Publications

2024

  1. Harvey, T.N., Gillard, G.B., Røsæg, L.L., Grammes, F., Monsen, Ø., Vik, J.O., Hvidsten, T.R., Sandve, S.R., 2024. The genome regulatory landscape of Atlantic salmon liver through smoltification. PLOS ONE 19, e0302388. https://doi.org/10.1371/journal.pone.0302388
  2. Royan, M.R., Hodne, K., Nourizadeh-Lillabadi, R., Weltzien, F.-A., Henkel, C., Fontaine, R., 2024. Day length regulates gonadotrope proliferation and reproduction via an intra-pituitary pathway in the model vertebrate Oryzias latipes. Commun Biol 7, 1–13. https://doi.org/10.1038/s42003-024-06059-y
  3. Kess, T., Lehnert, S.J., Bentzen, P., Duffy, S., Messmer, A., Dempson, J.B., Newport, J., Whidden, C., Robertson, M.J., Chaput, G., Breau, C., April, J., Gillis, C.-A., Kent, M., Nugent, C.M., Bradbury, I.R., 2024. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecology and Evolution 14, e11068. https://doi.org/10.1002/ece3.11068
  4. Lecomte, L., Árnyasi, M., Ferchaud, A.-L., Kent, M., Lien, S., Stenløkk, K., Sylvestre, F., Bernatchez, L., Mérot, C., 2024. Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations. Evolutionary Applications 17, e13653. https://doi.org/10.1111/eva.13653
  5. Harvey, T.N., Dvergedal, H., Grønvold, L., Jin, Y., Ødegård, J., Korsvoll, S.A., Knutsen, T.M., Hvidsten, T.R., Sandve, S.R., 2023. Linking genomic prediction for muscle fat content in Atlantic salmon to underlying changes in lipid metabolism regulation. Aquaculture 584, 740678 https://doi.org/10.1016/j.aquaculture.2024.740678
  6. Johnston, I.A., Kent, M.P., Boudinot, P., Looseley, M., Bargelloni, L., Faggion, S., Merino, G.A., Ilsley, G.R., Bobe, J., Tsigenopoulos, C.S., Robertson, J., Harrison, P.W., Martinez, P., Robledo, D., Macqueen, D.J., Lien, S., 2024. Advancing fish breeding in aquaculture through genome functional annotation. Aquaculture 583, 740589. https://doi.org/10.1016/j.aquaculture.2024.740589
  7. Mengkrog Holen, M., Tuveng, T.R., Kent, M.P., Vaaje-Kolstad, G., n.d. The gastric mucosa of Atlantic salmon (Salmo salar) is abundant in highly active chitinases. FEBS Open Bio n/a 14 (1), 23-26. https://doi.org/10.1002/2211-5463.13694
  8. Miera, C., Markussen, F.A.F., Cázarez-Márquez, F., Jaeger, C., Sandve, S.R., Simonneaux, V., Hazlerigg, D.G., Wood, S.H., 2024. Hypothalamic tanycytes as mediators of maternally programmed seasonal plasticity. Current Biology. https://doi.org/10.1016/j.cub.2023.12.042
  9. Lazado, C.C., Stiller, K.T., Timmerhaus, G., Megård Reiten, B.K., Nicolaysen, I.L., Carletto, D., Alipio, H.R.D., Bergstedt, J.H., Andersen, Ø., 2024. Mucosal and systemic physiological changes underscore the welfare risks of environmental hydrogen sulphide in post-smolt Atlantic salmon (Salmo salar). Ecotoxicology and Environmental Safety 270, 115897. https://doi.org/10.1016/j.ecoenv.2023.115897
  10. Monsen, Ø., Grønvold, L., Datsomor, A., Harvey, T., Kijas, J., Suh, A., Hvidsten, T.R., Sandve, S.R., 2024. The role of transposon activity in shaping cis-regulatory element evolution after whole genome duplication. BioRxiv. https://doi.org/10.1101/2024.01.02.573861

2023

  1. León, A.V.-P. de, Hoetzinger, M., Hensen, T., Gupta, S., Weston, B., Johnsen, S.M., Rasmussen, J.A., Clausen, C.G., Pless, L., Veríssimo, A.R.A., Rudi, K., Snipen, L., Karlsen, C.R., Limborg, M.T., Bertilsson, S., Thiele, I., Hvidsten, T.R., Sandve, S.R., Pope, P.B., Rosa, S.L.L., 2023. The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping. BioRxiv.  https://doi.org/10.1101/2023.12.10.570985
  2. Manunza, A., Ramirez-Diaz, J., Cozzi, P., Lazzari, B., Tosser-Klopp, G., Servin, B., Johansson, A.M., Grøva, L., Berg, P., Våge, D.I., Stella, A., 2023. Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe. Sci Rep 13, 20728. https://doi.org/10.1038/s41598-023-48005-8
  3. Nguyen, D.T., 2023. An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells. Bioinformatics 39, btad667. https://doi.org/10.1093/bioinformatics/btad667
  4. Pejšková, L., Rønning, S.B., Kent, M.P., Solberg, N.T., Høst, V., Thu-Hien, T., Wold, J.P., Lunde, M., Mosleth, E., Pisconti, A., Kolset, S.O., Carlson, C.R., Pedersen, M.E., 2023. Characterization of wooden breast myopathy: a focus on syndecans and ECM remodeling. Frontiers in Physiology 14. https://doi.org/10.3389/fphys.2023.1301804
  5. Bhattacharjee, P., Blagojevic, D., Lee, Y., Gillard, G.B., Grønvold, L., Hvidsten, T.R., Sandve, S.R., Lind, O.C., Salbu, B., Brede, D.A., Olsen, J.E., 2023. High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerant A. thaliana. BioRxiv. https://doi.org/10.1101/2023.11.20.562501
  6. Puvanendran, V., Burgerhout, E., Andersen, Ø., Kent, M., Hansen, Ø., Tengs, T., 2023. Intergenerational effects of early life-stage temperature modulation on gene expression and DNA methylation in Atlantic cod (Gadus morhua). Epigenetics 18, 2237759. https://doi.org/10.1080/15592294.2023.2237759
  7. Langille, B.L., Kess, T., Brachmann, M., Nugent, C.M., Messmer, A., Duffy, S.J., Holborn, M.K., Van Wyngaarden, M., Knutsen, T.M., Kent, M., Boyce, D., Gregory, R.S., Gauthier, J., Fairchild, E.A., Pietrak, M., Eddy, S., de Leaniz, C.G., Consuegra, S., Whittaker, B., Bentzen, P., Bradbury, I.R., 2023. Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic. Evolutionary Applications. https://doi.org/10.1111/eva.13590
  8. Andersen, Ø., Rubiolo, J.A., Pirolli, D., Aramburu, O., Pampín, M., Righino, B., Robledo, D., Bouza, C., De Rosa, M.C., Martínez, P., 2023. Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus). Sci Rep 13, 3019. https://doi.org/10.1038/s41598-023-29826-z
  9. Arzumanova, K., Rohlfs, R.V., Grønvold, L., Strand, M.A., Hvidsten, T.R., Sandve, S.R., 2023. Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model. Polyploidy: Methods and Protocols, Methods in Molecular Biology.  pp. 209–225. https://doi.org/10.1007/978-1-0716-2561-3_11
  10. Datsomor, A.K., Wilberg, R., Torgersen, J.S., Sandve, S.R., Harvey, T.N., 2023. Efficient transfection of Atlantic salmon primary hepatocyte cells for functional assays and gene editing. G3 Genes|Genomes|Genetics 13, jkad039. https://doi.org/10.1093/g3journal/jkad039
  11. Diblasi, C., Barson, N.J., Saitou, M., 2023. Resolving large-scale genome evolution in the high-throughput sequencing era: structural variants, genome rearrangement, and karyotype dynamics in animals. EcoEvoRxiv. doi: https://doi.org/10.32942/X2J59Q 
  12. Holen, M.M., Vaaje-Kolstad, G., Kent, M.P., Sandve, S.R., 2023. Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar). G3 Genes|Genomes|Genetics jkad069. doi: https://doi.org/10.1093/g3journal/jkad069
  13. Sahlström, H.M., Datsomor, A.K., Monsen, Ø., Hvidsten, T.R., Sandve, S.R., 2023. Functional validation of transposable element–derived cis-regulatory elements in Atlantic salmon. G3 Genes|Genomes|Genetics 13, jkad034. https://doi.org/10.1093/g3journal/jkad034
  14. Kwak, J.S., León-Tapia, M.Á., Diblasi, C., Manousi, D., Grønvold, L., Sandvik, G.K., Saitou, M., 2023. Functional and regulatory diversification of circadian rhythm period genes during the evolution of vertebrates. BioRxiv https://doi.org/10.1101/2023.03.09.531707
  15. Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Floi Bucao, C., Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W.-J., Zahm, M., Cabau, C., Klopp, C., Thompson, A.W., Robinson-Rechavi, M., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J.H., Berthelot, C., Roest Crollius, H., Guiguen, Y., 2023. Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575. https://doi.org/10.1126/science.abq4257
  16. Ager-Wick, E., Maugars, G., von Krogh, K., Fontaine, R., Weltzien, F.-A., Henkel, C., 2023. An RNA-seq time series of the medaka pituitary gland during sexual maturation. Sci Data 10, 62. https://doi.org/10.1038/s41597-023-01967-w
  17. Rahmad Royan, M., Siddique, K., Nourizadeh-Lillabadi, R., Weltzien, F.-A., Henkel, C., Fontaine, R., 2023. Functional and developmental heterogeneity of pituitary lactotropes in medaka. General and Comparative Endocrinology 330, 114144. https://doi.org/10.1016/j.ygcen.2022.114144

2022

  1. Holen, M. M., Sandve, S. R., Harvey, T. N., Jin, Y., Angell, I. L., Rudi, K., and Kent, M. P. (2022) The effect of dietary chitin on Atlantic salmon (<em>Salmo salar</em>) chitinase activity, gene expression, and microbial composition. bioRxiv, 2022.2005.2005.490722 doi: https://doi.org/10.1101/2022.05.05.490722
  2. Zakhartsev, M., Rotnes, F., Gulla, M., Øyås, O., van Dam, J. C. J., Suarez-Diez, M., Grammes, F., Hafþórsson, R. A., van Helvoirt, W., Koehorst, J. J., Schaap, P. J., Jin, Y., Mydland, L. T., Gjuvsland, A. B., Sandve, S. R., Martins dos Santos, V. A. P., and Vik, J. O. (2022) SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PLOS Computational Biology 18, e1010194. doi: https://doi.org/10.1371/journal.pcbi.1010194
  3. Leipart, V., Ludvigsen, J., Kent, M., Sandve, S., To, T.-H., Árnyasi, M., Kreibich, C. D., Dahle, B., and Amdam, G. V. (2022) Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites. Protein Science 31, e4369. doi: https://doi.org/10.1002/pro.4369
  4. Stenløkk, K., Saitou, M., Rud-Johansen, L., Nome, T., Moser, M., Árnyasi, M., Kent, M., Barson, N. J., and Lien, S. (2022) The emergence of supergenes from inversions in Atlantic salmon. Philosophical Transactions of the Royal Society B: Biological Sciences 377, doi: https://doi.org/10.1098/rstb.2021.0195
  5. Fjellheim, S., Young, D. A., Paliocha, M., Johnsen, S. S., Schubert, M., and Preston, J. C. (2022) Major niche transitions in Pooideae correlate with variation in photoperiodic flowering and evolution of CCT domain genes. J Exp Bot. doi: https://doi.org/10.1093/jxb/erac149
  6. La Rosa, S. L., Ostrowski, M. P., Vera-Ponce de Leon, A., McKee, L. S., Larsbrink, J., Eijsink, V. G., Lowe, E. C., Martens, E. C., and Pope, P. B. (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67, 102143. doi: https://doi.org/10.1016/j.mib.2022.102143
  7. Madsen-Osterbye, J., Abdelhalim, M., Baudement, M. O., and Collas, P. (2022) Local euchromatin enrichment in lamina-associated domains anticipates their repositioning in the adipogenic lineage. Genome Biol 23, 91. doi: https://1186/s13059-022-02662-6
  8. Ostrowski, M. P., La Rosa, S. L., Kunath, B. J., Robertson, A., Pereira, G., Hagen, L. H., Varghese, N. J., Qiu, L., Yao, T., Flint, G., Li, J., McDonald, S. P., Buttner, D., Pudlo, N. A., Schnizlein, M. K., Young, V. B., Brumer, H., Schmidt, T. M., Terrapon, N., Lombard, V., Henrissat, B., Hamaker, B., Eloe-Fadrosh, E. A., Tripathi, A., Pope, P. B., and Martens, E. C. (2022) Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 7, 556-569. doi: https://doi.org/10.1038/s41564-022-01093-0
  9. Perlman, D., Martinez-Alvaro, M., Morais, S., Altshuler, I., Hagen, L. H., Jami, E., Roehe, R., Pope, P. B., and Mizrahi, I. (2022) Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. Annu Rev Anim Biosci 10, 177-201. doi: https://doi.org/10.1146/annurev-animal-013020-020412
  10. Knutsen, T. M., Olsen, H. G., Ketto, I. A., Sundsaasen, K. K., Kohler, A., Tafintseva, V., Svendsen, M., Kent, M. P., and Lien, S. (2022) Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition. Genetics Selection Evolution 54, 35. doi: https://doi.org/10.1186/s12711-022-00731-9
  11. Mérot, C., Stenløkk, K. S. R., Venney, C., Laporte, M., Moser, M., Normandeau, E., Árnyasi, M., Kent, M., Rougeux, C., Flynn, J. M., Lien, S., and Bernatchez, L. Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. doi: https://doi.org/10.1111/mec.16468
  12. Holborn, M. K., Einfeldt, A. L., Kess, T., Duffy, S. J., Messmer, A. M., Langille, B. L., Gauthier, J., Bentzen, P., Knutsen, T. M., Kent, M., Boyce, D., and Bradbury, I. R. Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway. Molecular Ecology Resources, 22, 1427– 1439. doi: 10.1111/1755-0998.13565
  13. Bradbury, I. R., Lehnert, S. J., Kess, T., Van Wyngaarden, M., Duffy, S., Messmer, A., Wringe, B., Karoliussen, S., Dempson, J. B., Fleming, I. A., Solberg, M. F., Glover, K. A., and Bentzen, P. (2022) Genomic evidence of recent European introgression into North American farmed and wild Atlantic Salmon. Evolutionary Applications. doi: https://doi.org/10.1111/eva.13454
  14. van Son, M., Våge, D. I., Skaugen, M., Tremoen, N. H., Gaustad, A. H., Zeremichael, T. T., Myromslien, F. D., and Grindflek, E. (2022) Protein profiling of testicular tissue from boars with different levels of hyperactive sperm motility. Acta Veterinaria Scandinavica 64, 21. doi: https://doi.org/10.1186/s13028-022-00642
  15. Datsomor, A. K., Gillard, G., Jin, Y., Olsen, R. E., and Sandve, S. R. (2022) Molecular Regulation of Biosynthesis of Long Chain Polyunsaturated Fatty Acids in Atlantic Salmon. Mar Biotechnol (NY) 24, 661-670 doi: https://doi.org/10.1007/s10126-022-10144-w
  16. Nguyen, D. T., Tran, T. T. H., Tran, M. H., Tran, K., Pham, D., Duong, N. T., Nguyen, Q., and Vo, N. S. (2022) A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations. Scientific Reports 12, 17556 doi: https://doi.org/10.1038/s41598-022-22215-y
  17. Sinclair-Waters, M., Nome, T., Wang, J., Lien, S., Kent, M. P., Sægrov, H., Florø-Larsen, B., Bolstad, G. H., Primmer, C. R., and Barson, N. J. (2022) Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods. Heredity. https://doi.org/10.1038/s41437-022-00570-w
  18. Wenne, R., Zbawicka, M., Prądzińska, A., Kotta, J., Herkül, K., Gardner, J. P. A., Apostolidis, A. P., Poćwierz-Kotus, A., Rouane-Hacene, O., Korrida, A., Dondero, F., Baptista, M., Reizopoulou, S., Hamer, B., Sundsaasen, K. K., Árnyasi, M., and Kent, M. P. (2022) Molecular genetic differentiation of native populations of Mediterranean blue mussels, Mytilus galloprovincialis Lamarck, 1819, and the relationship with environmental variables. The European Zoological Journal 89, 755-784. https://doi.org/10.1080/24750263.2022.2086306
  19. Kwak, J. S., and Kim, K. H. (2022) Effect of CRISPR/Cas9-mediated knockout of either IRF-3 or IRF-5 gene in Epithelioma papulosum cyprini cells on type I interferon response and NF-κB activity. Fish & Shellfish Immunology, 108463. https://doi.org/10.1016/j.fsi.2022.108463

2021

  1. Watson, K. B., Lehnert, S. J., Bentzen, P., Kess, T., Einfeldt, A., Duffy, S., Perriman, B., Lien, S., Kent, M., and Bradbury, I. R. Environmentally associated chromosomal structural variation influences fine-scale population structure of atlantic salmon (Salmo salar). Molecular Ecology. Doi: 1111/mec.16307
  2. Bernaś, R., Wąs-Barcz, A., Árnyasi, M., Dębowski, P., Radtke, G., Poćwierz-Kotus, A., and Berrebi, P. (2021) Evidence of unidirectional gene flow in a fragmented population of Salmo trutta L. Scientific Reports 11, 23417. Doi: 1038/s41598-021-02975-9
  3. Saitou, M., Masuda, N., and Gokcumen, O. (2021) Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Molecular Biology and Evolution. Doi: 1093/molbev/msab313
  4. Gundappa, M. K., To, T.-H., Grønvold, L., Martin, S. A. M., Lien, S., Geist, J., Hazlerigg, D., Sandve, S. R., and Macqueen, D. J. (2021) Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution. Molecular Biology and Evolution. Doi: 1093/molbev/msab310
  5. Hansen, T., Fjelldal, P., Lien, S., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, S., Chow, W., Howe, K., Torrance, J., Wood, J., Sims, Y., Haggerty, L., Challis, R., Threlfall, J., Mead, D., Durbin, R., and Blaxter, M. (2021) The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 3 approved]. Wellcome Open Res 2021, 6:108
  6. Saitou, M., Resendez, S., Pradhan Apoorva, J., Wu, F., Lie Natasha, C., Hall Nancy, J., Zhu, Q., Reinholdt, L., Satta, Y., Speidel, L., Nakagome, S., Hanchard Neil, A., Churchill, G., Lee, C., Atilla-Gokcumen, G. E., Mu, X., and Gokcumen, O. Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Science Advances 7. Doi: 1126/sciadv.abi4476
  7. Skern-Mauritzen, R., Malde, K., Eichner, C., Dondrup, M., Furmanek, T., Besnier, F., Komisarczuk, A. Z., Nuhn, M., Dalvin, S., Edvardsen, R. B., Klages, S., Huettel, B., Stueber, K., Grotmol, S., Karlsbakk, E., Kersey, P., Leong, J. S., Glover, K. A., Reinhardt, R., Lien, S., Jonassen, I., Koop, B. F., and Nilsen, F. (2021) The salmon louse genome: Copepod features and parasitic adaptations. Genomics 113, 3666-3680. Doi: 1016/j.ygeno.2021.08.002
  8. Krabbenhoft, T. J., MacGuigan, D. J., Backenstose, N. J. C., Waterman, H., Lan, T., Pelosi, J. A., Tan, M., and Sandve, S. R. (2021) Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly-Conserved Synteny Following a Catostomid-Specific Whole Genome Duplication. Genome biology and evolution. Doi: 1093/gbe/evab190
  9. Kent, M., Moser, M., Boman, I. A., Lindtveit, K., Árnyasi, M., Sundsaasen, K. K., and Våge, D. I. (2021) Insertion of an endogenous Jaagsiekte sheep retrovirus element into the BCO2 – gene abolishes its function and leads to yellow discoloration of adipose tissue in Norwegian Spælsau (Ovis aries). BMC Genomics 22, 492. Doi: 1186/s12864-021-07826-5
  10. Saha, A., Kent, M., Hauser, L., Drinan, D. P., Nielsen, E. E., Westgaard, J.-I., Lien, S., and Johansen, T. (2021) Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella. PLOS ONE 16. Doi: 1371/journal.pone.0251976
  11. West, A. C., Mizoro, Y., Wood, S. H., Ince, L. M., Iversen, M., Jørgensen, E. H., Nome, T., Sandve, S. R., Martin, S. A. M., Loudon, A. S. I., and Hazlerigg, D. G. (2021) Immunologic Profiling of the Atlantic Salmon Gill by Single Nuclei Transcriptomics. Doi: 10.3389/fimmu.2021.669889
  12. Gillard, G. B., Grønvold, L., Røsæg, L. L., Holen, M. M., Monsen, Ø., Koop, B. F., Rondeau, E. B., Gundappa, M. K., Mendoza, J., Macqueen, D. J., Rohlfs, R. V., Sandve, S. R., and Hvidsten, T. R. (2021) Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biology 22, 103. Doi: 1186/s13059-021-02323-0
  13. Martínez, P., Robledo, D., Taboada, X., Blanco, A., Moser, M., Maroso, F., Hermida, M., Gómez-Tato, A., Álvarez-Blázquez, B., Cabaleiro, S., Piferrer, F., Bouza, C., Lien, S., and Viñas, A. M. (2021) A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Doi: https://doi.org/10.1016/j.ygeno.2021.04.007
  14. Jin, Y., Harvey, T. N., Bartosova, Z., Hassani, S., Bruheim, P., Sandve, S. R., and Vik, J. O. (2021) Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon. Journal of Agricultural and Food Chemistry. Doi: 1021/acs.jafc.0c07281
  15. Iversen, M., Mulugeta, T., West, A., Jørgensen, E. H., Martin, S. A. M., Sandve, S. R., and Hazlerigg, D. (2021) Photoperiod-dependent developmental reprogramming of the transcriptional response to seawater entry in Atlantic salmon (Salmo salar). G3 Genes|Genomes|Genetics. Doi: 1093/g3journal/jkab072
  16. Strand, M. A., Jin, Y., Sandve, S. R., Pope, P. B., and Hvidsten, T. R. (2021) Transkingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon. Computational and Structural Biotechnology Journal. Doi: 1016/j.csbj.2021.01.038
  17. Mariussen, E., Fjellsbø, L., Frømyr, T. R., Johnsen, I. V., Karsrud, T. E., and Voie, Ø. A. (2021) Toxic effects of gunshot fumes from different ammunitions for small arms on lung cells exposed at the air liquid interface. Toxicology in Vitro 72, 105095. Doi: 1016/j.tiv.2021.105095

2020

  1. Clark, E. L., Archibald, A. L., Daetwyler, H. D., Groenen, M. A. M., Harrison, P. W., Houston, R. D., Kühn, C., Lien, S., Macqueen, D. J., Reecy, J. M., Robledo, D., Watson, M., Tuggle, C. K., and Giuffra, E. (2020) From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome Biology 21, 285. Doi: 10.1186/s13059-020-02197-8
  2. Guellil, M., Kersten, O., Namouchi, A., Luciani, S., Marota, I., Arcini, C. A., Iregren, E., Lindemann, R. A., Warfvinge, G., Bakanidze, L., Bitadze, L., Rubini, M., Zaio, P., Zaio, M., Neri, D., Stenseth, N. C., and Bramanti, B. (2020) A genomic and historical synthesis of plague in 18th century Eurasia. 117. Doi: 1073/pnas.2009677117
  3. Jin, Y., Datsomor, A. K., Olsen, R. E., Vik, J. O., Torgersen, J. S., Edvardsen, R. B., Wargelius, A., Winge, P., and Grammes, F. (2020) Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar). BMC Genomics 21, 805, doi: 1186/s12864-020-07218-1
  4. Dvergedal, H., Sandve, S. R., Angell, I. L., Klemetsdal, G., and Rudi, K. (2020) Association of gut microbiota with metabolism in juvenile Atlantic salmon. Microbiome 8, 160. Doi: 1186/s40168-020-00938-2
  5. Dvergedal, H., Harvey, T. N., Jin, Y., Ødegård, J., Grønvold, L., Sandve, S. R., Våge, D. I., Moen, T., and Klemetsdal, G. (2020) Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar). Genetics Selection Evolution 52, 66. Doi: 1186/s12711-020-00587-x
  6. Bertolotti, A. C., Layer, R. M., Gundappa, M. K., Gallagher, M. D., Pehlivanoglu, E., Nome, T., Robledo, D., Kent, M. P., Røsæg, L. L., Holen, M. M., Mulugeta, T. D., Ashton, T. J., Hindar, K., Sægrov, H., Florø-Larsen, B., Erkinaro, J., Primmer, C. R., Bernatchez, L., Martin, S. A. M., Johnston, I. A., Sandve, S. R., Lien, S., and Macqueen, D. J. (2020) The structural variation landscape in 492 Atlantic salmon genomes. Nature Communications 11, 5176. doi: 1038/s41467-020-18972-x
  7. West, A. C., Iversen, M., Jørgensen, E. H., Sandve, S. R., Hazlerigg, D. G., and Wood, S. H. (2020) Diversified regulation of circadian clock gene expression following whole genome duplication. PLOS Genetics 16, e1009097. Doi: 1371/journal.pgen.1009097
  8. Johansen, T., Besnier, F., Quintela, M., Jorde, P. E., Glover, K. A., Westgaard, J.-I., Dahle, G., Lien, S., and Kent, M. P. (2020) Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L. Evolutionary Applications. Doi: 10.1111/eva.13070
  9. van Son, M., Tremoen, N. H., Gaustad, A. H., Våge, D. I., Zeremichael, T. T., Myromslien, F. D., and Grindflek, E. (2020) Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility. BMC Veterinary Research 16, Doi: 10.1186/s12917-020-02373-9
  10. Kirubakaran, T. G., Andersen, Ø., Moser, M., Árnyasi, M., McGinnity, P., Lien, S., and Kent, M. (2020) A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea. G DOI: 10.1534/g3.120.401423
  11. Wenne, R., Bernaś, R., Kijewska, A., Poćwierz-Kotus, A., Strand, J., Petereit, C., Plauška, K., Sics, I., Árnyasi, M., and Kent, M. P. (2020) SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea. Scientific Reports 10, 9738. Doi: /10.1038/s41598-020-66518-4
  12. Niskanen, A. K., Billing, A. M., Holand, H., Hagen, I. J., Araya-Ajoy, Y. G., Husby, A., Rønning, B., Myhre, A. M., Ranke, P. S., Kvalnes, T., Pärn, H., Ringsby, T. H., Lien, S., Sæther, B.-E., Muff, S., and Jensen, H. (2020) Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation. PNAS. Doi: 1073/pnas.1909599117
  13. Berg, P., Groeneveld, L. F., Brekke, C., Våge, D. I., Sørheim, K. M., and Grøva, L. (2020) Genetic characterization of a small closed island population of Norwegian coastal goat. Acta Agriculturae Scandinavica, Section A — Animal Science 69, 47-52. Doi: 1080/09064702.2020.1729852
  14. Wenne, R., Zbawicka, M., Bach, L., Strelkov, P., Gantsevich, M., Kukliński, P., Kijewski, T., McDonald, J. H., Sundsaasen, K. K., Árnyasi, M., Lien, S., Kaasik, A., Herkül, K., and Kotta, J. (2020) Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors. 11, 530. Doi: 3390/genes11050530
  15. Jin, Y., Olsen, R. E., Harvey, T. N., Østensen, M.-A., Li, K., Santi, N., Vadstein, O., Magnar Bones, A., Vik, J. O., Sandve, S. R., and Olsen, Y. (2020) Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism. Molecular Ecology. Doi: 10.1111/mec.15446
  16. Iversen, M., Mulugeta, T., Gellein Blikeng, B., West, A. C., Jørgensen, E. H., Rød Sandven, S., and Hazlerigg, D. (2020) RNA profiling identifies novel, photoperiod-history dependent markers associated with enhanced saltwater performance in juvenile Atlantic salmon. PLOS ONE 15. Doi: 10.1371/journal.pone.0227496
  17. Lieven, C., Beber, M. E., Olivier, B. G., …, Vik, J. O., …, and Zhang, C. (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. Doi: 1038/s41587-020-0446-y
  18. Løvmo, S. D., Madaro, A., Whatmore, P., Bardal, T., Ostensen, M.-A., Sandve, S. R., and Olsen, R. E. (2020) Mid and hindgut transcriptome profiling analysis of Atlantic salmon (Salmon salar) under unpredictable chronic stress. 7. R. Soc. open sci. Doi: 10.1098/rsos.191480
  19. Sinclair-Waters, M., Ødegård, J., Korsvoll, S. A., Moen, T., Lien, S., Primmer, C. R., and Barson, N. J. (2020) Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. Genetics Selection Evolution 52, 9. Doi: 1186/s12711-020-0529-8
  20. Bernaś, R., Poćwierz-Kotus, A., Árnyasi, M., Kent, P., Lien, S., and Wenne, R. (2020) Genetic Differentiation in Hatchery and Stocked Populations of Sea Trout in the Southern Baltic: Selection Evidence at SNP Loci. 11, 184. doi: 3390/genes11020184
  21. Olsen, H. F., Tenhunen, S., Dolvik, N. I., Våge, D. I., and Klemetsdal, G. (2020) Segment-based coancestry, additive relationship and genetic variance within and between the Norwegian and the Swedish Fjord horse populations. Acta Agriculturae Scandinavica, Section A — Animal Science, 1-9. Doi: 1080/09064702.2019.1711155
  22. Bláhová, Z., Harvey, T. N., Pšenička, M., and Mráz, J. (2020) Assessment of Fatty Acid Desaturase (Fads2) Structure-Function Properties in Fish in the Context of Environmental Adaptations and as a Target for Genetic Engineering. 10, 206. doi: 3390/biom10020206
  23. Hagen, I. J., Lien, S., Billing, A. M., Elgvin, T. O., Trier, C., Niskanen, A. K., Tarka, M., Slate, J., Sætre, G.-P., and Jensen, H. A genome-wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. doi: 1111/1755-0998.13134
  24. Kess, T., Bentzen, P., Lehnert, S. J., Sylvester, E. V. A., Lien, S., Kent, M. P., Sinclair-Waters, M., Morris, C., Wringe, B., Fairweather, R., and Bradbury, I. R. (2019) Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish. doi: 1002/ece3.5828

2019

  1. Skedsmo, F. S., Malachin, G., Vage, D. I., Hammervold, M. M., Salvesen, O., Ersdal, C., Ranheim, B., Stafsnes, M. H., Bartosova, Z., Bruheim, P., Jaderlund, K. H., Matiasek, K., Espenes, A., and Tranulis, M. A. (2020) Demyelinating polyneuropathy in goats lacking prion protein. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 34, 2359-2375. Doi: 1096/fj.201902588R
  2. To, T.-H., and Pederson, S. (2019) strandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seq. Journal of Open Source Software 4, 1145. Doi: 21105/joss.01145
  3. Lesne, A., Baudement, M.-O., Rebouissou, C., and Forné, T. (2019) Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression. 10, 1049. doi 3390/genes10121049
  4. Andersen, Ø., Vieira, V., Dessen, J.-E., and Johnston, I. A. (2019) Influence of feed ration size on somatic and muscle growth in landlocked dwarf and farmed Atlantic salmon Salmo salar. 94, 614-620. doi: 10.1111/jfb.13942
  5. Helgeland, H., Sodeland, M., Zoric, N., Torgersen, J. S., Grammes, F., von Lintig, J., Moen, T., Kjøglum, S., Lien, S., and Våge, D. I. (2019) Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color. Scientific Reports 9, 20061. doi: 1038/s41598-019-56438-3
  6. Tremoen, N. H., Van Son, M., Andersen-Ranberg, I., Grindflek, E., Myromslien, F. D., Gaustad, A. H., and Våge, D. I. (2019) Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs. Acta Veterinaria Scandinavica 61, 58. doi: 10.1186/s13028-019-0493-x
  7. Pearse, D. E., Barson, N. J., Nome, T., Gao, G., Campbell, M. A., Abadía-Cardoso, A., Anderson, E. C., Rundio, D. E., Williams, T. H., Naish, K. A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D. R., Rondeau, E. B., Brieuc, M. S. O., Sandve, S. R., Miller, M. R., Cedillo, L., Baruch, K., Hernandez, A. G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J. C., Lindley, S. T., Koop, B. F., Thorgaard, G. H., Palti, Y., and Lien, S. (2019) Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology & Evolution 3, 1731-1742. doi: 1038/s41559-019-1044-6
  8. Rodríguez-Ramilo, S. T., Baranski, M., Moghadam, H., Grove, H., Lien, S., Goddard, M. E., Meuwissen, T. H. E., and Sonesson, A. K. (2019) Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations. Genetics Selection Evolution 51, 61. Doi: org/10.1186/s12711-019-0503-5
  9. Gabián, M., Morán, P., Fernández, A. I., Villanueva, B., Chtioui, A., Kent, M. P., Covelo-Soto, L., Fernández, A., and Saura, M. (2019) Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data. BMC Genomics 20, 764. doi: 10.1186/s12864-019-6104-4
  10. Bekkevold, D., Höjesjö, J., Nielsen, E. E., Aldvén, D., Als, T. D., Sodeland, M., Kent, M. P., Lien, S., and Hansen, M. M. Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients. doi: 10.1111/eva.12877
  11. Harvey, T. N., Sandve, S. R., Jin, Y., Vik, J. O., and Torgersen, J. S. (2019) Liver slice culture as a model for lipid metabolism in fish. PeerJ 7, e7732. Doi: https://doi.org/10.7717/peerj.7732
  12. Sargent, D. J., Buti, M., Šurbanovski, N., Brurberg, M. B., Alsheikh, M., Kent, M. P., and Davik, J. (2019) Identification of QTLs for powdery mildew (Podosphaera aphanis; syn. Sphaerotheca macularis f. sp. fragariae) susceptibility in cultivated strawberry (Fragaria ×ananassa). PLOS ONE 14, e0222829.  doi: 1371/journal.pone.0222829
  13. Bratlie, S., Halvorsen, K., Myskja, B. K., Mellegård, H., Bjorvatn, C., Frost, P., Heiene, G., Hofmann, B., Holst‐Jensen, A., Holst‐Larsen, T., Malnes, R. S., Paus, B., Sandvig, B., Sjøli, S. I., Skarstein, B., Thorseth, M. B., Vagstad, N., Våge, D. I., and Borge, O. J. (2019) A novel governance framework for GMO. A tiered, more flexible regulation for GMOs would help to stimulate innovation and public debate, e47812. doi: 15252/embr.201947812
  14. Conte, M. A., Joshi, R., Moore, E. C., Nandamuri, S. P., Gammerdinger, W. J., Roberts, R. B., Carleton, K. L., Lien, S., and Kocher, T. D. (2019) Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. GigaScience 8. doi 10.1093/gigascience/giz030
  15. Danzmann, R. G., Norman, J. D., Rondeau, E. B., Messmer, A. M., Kent, M. P., Lien, S., Igboeli, O., Fast, M. D., and Koop, B. F. (2019) A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Molecular genetics and genomics : MGG 294, 343-363. doi: 10.1007/s00438-018-1513-7
  16. Datsomor, A. K., Zic, N., Li, K., Olsen, R. E., Jin, Y., Vik, J. O., Edvardsen, R. B., Grammes, F., Wargelius, A., and Winge, P. (2019) CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes. Scientific Reports 9, 7533. Doi: 1038/s41598-019-43862-8
  17. Jin, Y., Angell, I. L., Sandve, S. R., Snipen, L. G., Olsen, Y., and Rudi, K. (2019) Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at sea. Aquaculture Environment Interactions 11, 31-39. doi: 3354/aei00297
  18. Kess, T., Bentzen, P., Lehnert, S. J., Sylvester, E. V. A., Lien, S., Kent, M. P., Sinclair-Waters, M., Morris, C. J., Regular, P., Fairweather, R., and Bradbury, I. R. (2019) A migration-associated supergene reveals loss of biocomplexity in Atlantic cod. Science Advances doi: 10.1126/sciadv.aav2461
  19. Kirubakaran, T. G., Andersen, Ø., De Rosa, M. C., Andersstuen, T., Hallan, K., Kent, M. P., and Lien, S. (2019) Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod. Scientific Reports 9, 116. doi: 1038/s41598-018-36748-8
  20. Lehnert, S. J., Bentzen, P., Kess, T., Lien, S., Horne, J. B., Clément, M., and Bradbury, I. R. Chromosome polymorphisms track trans-Atlantic divergence and secondary contact in Atlantic salmon. Molecular ecology doi: 10.1111/mec.15065
  21. Lehnert, S. J., Kess, T., Bentzen, P., Kent, M. P., Lien, S., Gilbey, J., Clément, M., Jeffery, N. W., Waples, R. S., and Bradbury, I. R. (2019) Genomic signatures and correlates of widespread population declines in salmon. Nature Communications 10, 2996. Doi: 1038/s41467-019-10972-w
  22. Maremonti, E., Eide, D. M., Oughton, D. H., Salbu, B., Grammes, F., Kassaye, Y. A., Guédon, R., Lecomte-Pradines, C., and Brede, D. A. (2019) Gamma radiation induces life stage-dependent reprotoxicity in Caenorhabditis elegans via impairment of spermatogenesis. Science of The Total Environment 695, 133835 Doi: 1016/j.scitotenv.2019.133835
  23. Minniti, G., Rød Sandve, S., Padra, J. T., Heldal Hagen, L., Lindén, S., Pope, P. B., Ø. Arntzen, M., and Vaaje-Kolstad, G. (2019) The Farmed Atlantic Salmon (Salmo salar) Skin–Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community. Genes 10, 515. Doi: 3390/genes10070515
  24. Mulugeta, T. D., Nome, T., To, T.-H., Gundappa, M. K., Macqueen, D. J., Våge, D. I., Sandve, S. R., and Hvidsten, T. R. (2019) SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. BMC Genomics 20, 694. Doi: 1186/s12864-019-6051-0
  25. Schubert, M., Groenvold, L., Sandve, S. R., Hvidsten, T. R., and Fjellheim, S. (2019) Evolution of cold acclimation and its role in niche transition in the temperate grass subfamily Pooideae. Plant Physiology, 10.1104/pp.18.01448
  26. Sävilammi, T., Primmer, C. R., Varadharajan, S., Guyomard, R., Guiguen, Y., Sandve, S. R., Vøllestad, L. A., Papakostas, S., and Lien, S. (2019) The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3: Genes|Genomes|Genetics, g3. doi: 10.1534/g3.118.200919
  27. Andrew, S. C., Taylor, M. P., Lundregan, S., Lien, S., Jensen, H., and Griffith, S. C. (2018) Signs of adaptation to trace metal contamination in a common urban bird. Science of The Total Environment 650, 8. doi: 10.1016/j.scitotenv.2018.09.052

Popular scientific publications 2019

  1. Lien, S. (2019) Supergen leder hunn-ørreten til havet. Forskning.no.
  2. Gørbitz, C. H., Jakobsen, K. S., Sandve, S. R., Goksøyr, A., Brautaset, T., Jørgensen, T. Ø. (2019) Internasjonalt forskningsprosjekt vil kartlegge arters DNA før det er for sent. Aftenposten Viten.
2018
  1. Jin, Y., Olsen, R. E., Østensen, M.-A., Gillard, G. B., Li, K., Harvey, T. N., Santi, N., Vadstein, O., Vik, J. O., Sandve, S. R., and Olsen, Y. (2019) Transcriptional regulation of lipid metabolism when salmon fry switches from endogenous to exogenous feeding. Aquaculture. doi: 1016/j.aquaculture.2018.12.089
  2. Danzmann, R. G., Norman, J. D., Rondeau, E. B., Messmer, A. M., Kent, M. P., Lien, S., Igboeli, O., Fast, M. D., and Koop, B. F. (2018) A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Molecular genetics and genomics : MGG doi: 10.1007/s00438-018-1513-7
  3. Gao, G., Nome, T., Pearse, D. E., Moen, T., Naish, K. A., Thorgaard, G. H., Lien, S., and Palti, Y. (2018) A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing. Frontiers in Genetics 9. doi: 10.3389/fgene.2018.00147
  4. Gillard, G., Harvey, T. N., Gjuvsland, A., Jin, Y., Thomassen, M., Lien, S., Leaver, M., Torgersen, J. S., Hvidsten, T. R., Vik, J. O., and Sandve, S. R. (2018) Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon. Molecular Ecology 27, 1200-1213. doi: 10.1111/mec.14533
  5. Grindflek, E. A.-O. h. o. o., Hansen, M. H. S., Lien, S., and van Son, M. (2018) Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14. BMC Genomics 19 doi: 10.1186/s12864-018-4812-9
  6. Hillestad, B., Woolliams, J. A., Boison, S. A., Grove, H., Meuwissen, T., Våge, D. I., and Klemetsdal, G. (2018) Detection of runs of homozygosity in Norwegian Red: Density, criteria and genotyping quality control. Acta Agriculturae Scandinavica, Section A — Animal Science 67, 107-116 doi: 10.1080/09064702.2018.1501088
  7. IWGSC (The International Wheat Genome Sequencing Consortium), Appels, R., …, Sandve, S., …, and Uauy, C. (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361. doi: 10.1126/science.aar7191
  8. Jeffery, N. W., Wringe, B. F., McBride, M. C., Hamilton, L. C., Stanley, R. R. E., Bernatchez, L., Kent, M., Clément, M., Gilbey, J., Sheehan, T. F., Bentzen, P., and Bradbury, I. R. (2018) Range-wide regional assignment of Atlantic salmon (Salmo salar) using genome wide single-nucleotide polymorphisms. Fisheries Research 206, 163-175. doi: 10.1016/j.fishres.2018.05.017
  9. Jin, Y., Olsen, R. E., Gillard, G. B., Ostensen, M. A., Korsvoll, S. A., Santi, N., Vik, J. O., Sandve, S. R., and Olsen, Y. (2018) A systemic study of lipid metabolism regulation in salmon fingerlings and early juveniles fed plant oil. Br J Nutr 120, 653-664. doi: 10.1017/S0007114518001885
  10. Jin, Y., Olsen, R. E., Østensen, M.-A., Gillard, G. B., Korsvoll, S. A., Santi, N., Gjuvsland, A. B., Vik, J. O., Torgersen, J. S., Sandve, S. R., and Olsen, Y. (2018) Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry. BMC Genomics 19, 253. doi: 10.1186/s12864-018-4651-8
  11. Joshi, R., Arnyasi, M., Lien, S., Gjoen, H. M., Alvarez, A. T., and Kent, M. (2018) Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus). Front Genet 9, 472. Doi: 10.3389/fgene.2018.00472
  12. Kijas, J., McWilliam, S., Naval Sanchez, M., Kube, P., King, H., Evans, B., Nome, T. A.-O. h. o. o. X., Lien, S., and Verbyla, K. (2018) Evolution of Sex Determination Loci in Atlantic Salmon. Scientific Reports 8. doi: 10.1038/s41598-018-23984-1
  13. Knutsen, T. M., Olsen, H. G., Tafintseva, V., Svendsen, M., Kohler, A., Kent, M. P., and Lien, S. (2018) Unravelling genetic variation underlying de novo-synthesis of bovine milk fatty acids. Scientific Reports 8, 2179. doi: 10.1038/s41598-018-20476-0
  14. Lin, Y. C., Wang, J., Delhomme, N., Schiffthaler, B., Sundstrom, G., Zuccolo, A., Nystedt, B., Hvidsten, T. R., de la Torre, A., Cossu, R. M., Hoeppner, M. P., Lantz, H., Scofield, D. G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K. M., Mahler, N., Leitch, I. J., Pellicer, J., Park, E. J., Van Montagu, M., Van de Peer, Y., Grabherr, M., Jansson, S., Ingvarsson, P. K., and Street, N. R. (2018) Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America 115, E10970-e10978. doi: 1073/pnas.1801437115
  15. Lundregan, S. L., Hagen, I. J., Gohli, J., Niskanen, A. K., Kemppainen, P., Ringsby, T. H., Kvalnes, T., Pärn, H., Rønning, B., Holand, H., Ranke, P. S., Båtnes, A. S., Selvik, L.-K., Lien, S., Sæther, B.-E., Husby, A., and Jensen, H. (2018) Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis. Molecular Ecology 27, 3498-3514. doi: 10.1111/mec.14811
  16. Messmer, A. M., Leong, J. S., Rondeau, E. B., Mueller, A., Despins, C. A., Minkley, D. R., Kent, M. P., Lien, S., Boyce, B., Morrison, D., Fast, M. D., Norman, J. D., Danzmann, R. G., and Koop, B. F. (2018) A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. LID – S1874-7787(17)30254-4 [pii] LID – 10.1016/j.margen.2018.03.005 [doi]. Marine Genomics. Doi: 10.1016/j.margen.2018.03.005
  17. Rudi, K., Angell, I. L., Pope, P. B., Vik, J. O., Sandve, S. R., and Snipen, L.-G. (2018) Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon. Applied and Environmental Microbiology 84, e01974-01917. doi: 10.1128/AEM.01974-17
  18. Sandve, S. R., Rohlfs, R. V., and Hvidsten, T. R. (2018) Subfunctionalization versus neofunctionalization after whole-genome duplication. Nature Genetics 50, 908-909. doi: 10.1038/s41588-018-0162-4
  19. Sinclair-Waters, M., Bentzen, P., Morris, C. J., Ruzzante, D. E., Kent, M. P., Lien, S., and Bradbury, I. R. (2018) Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area. Canadian Journal of Fisheries and Aquatic Sciences, 1-11. doi: 10.1139/cjfas-2017-0254
  20. Sinclair-Waters, M., Bradbury, I. R., Morris, C. J., Lien, S., Kent, M. P., and Bentzen, P. (2018) Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic. Molecular ecology 27, 339-351. doi: 1111/mec.14442
  21. Tekle, K. M., Gundersen, S., Klepper, K., Bongo, L. A., Raknes, I. A., Li, X., Zhang, W., Andreetta, C., Mulugeta, T. D., Kalas, M., Rye, M. B., Hjerde, E., Antony Samy, J. K., Fornous, G., Azab, A., Vage, D. I., Hovig, E., Willassen, N. P., Drablos, F., Nygard, S., Petersen, K., and Jonassen, I. (2018) Norwegian e-Infrastructure for Life Sciences (NeLS). F1000Research 7 doi: 10.12688/f1000research.15119.1.
  22. Tremoen, N. H., Gaustad, A. H., Andersen-Ranberg, I., van Son, M., Zeremichael, T. T., Frydenlund, K., Grindflek, E., Våge, D. I., and Myromslien, F. D. (2018) Relationship between sperm motility characteristics and ATP concentrations, and association with fertility in two different pig breeds. Animal Reproduction Science 193, 226-234 doi: 10.1016/j.anireprosci.2018.04.075
  23. Varadharajan, S., Sandve, S. R., Gillard, G. B., Tørresen, O. K., Mulugeta, T. D., Hvidsten, T. R., Lien, S., Vøllestad, L. A., Jentoft, S., Nederbragt, A. J., and Jakobsen, K. S. (2018) The grayling genome reveals selection on gene expression regulation after whole genome duplication. Genome Biology and Evolution, evy201-evy201. Doi: 10.1093/gbe/evy201
  24. Wang, J., Ding, J., Tan, B., Robinson, K. M., Michelson, I. H., Johansson, A., Nystedt, B., Scofield, D. G., Nilsson, O., Jansson, S., Street, N. R., and Ingvarsson, P. K. (2018) A major locus controls local adaptation and adaptive life history variation in a perennial plant. Genome Biology 19, 72. doi: 1186/s13059-018-1444-y
  25. Zueva, K. J., Lumme, J., Veselov, A. E., Kent, M. P., and Primmer, C. R. (2018) Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar). Marine Genomics 39, 26-38. doi: 1016/j.margen.2018.01.001

Popular scientific publications 2018:

  1. Joshi, R. and Kent, M. (2018). New resources could improve breeding programs of this important aquaculture species. ScienceNordic
  2. Tørresen, O.J., Skrede I., Sandve S. R., Jentoft S., Jakobsen K. S., Borge O. J. Gendykk i norsk natur gir ny kunnskap. Forskning.no.

2017

  1. Andersson, A., Jansson, E., Wennerström, L., Chiriboga, F., Arnyasi, M., Kent, M. P., Ryman, N., and Laikre, L. (2017) Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes. Conservation Genetics 18, 1213-1227. doi: 10.1007/s10592-017-0972-4
  2. Elgvin, T. O., Trier, C. N., Tørresen, O. K., Hagen, I. J., Lien, S., Nederbragt, A. J., Ravinet, M., Jensen, H., and Sætre, G.-P. (2017) The genomic mosaicism of hybrid speciation. Science Advances 3. doi: 10.1126/sciadv.1602996
  3. Kemppainen, P., Rønning, B., Kvalnes, T., Hagen, I. J., Ringsby, T. H., Billing, A. M., Pärn, H., Lien, S., Husby, A., Sæther, B.-E., and Jensen, H. (2017) Controlling for P-value inflation in allele frequency change in experimental evolution and artificial selection experiments. Molecular Ecology Resources 17, 770-782. doi: 10.1111/1755-0998.12631
  4. Ketto, I. A., Knutsen, T. M., Øyaas, J., Heringstad, B., Ådnøy, T., Devold, T. G., and Skeie, S. B. (2017) Effects of milk protein polymorphism and composition, casein micelle size and salt distribution on the milk coagulation properties in Norwegian Red cattle. International Dairy Journal 70, 55-64. doi: 10.1016/j.idairyj.2016.10.010
  5. Linløkken, A. N., Haugen, T. O., Kent, M. P., and Lien, S. (2017) Genetic differences between wild and hatchery-bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits. Ecology and Evolution 7, 4963-4972. doi: 10.1002/ece3.3070
  6. Liu, L., Ang, K. P., Elliott, J. A. K., Kent, M. P., Lien, S., MacDonald, D., and Boulding, E. G. (2017) A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits. Evolutionary Applications 10, 276-296. doi: 10.1111/eva.12450
  7. Macqueen, D. J., Primmer, C. R., Houston, R. D., Nowak, B. F., Bernatchez, L., Bergseth, S., Davidson, W. S., Gallardo-Escárate, C., Goldammer, T., Guiguen, Y., Iturra, P., Kijas, J. W., Koop, B. F., Lien, S., Maass, A., Martin, S. A. M., McGinnity, P., Montecino, M., Naish, K. A., Nichols, K. M., Ólafsson, K., Omholt, S. W., Palti, Y., Plastow, G. S., Rexroad, C. E., Rise, M. L., Ritchie, R. J., Sandve, S. R., Schulte, P. M., Tello, A., Vidal, R., Vik, J. O., Wargelius, A., Yáñez, J. M., Primmer, C. R., Macqueen, D. J., Houston, R. D., Nowak, B. F., Davidson, W. S., Lien, S., Koop, B. F., and Consortium, T. F. (2017) Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics 18, 484. doi: 10.1186/s12864-017-3862-8
  8. Mähler, N., Wang, J., Terebieniec, B. K., Ingvarsson, P. K., Street, N. R., and Hvidsten, T. R. (2017) Gene co-expression network connectivity is an important determinant of selective constraint. PLoS Genetics 13, e1006402. doi: 10.1371/journal.pgen.1006402
  9. Olsen, H., Knutsen, T. M., Kohler, A., Svendsen, M., Gidskehaug, L., Grove, H., Nome, T., Sodeland, M., Sundsaasen, K., Kent, M., Martens, H., and Lien, S. (2017) Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13 Genetics Selection Evolution. Vol. 49. doi: 10.1186/s12711-017-0294-5
  10. Pedersen, S., Liu, L., Glebe, B., Leadbeater, S., Lien, S., and Boulding, E. G. (2017) Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first- and second-generation backcrosses between European and North American Atlantic salmon (Salmo salar). Genome 61, 33-42. doi: 10.1139/gen-2017-0026
  11. Robertson, F. M., Gundappa, M. K., Grammes, F., Hvidsten, T. R., Redmond, A. K., Lien, S., Martin, S. A. M., Holland, P. W. H., Sandve, S. R., and Macqueen, D. J. (2017) Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biology 18, 111. doi: 10.1186/s13059-017-1241-z
  12. Samy, J. K. A., Mulugeta, T. D., Nome, T., Sandve, S. R., Grammes, F., Kent, M. P., Lien, S., and Våge, D. I. (2017) SalmoBase: an integrated molecular data resource for Salmonid species. BMC Genomics 18, 482. doi: 10.1186/s12864-017-3877-1
  13. Sinclair-Waters, M., Bradbury, I. R., Morris, C. J., Lien, S., Kent, M. P., and Bentzen, P. (2017) Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic. Molecular Ecology 27, 339-351. Doi: 10.1111/mec.14442
  14. Tørresen, O. K., Star, B., Jentoft, S., Reinar, W. B., Grove, H., Miller, J. R., Walenz, B. P., Knight, J., Ekholm, J. M., Peluso, P., Edvardsen, R. B., Tooming-Klunderud, A., Skage, M., Lien, S., Jakobsen, K. S., and Nederbragt, A. J. (2017) An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 18, 95. doi: 10.1186/s12864-016-3448-x
  15. van Son, M., Agarwal, R., Kent, M. P., Grove, H., Grindflek, E., and Lien, S. (2017) Exploiting whole genome sequence data to fine map and characterize candidate genes within a quantitative trait loci region affecting androstenone on porcine chromosome 5. Animal Genetics 48, 653-659. doi: 10.1111/age.12615
  16. van Son, M., Enger, E. G., Grove, H., Ros-Freixedes, R., Kent, M. P., Lien, S., and Grindflek, E. (2017) Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs. BMC Genomics 18, 369. doi: 10.1186/s12864-017-3752-0
  17. van Son, M., Tremoen, N. H., Gaustad, A. H., Myromslien, F. D., Våge, D. I., Stenseth, E.-B., Zeremichael, T. T., and Grindflek, E. (2017) RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars. BMC Veterinary Research 13, 362 doi: 10.1186/s12917-017-1279-x

2016

  1. Bou, M., Todorčević, M., Torgersen, J., Škugor, S., Navarro, I., and Ruyter, B. (2016) De novo lipogenesis in Atlantic salmon adipocytes. Biochimica et Biophysica Acta (BBA) – General Subjects 1860, 86-96. doi:1016/j.bbagen.2015.10.022
  2. Gjuvsland, A. B., Zörgö, E., Samy, J. K., Stenberg, S., Demirsoy, I. H., Roque, F., Maciaszczyk‐Dziubinska, E., Migocka, M., Alonso‐Perez, E., Zackrisson, M., Wysocki, R., Tamás, M. J., Jonassen, I., Omholt, S. W., and Warringer, J. (2016) Disentangling genetic and epigenetic determinants of ultrafast adaptation. Molecular Systems Biology doi: 10.15252/msb.20166951
  3. Hermansen, R. A., Hvidsten, T. R., Sandve, S. R., and Liberles, D. A. (2016) Extracting functional trends from whole genome duplication events using comparative genomics. Biological Procedures Online 18, 11. doi:1186/s12575-016-0041-2
  4. Ingvarsson, P. K., Hvidsten, T. R., and Street, N. R. (2016) Towards integration of population and comparative genomics in forest trees. New Phytologist 212, 338-344. doi:1111/nph.14153
  5. Jørgensen, M. H., Elameen, A., Hofman, N., Klemsdal, S., Malaval, S., and Fjellheim, S. (2016) What’s the meaning of local? Using molecular markers to define seed transfer zones for ecological restoration in Norway. Evolutionary Applications 9, 673-684. doi:1111/eva.12378 
  6. Khan, U. W., Øverli, Ø., Hinkle, P. M., Pasha, F. A., Johansen, I. B., Berget, I., Silva, P. I. M., Kittilsen, S., Höglund, E., Omholt, S. W., and Våge, D. I. (2016) A novel role for pigment genes in the stress response in rainbow trout (Oncorhynchus mykiss). Scientific Reports 6, 28969. doi:1038/srep28969
  7. Kirubakaran, T. G., Grove, H., Kent, M. P., Sandve, S. R., Baranski, M., Nome, T., De Rosa, M. C., Righino, B., Johansen, T., Otterå, H., Sonesson, A., Lien, S., and Andersen, Ø. (2016) Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod. Molecular Ecology 25, 2130-2143. doi:1111/mec.13592
  8. Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., von Schalburg, K., Rondeau, E. B., Di Genova, A., Samy, J. K. A., Olav Vik, J., Vigeland, M. D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D. R., Yorke, J. A., Nederbragt, A. J., Tooming-Klunderud, A., Jakobsen, K. S., Jiang, X., Fan, D., Hu, Y., Liberles, D. A., Vidal, R., Iturra, P., Jones, S. J. M., Jonassen, I., Maass, A., Omholt, S. W., and Davidson, W. S. (2016) The Atlantic salmon genome provides insights into rediploidization. Nature 533, 200. doi:1038/nature17164
  9. Linløkken, A. N., Haugen, T. O., Mathew, P. K., Johansen, W., and Lien, S. (2016) Comparing estimates of number of breeders Nb based on microsatellites and single nucleotide polymorphism of three groups of brown trout (Salmo trutta L.). Fisheries Management and Ecology 23, 152-160. doi:1111/fme.12169
  10. Lorenz, S., Barøy, T., Sun, J., Nome, T., Vodák, D., Bryne, J.-C., Håkelien, A.-M., Fernandez-Cuesta, L., Möhlendick, B., Rieder, H., Szuhai, K., Zaikova, O., Ahlquist, T. C., Thomassen, G. O. S., Skotheim, R. I., Lothe, R. A., Tarpey, P. S., Campbell, P., Flanagan, A., Myklebost, O., and Meza-Zepeda, L. A. (2016) Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations. Oncotarget 7, 5273-5288. doi:18632/oncotarget.6567
  11. McKeown, M., Schubert, M., Marcussen, T., Fjellheim, S., and Preston, J. C. (2016) Evidence for an Early Origin of Vernalization Responsiveness in Temperate Pooideae Grasses. Plant Physiology 172, 416-426. doi:1104/pp.16.01023
  12. Obudulu, O., Bygdell, J., Sundberg, B., Moritz, T., Hvidsten, T. R., Trygg, J., and Wingsle, G. (2016) Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics 17, 119. doi:1186/s12864-016-2458-z
  13. Olsen, H. G., Knutsen, T. M., Lewandowska-Sabat, A. M., Grove, H., Nome, T., Svendsen, M., Arnyasi, M., Sodeland, M., Sundsaasen, K. K., Dahl, S. R., Heringstad, B., Hansen, H. H., Olsaker, I., Kent, M. P., and Lien, S. (2016) Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production. Genetics, Selection, Evolution : GSE 48, 79. doi:1186/s12711-016-0257-2
  14. Pritchard, V. L., Erkinaro, J., Kent, M. P., Niemelä, E., Orell, P., Lien, S., and Primmer, C. R. (2016) Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees. Evolutionary Applications 9, 1017-1031. doi:1111/eva.12407
  15. Rostgaard Nielsen, L., Brandes, U., Dahl Kjær, E., and Fjellheim, S. (2016) Introduced Scotch broom (Cytisus scoparius) invades the genome of native populations in vulnerable heathland habitats. Molecular Ecology 25, 2790-2804. doi:1111/mec.13666
  16. Sodeland, M., Jorde, P. E., Lien, S., Jentoft, S., Berg, P. R., Grove, H., Kent, M. P., Arnyasi, M., Olsen, E. M., and Knutsen, H. (2016) “Islands of Divergence” in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements. Genome Biology and Evolution 8, 1012-1022. doi:1093/gbe/evw057
  17. Sveen, L. R., Timmerhaus, G., Torgersen, J. S., Ytteborg, E., Jørgensen, S. M., Handeland, S., Stefansson, S. O., Nilsen, T. O., Calabrese, S., Ebbesson, L., Terjesen, B. F., and Takle, H. (2016) Impact of fish density and specific water flow on skin properties in Atlantic salmon (Salmo salar L.) post-smolts. Aquaculture 464, 629-637. doi:1016/j.aquaculture.2016.08.012

Popular scientific publications 2016:

  1. Andersen Ø., Lien S. (2016) Torsk eller skrei? Gåten er endelig løst. Aftenposten Viten
  2. Sverdrup-Thygeson A., Sandve S. R., Hvidsten T. R. (2016) Verdens rareste dyr ble nettopp litt rarere. Aftenposten

Link to publications in the period 2003-2015