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    • Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management 

      Maduna, Simo; Vivian-Smith, Adam; Jónsdóttir, Ólöf Dóra Bartels; Imsland, Albert; Klutsch, Cornelya; Nyman, Tommi; Eiken, Hans Geir; Hagen, Snorre (Journal article; Peer reviewed, 2020)
      The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the ...

    • Genome-wide analysis of Atlantic salmon (Salmo salar) mucin genes and their role as biomarkers 

      Sveen, Lene Rydal; Grammes, Fabian Thomas; Ytteborg, Elisabeth; Takle, Harald Rune; Jørgensen, Sven Martin (Peer reviewed; Journal article, 2017-10-08)
      The aim of this study was to identify potential mucin genes in the Atlantic salmon genome and evaluate tissue-specific distribution and transcriptional regulation in response to aquaculture- relevant stress conditions in ...

    • Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns 

      Fortunato, Sofia; Adamski, Marcin; Bergum, Brith; Guder, Corina; Jordal, Signe; Rapp, Hans Tore; Leininger, Sven; Zwafink, Christin; Adamska, Maja (Peer reviewed; Journal article, 2012-06-23)
      Background: Sox genes are HMG-domain containing transcription factors with important roles in developmental processes in animals; many of them appear to have conserved functions among eumetazoans. Demosponges have fewer ...

    • Genome-wide DNA methylation profiling of non-small cell lung carcinomas 

      Carvalho, Rejane Hughes; Haberle, Vanja; Hou, Jun; van Gent, Teus; Thongjuea, Supat; van Ijcken, Wilfred F.J.; Kockx, Christel; Brouwer, Rutger; Rijkers, Erikjan; Sieuwerts, Anieta; Foekens, John; van Vroonhoven, Mirjam; Aerts, Joachim; Grosveld, Frank; Lenhard, Boris; Philipsen, Sjaak (Peer reviewed; Journal article, 2012-06-22)
      Background: Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important ...

    • The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation 

      Soler, Eric; Andrieu-Soler, Charlotte; Boer, Ernie de; Bryne, Jan Christian; Thongjuea, Supat; Stadhouders, Ralph; Palstra, Robert-Jan; Stevens, Mary; Kockx, Christel; IJcken, Wilfred van; Hou, Jun; Steinhoff, Christine; Rijkers, Erikjan; Lenhard, Boris; Grosveld, Frank (Peer reviewed; Journal article, 2010)
      One of the complexes formed by the hematopoietic transcription factor Gata1 is a complex with the Ldb1 (LIM domain-binding protein 1) and Tal1 proteins. It is known to be important for the development and differentiation ...

    • Genome-wide SNP analyses reveal population structure of Portunus pelagicus alongVietnam coastline 

      Dang, BT; Rahman, MA; Tran, SQ; Glenner, Henrik (Peer reviewed; Journal article, 2019-11-05)
      The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure ...

    • Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages 

      Kerou, Melina; Ponce-Toledo, Rafael I.; Zhao, Rui; Abby, Sophie S.; Hirai, Miho; Nomaki, Hidetaka; Takaki, Yoshihiro; Nunoura, Takuro; Jørgensen, Steffen Leth; Schleper, Christa (Journal article; Peer reviewed, 2021)
      Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem ...

    • Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia: Rhizocephala) 

      Martin, Sebastian; Lesny, Peter; Glenner, Henrik; Hecht, Jochen; Vilcinskas, Andreas; Bartolomaeus, Thomas; Podsiadlowski, Lars (Journal article; Peer reviewed, 2022)
      The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of ...

    • Genomic analysis of pasteurella atlantica provides insight on its virulence factors and phylogeny and highlights the potential of reverse vaccinology in aquaculture 

      Ellul, Rebecca Marie; Kalatzis, Panos G.; Frantzen, Cyril Alexander; Haugland, Gyri Teien; Gulla, Snorre; Colquhoun, Duncan John; Middelboe, Mathias; Wergeland, Heidrun Inger; Rønneseth, Anita (Journal article; Peer reviewed, 2021)
      Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology ...

    • Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L 

      Johansen, Torild; Besnier, Francois; Sanchez, Maria Quintela; Jorde, Per Erik; Glover, Kevin; Westgaard, Jon-Ivar; Dahle, Geir; Lien, Sigbjørn; Kent, Matthew Peter (Journal article; Peer reviewed, 2020)
      Challenging long‐held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor ...

    • Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis) 

      Økland, Arnfinn Lodden; Nylund, Are; Øvergård, Aina-Cathrine; Blindheim, Steffen H.; Watanabe, Kuninori; Grotmol, Sindre; Arnesen, Carl-Erik; Plarre, Heidrun (Peer reviewed; Journal article, 2014-11-17)
      Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for ...

    • Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon 

      Bradbury, Ian R.; Lehnert, Sarah Jean; Kess, Tony; Van Wyngaarden, Mallory; Duffy, Steven; Messmer, Amber M.; Wringe, Brendan; Karoliussen, Silje; Dempson, J. Brian; Fleming, Ian A.; Solberg, Monica Favnebøe; Glover, Kevin Alan; Bentzen, Paul (Journal article; Peer reviewed, 2022)
      Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree ...

    • The Genomic HyperBrowser: an analysis web server for genome-scale data 

      Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo; Hovig, Johannes Eivind (Peer reviewed; Journal article, 2013-04-30)
      The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable ...

    • Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) 

      Ward, Naomi; Larsen, Øivind; Sakwa, James; Bruseth, Live; Khouri, Hoda; Durkin, A. Scott; Dimitrov, George; Jiang, Lingxia; Scanlan, David; Kang, Katherine H.; Lewis, Matt; Nelson, Karen E.; Methé, Barbara; Wu, Martin; Heidelberg, John F.; Paulsen, Ian T.; Fouts, Derrick; Ravel, Jacques; Tettelin, Hervé; Ren, Qinghu; Read, Tim; DeBoy, Robert T.; Seshadri, Rekha; Salzberg, Steven L.; Jensen, Harald B.; Birkeland, Nils-Kåre; Nelson, William C.; Dodson, Robert J.; Grindhaug, Svenn Helge; Holt, Ingeborg; Eidhammer, Ingvar; Jonassen, Inge; Vanaken, Susan; Utterback, Terry; Feldblyum, Tamara V.; Fraser, Claire M.; Lillehaug, Johan; Eisen, Jonathan A. (Peer reviewed; Journal article, 2004-09-21)
      Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing ...

    • Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes 

      Yasuike, Motoshige; Leong, Jong; Jantzen, Stuart G.; Schalburg, Kristian R. von; Nilsen, Frank; Jones, Simon R. M.; Koop, Ben F. (Peer reviewed; Journal article, 2011-07-12)
      Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant ...

    • Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production 

      Maduna, Simo; Jónsdóttir, Ólöf Dóra Bartels; Imsland, Albert; Gíslason, Davíð; Reynolds, Patrick; Kapari, Lauri Teemu; Hangstad, Thor Arne; Meier, Kristian; Hagen, Snorre (Journal article; Peer reviewed, 2023-09-26)
      Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used ...

    • Genotyping errors in a calibrated DNA register: implications for identification of individuals 

      Haaland, Øystein; Glover, Kevin; Seliussen, Bjørghild Breistein; Skaug, Hans J. (Peer reviewed; Journal article, 2011-04-20)
      Background: The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. ...

    • Genotyping of Tenacibaculum maritimum isolates from farmed Atlantic salmon in Western Canada 

      Frisch, Kathleen Marie; Småge, Sverre Bang; Brevik, Øyvind Jakobsen; Duesund, Henrik; Nylund, Are (Peer reviewed; Journal article, 2018-01)
      Mouthrot infections (bacterial stomatitis) have a significant impact on the Atlantic salmon aquaculture industry in Western Canada due to economic losses and fish welfare. Bacteria isolated from lesions in the field have ...

    • Genotyping tool for salmonid gill pox virus (SGPV) obtained from farmed and wild Atlantic salmon (Salmo salar) 

      Nylund, Are; Macintyre, Thomas Kloster-Jensen; Mohammadi, Faezeh; Lagadec, Erwan; Plarre, Heidrun (Journal article; Peer reviewed, 2023)
      Poxviruses are common viruses found in vertebrate species. In 2006, the first poxvirus associated with salmon, salmonid gill poxvirus (SGPV), was identified during an outbreak of gill disease at a smolt production site in ...

    • A gentle tutorial on accelerated parameter and confidence interval estimation for hidden Markov models using Template Model Builder 

      Bacri, Timothee Raphael Ferdinand; Berentsen, Geir Drage; Bulla, Jan; Hølleland, Sondre Nedreås (Journal article; Peer reviewed, 2022)
      A very common way to estimate the parameters of a hidden Markov model (HMM) is the relatively straightforward computation of maximum likelihood (ML) estimates. For this task, most users rely on user-friendly implementation ...