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Contributing lab-members (past and present) emboldened

Up to date list: see Dan's Google Scholar Page

Peer-reviewed articles:

72. Johnston IA^, Kent MP, Boudinot, P, Looseley M, Bargelloni L, Faggion S, Merino GA, Ilsley GR, Bobe J, Tsigenopoulos CS, Robertson R, Harrison PW, Martinez M, Robledo D, Macqueen DJ * ^, Lien S *. 2024.  Advancing fish breeding in aquaculture through genome functional annotation. Aquaculture. 740589. doi: 10.1016/j.aquaculture.2024.740589.  * Equal contribution, ^ Corresponding authors.

71. Andresen AMS, Taylor RS, Grimholt U, Ruiz Daniels R, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ *, Fosse JH *. 2024. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. Fish Shellfish Immunol. 109357. doi: 10.1016/j.fsi.2024.109357. * Equal contribution and shared correspondence


70. Sun J, Ruiz Daniels R, Balic A, Andresen AMS, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SAM, Fosse JH, Taylor RS, Macqueen DJ. 2024. Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. Fish Shellfish Immunol. 109358. doi: 10.1016/j.fsi.2024.109358.


69. Matz H, Taylor RS, Redmond AK, Hill TM, Ruiz Daniels R, Beltran M, Henderson NC, Macqueen DJ, Dooley H. 2023. Organized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers. Cell Reports. 42: 112664


68. Clark T, Naseer S, Gundappa MK, Laurent A, Perquis A, Collet B, Macqueen DJ, Martin SAM, Boudinot P. 2023. Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes. Genomics. 115: 110663.


67. Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. 2023. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nat Commun. 14: 2879. doi: 10.1038/s41467-023-38714-z.

66. Ruiz Daniels R, Taylor RS, Dobie, R, Salisbury S, Clark E, Macqueen DJ, Robledo D. 2023. A versatile nuclei extraction protocol for single nucleus sequencing in non-model species – optimization in various Atlantic salmon tissues. PLoS One.  7: 18: e0285020. doi: 10.1371/journal.pone.0285020 

65. Ruiz Daniels RTaylor RT, Robledo D, Macqueen DJ. 2023. Single cell genomics as a transformative approach for aquaculture research and innovation. Reviews in Aquaculture.

64. Taylor RTRuiz Daniels R,  Dobie R, Naseer S, Clark T, Henderson N,  Boudinot P,  Martin SA, Macqueen DJ. 2022. Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida. Front. Immunol. doi: 10.3389/fimmu.2022.984799

63. Bean TP, Tanguy A, Peñaloza C, Gundappa MK, Boutet I, Houston RD, Macqueen DJ, Boudry P. 2022. Two parallel chromosome‐level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis. Evol Appl. doi: 10.1111/eva.13465


62. Gundappa MK, Peñaloza C, Regan T, Boutet I, Tanguy A, Houston RD, Bean TP, Macqueen DJ. 2022. Chromosome level reference genome for European flat oyster (Ostrea edulis L.). Evol Appl.


61. Peñaloza C, Preston J, Green M, Helmer L,  Kean-Hammerson J, Nascimento-Schulze JC, Minardi D, Gundappa MKMacqueen DJ
Hamilton J, Houston RD, Bean TP. 2022. Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis). Front. Genet. 13: 926638. doi: 10.3389/fgene.2022.926638


60. Sambade IM, Casanova A ,Blanco A, Gundappa MK, Bean TP, Macqueen DJ, Houston RD,  Villalba A, Vera M, Kamermans P, Martínez P. 2022. A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae. Evol Appl.


59. Bakke FK, Gundappa MK, Matz H, Stead DA, Macqueen DJ, Dooley H. 2022. Exploration of the Nurse Shark (Ginglymostoma cirratum) Plasma Immunoproteome Using High-Resolution LC-MS/MS. Front Immunol. 13:873390. doi: 10.3389/fimmu.2022.873390.


58. Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S, Karlsen M. 2021. Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses. 13: 2549. doi: 10.3390/v13122549.

57. Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist, J, Hazlerigg D, Sandve SR, Macqueen DJ. 2021. Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution. Mol. Biol. Evol. 2021;msab310. doi:10.1093/molbev/msab310

56. Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. 2021. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol. 22: 103. doi: 10.1186/s13059-021-02323-0.

55. Clark EL, Archibald AL, Daetwyler HD, Groenen MAM, Harrison PW, Houston RD, Kühn C, Lien S, Macqueen DJ, Reecy JM, Robledo D, Watson M, Tuggle CK, Giuffra E. 2020. From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome Biol. 21: 285. doi: 10.1186/s13059-020-02197-8. 

54. Bertolotti AC, Layer RM, Gundappa MK, Gallagher MD, Pehlivanoglu E, Nome T, Robledo D, Kent MP, Røsæg LL, Holen MH, Mulugeta TD, Ashton TJ, Hindar K, Sægrov H, Florø-Larsen B, Erkinaro J, Primmer CR, Bernatchez L, Martin SAM, Johnston IA, Sandve SR, Lien S, Macqueen DJ. 2020. The structural variation landscape in 492 Atlantic salmon genomes. Nature Commun. 11: 5176.

53. Bakke FK, Monte M, Stead DA, Cornulier T, Causey DR, Douglas A, Macqueen DJ*, Dooley H*. 2020. Plasma proteome responses in salmonid fish following immunization. Front. Immunol. doi: 10.3389/fimmu.2020.581070 * Joint corresponding and senior author 

52. Tighe AJ, Gallagher MD, Carlsson J, Matejusova I, Swords F, Macqueen DJ, Ruane NM. 2020. Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7). Dis. Aquat. Org. DOI:


51. Gallagher MD, Karlsen M, Petterson E, Haugland O, Matejusova I, Macqueen DJ. 2020. Whole Genome Sequencing of SAV reveals repeated seeding events of viral strains in Norwegian aquaculture. Front. Microbiol. 11: 740.

50. Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Yehwa J, Jenkins TL, Counter Selly S-L, Martin SAM, Stevens J, Santos E, Davie A, Robledo R. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat. Rev. Genet. 21: 389–409

49. Gallagher MD, Ruane NM, Matejusova I, Macqueen DJ. 2020. Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations. Aquaculture. 522: 735117

48. Clark TC, Tinsley J, Sigholt T, Macqueen DJ, Martin SAM. 2020. Arginine, ornithine and citrulline supplementation in rainbow trout (Oncorhynchus mykiss): Free amino acid dynamics and gene expression responses to bacterial infection with Aeromonas salmonicida. Fish. Shellfish Immunol. 98: 374-390


47. Clark TC, Tinsley J, Sigholt T, Macqueen DJ, Martin SAM. 2020. Supplementation of arginine, ornithine and citrulline in rainbow trout (Oncorhynchus mykiss): effects on growth, free amino acid levels and gene expression responses in plasma and tissue. Comp. Biochem. Physiol. A. 241: 110632.

46. Kim J-H, Macqueen DJ, Winton JR, Hansen JD, Park H, Devlin RH. 2019. Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon. BMC Genomics. 20: 1024.

45. Mulugeta TD, Nome T, To TH, Gundappa MK, Macqueen DJ, Våge DI; Sandve SR, Hvidsten TR. 2019. SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. BMC Genomics. 20: 694.

44. Causey DR, Kim JH, Devlin RH, Martin SAM, Macqueen DJ. 2019. The AMPK system of salmonid fishes was expanded through genome duplication and is regulated by growth and immune status in muscle. Sci. Rep. 9: 9819


43. Redmond AK, Zou J, Secombes CJ, Macqueen DJ, Dooley H. 2019. Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons: Front. Immunol. 10:1558.


42. Denker E, Ebbesson L, Hazlerigg DH, Macqueen DJ. 2019. Phylogenetic reclassification of melatonin receptors to include Mel1d as a new ancestral vertebrate family member. G3: Bethesda. 9: 3225-3238


41. Clark T, Tinsley J, Sigholt, Macqueen DJ, Martin SAM. 2019. Rainbow trout urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation. Fish. Shellfish Imm. 89: 290-300


40. Causey DR, Kim JH, Stead DA, Devlin RH, Martin SAM, Macqueen DJ. 2019. Proteomic comparison of selective breeding and growth hormone transgenesis in fish: Unique pathways to enhanced growth. J. Proteomics. 192: 114-124.

39. Gallagher MD, Matejusova I, Nguyen L, Ruane NM, Falk N, Macqueen DJ. 2018. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Sci. Rep.  8: 16307


38. Houston RD, Macqueen DJ. 2018. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Animal Genet.

37. Redmond AK, Macqueen DJ, Dooley H. 2018. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evol. Biol. 18: 169

36. Causey DR, Potz M, Stead DA, Secombes CJ, Macqueen DJ. 2018. High-throughput proteomic expression profiling of the fish liver response to bacterial challenge. BMC Genomics. 19: 719

35. Redmond AK, Ohta Y, Criscitiello MF, Macqueen DJ, Flajnik MF, Dooley M. Haptoglobin is a divergent MASP family member that neofunctionalized to recycle hemoglobin via CD163 in mammals. J. Immunol. pii: ji1800508.


34. Alzaid A, Kim J-H, Devlin RH, Martin SAM, Macqueen DJ. 2018. Growth hormone transgenesis in coho salmon disrupts muscle immune function impacting cross-talk with growth systems. J. Exp. Biol. 221 pii: jeb173146.


33. Garcia de la Serrana D, Macqueen DJ. 2018. The insulin-like growth factor binding proteins of teleost fish (Review). Front. Endocrinol. doi: 10.3389/fendo.2018.00080

32. 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, Rise MR, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM (The FAASG Consortium. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.  BMC Genomics. 18:484.

31. Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien, S. Martin SAM, Holland PW, Sandve SR, Macqueen DJ. 2017. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18:111. 

30. Pettinello R, Redmond AK, Secombes CJ, Macqueen DJ, Dooley H. 2017. Evolutionary history of the T cell receptor complex as revealed by small-spotted catshark (Scyliorhinus canicula). Dev. Comp. Immunol. 74:125-135.

29. Garcia de la Serrana, D, Fuentes EN, Martin SAM, Johnston IA. Macqueen DJ. 2017. Divergent regulation of insulin-like growth factor binding protein genes in cultured Atlantic salmon myotubes under different models of catabolism and anabolism. Gen. Comp. Endocrinol. Pii: S0016-6480(16)30399-9.


28. Gallagher M, Macqueen DJ. 2016. Evolution and expression of tissue globins in ray-finned fishes. Genome Biol. Evol. 9:32-47.


27. Alzaid A, Martin SAM, Macqueen DJ. 2016. The complete salmonid IGF-IR gene family and its transcriptional response to disease. Sci. Rep. 6: 34806.


26. Lappin FM, Shaw RL, Macqueen DJ. 2016. Targeted sequencing for high-resolution evolutionary analyses following recent genome duplication: proof of concept for key components of the salmonid insulin-like growth factor axis. Mar. Genomics. 30:15-26. Invited contribution to special issue.


25. Alzaid A, Jouneau L, Wang T, Secombes CJ, Boudinot P, Macqueen DJ*, Martin SAM*. 2016. Cross-talk between growth and immunity: coupling of the insulin-like growth factor axis to conserved cytokine pathway in rainbow trout. Endocrinology. 157:1942-1955. [*joint senior/corresponding authors]


24. Macqueen DJ, Gubry-Rangin C. 2016. Molecular adaptation of Ammonia Monooxygenase during repeated pH specialization in Archaea. Mol. Ecol. 25:1986-99.


23. Castro R, Jouneau L, Tacchi L, Macqueen DJ, Alzaid A, Secombes CJ, Martin SAM, Boudinot P. 2015. Disparate developmental patterns of immune responses to bacterial and viral infections in fish. Sci. Rep. 5: 15458.

22. Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. 2015. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc. Natl. Acad. Sci. USA. 30:  9370–9375.

21. Macqueen DJ, Fuentes EN, Valdés JA, Molina A, Martin SAM. 2014. The vertebrate muscle-specific RING finger protein family includes MuRF4 – a novel and widely conserved E3-ubiquitin ligase. FEBS Lett. 588: 4390-4397.

20. Macqueen DJ, Garcia de la Serrana D, Johnston, IA. 2014. Cardiac myoglobin deficit has evolved repeatedly in teleost fish. Biol. Lett. 10: 20140225.

19. Bruno DW, Noguera PA, Black J, Murray W, Macqueen DJ, Matejusova I. 2014. Identification of a wild reservoir of salmonid alphavirus in common dab Limanda limanda with emphasis on virus culture and sequencing. Aquacult. Environ. Interac. 5: 89-98.

18. Macqueen DJ, Wilcox A. 2014. Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression Analyses. Open. Biol. 4: 130219.

17. Macqueen DJ, Johnston, IA. 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. Soc. Biol. B. 281: 20132881.

16. Macqueen DJ, Garcia de la Serrana D, Johnston IA. 2013. Evolution of ancient functions in the vertebrate insulin-like growth factor system uncovered by study of duplicated salmonid fish genomes. Mol. Biol. Evol. 30:1060-1076.

15. Johnston IA, Kristjánsson BK, Vieira VLA, Paxton CGM, Macqueen DJ, Bell, MA. 2012.  Universal scaling rules predict evolutionary patterns of myogenesis in species with indeterminate growth. Proc. R. Soc. B. 279: 2255-2261.

14. Macqueen DJ, Kristjánsson BK, Paxton CGM, Vieira VLA, Johnston IA. 2011. The parallel evolution of dwarfism in Arctic charr is accompanied by adaptive divergence in mTOR-pathway gene expression. Mol. Ecol. 20: 3167–3184. 

13. Johnston IA, Bower NI, Macqueen DJ. 2011. Growth and the regulation of myotomal muscle mass in teleost fish (Review). J. Exp. Biol. 214: 1617-1628.

12. Macqueen DJ, Delbridge ML, Manthri S, Johnston IA. 2010. A newly classified vertebrate calpain protease, directly ancestral to CAPN1 and 2, episodically evolved a restricted physiological function in placental mammals. Mol. Biol. Evol. 27: 1886-1902. 

11. Macqueen DJ, Kristjánsson BK, Johnston IA. 2010. Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism. Physiol. Genomics 42: 134-148.

10. Macqueen DJ, Bower NI, Johnston IA. 2010. Positioning the expanded akirin gene family of Atlantic salmon within the transcriptional networks of myogenesis. Biochem. Biophys. Res. Commun. 400: 599-605.

9. Macqueen DJ, Meischke L, Manthri S, Anwar A, Solberg C, Johnston IA. 2010. Characterisation of capn1, capn2-like, capn3 and capn11 genes in Atlantic halibut (Hippoglossus hippoglossus L.): Transcriptional regulation across tissues and in skeletal muscle at distinct nutritional states. Gene 453: 45-58. 

8. Johnston IA, Lee HT, Macqueen DJ, Paranthaman K, Kawashima C, Anwar A, Kinghorn JR, Dalmay T. 2009. Embryonic temperature affects muscle fibre recruitment in adult zebrafish: genome-wide changes in gene and microRNA expression associated with the transition from hyperplastic to hypertrophic growth phenotypes. J. Exp. Biol. 212:1781-1793.

7. Macqueen DJ, Johnston IA. 2009. Evolution of the multifaceted eukaryotic akirin gene family. BMC Evol. Biol. 9: 34. 

6. Macqueen DJ, Robb DH, Olsen T, Melstveit L, Paxton CG, Johnston IA. 2008. Temperature until the 'eyed stage' of embryogenesis programmes the growth trajectory and muscle phenotype of adult Atlantic salmon. Biol. Lett. 4: 294-298. 

5. Macqueen DJ, Johnston IA. 2008. An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes. PLoS One 3: e1567. 

4. Fernandes JM, Macqueen DJ (co-first author), Lee HT, Johnston IA. Genomic, evolutionary, and expression analyses of cee, an ancient gene involved in normal growth and development. 2008. Genomics 91: 315-325.

3. Macqueen DJ, Johnston IA. 2008. Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses. Dev. Genes Evol. 218:1-14.

2. Macqueen DJ, Robb D, Johnston IA. 2007. Temperature influences the coordinated expression of myogenic regulatory factors during embryonic myogenesis in Atlantic salmon (Salmo salar L.). J. Exp. Biol. 210: 2781-2794.

1. Macqueen DJ, Johnston IA. 2006. A novel salmonid myoD gene is distinctly regulated during development and probably arose by duplication after the genome tetraploidization. FEBS Lett. 580: 4996-5002.


Peer-reviewed book chapters

2. Taylor RS, Ruiz Daniels R, Perojil Morata D, Gundappa MK, Macqueen DJ. 2021. Evolution of ray-finned fish genomes: Status and directions with a primer on microRNA characterization. In: Cellular and Molecular Approaches in Fish Biology (Editors: Ignacio Fernandez & Jorge Fernandes). Academic Press. ISBN: 9780128222737 (In Production)


1. Johnston, IA, Macqueen DJ, Watabe, S. 2008. Molecular biotechnology of development and growth in fish muscle. In Fisheries for Global Welfare and Environment, 5th World Fisheries Congress, 2008 pp. 241–262. K. Tsukamoto, T. Kawamura, T. Takeuchi, T. D. Beard, Jr. and M. J. Kaiser, eds. Terrapub, Tokyo.

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