ames, IA. pp. 339-348.

Booman M and Rise ML. 2012. Genomic tools for understanding the molecular basis of production-relevant traits in finfish. In Aquaculture Biotechnology (eds. G.L. Fletcher and M.L. Rise), Wiley-Blackwell, Ames, IA. pp. 3-20.

Rise ML, Liu ZJ, Douglas SE, Brown LL, Nash JHE, and McFall-Ngai MJ. 2009. Aquaculture-related applications of DNA microarray technology. In Molecular Research in Aquaculture (ed. K. Overturf), Wiley-Blackwell, Ames, IA. pp. 63-101.

Rise ML, von Schalburg KR, Cooper GA, and Koop BF. 2007. Salmonid DNA microarrays and other tools for functional genomics research. In Aquaculture Genome Technologies (ed. Z. Liu), Blackwell Publishing, Ames, IA. pp. 369-411.

Carvan MJ, Rise ML, and Klaper RD. 2005. Genomic Technologies in Biomonitoring. In Water Encyclopedia, Vol. 5, Water Quality and Resource Development (ed. J.H. Lehr, J. Keeley, and J. Lehr), John Wiley and Sons, New York.


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