Blar i forfatter "Willassen, Nils Peder"

Viser treff 21-29 av 29

    • The metagenomic data life-cycle: standards and best practices 

      Ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Fosso, Bruno; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder; Cochrane, Guy (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-08-01)
      Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine ...

    • Norwegian e-Infrastructure for Life Sciences (NeLS) 

      Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander; Li, Xiaxi; Zhang, Wei; Andreetta, Christian; Mulugeta, Teshome Dagne; Kalaš, Matúš; Rye, Morten Beck; Hjerde, Erik; Antony Samy, Jeevan Karloss; Fornous, Ghislain; Azab, Abdulrahman; Våge, Dag Inge; Hovig, Eivind; Willassen, Nils Peder; Drabløs, Finn; Nygård, Ståle; Petersen, Kjell; Jonassen, Inge (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-06-29)
      The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may ...

    • Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa 

      Karlsen, Christian; Hjerde, Erik; Klemetsen, Terje; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-04-20)
      Background: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight ...

    • Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species 

      Klemetsen, Terje; Karlsen, Christian René; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-02-18)
      Genus Aliivibrio is known to harbor species exhibiting bioluminescence as well as pathogenic behavior affecting the fish farming industry. Current phylogenetic understanding of Aliivibrio has largely remained dormant after reclassification disentangled it from the Vibrio genus in 2007. There is growing evidence of wider diversity, but until now the lack of genomes and selective use of type strains ...

    • Presence of acyl-homoserine lactones in 57 members of the Vibrionaceae family 

      Purohit, Amit Anand; Johansen, Jostein a; Hansen, Hilde; Leiros, Hanna-Kirsti S.; Kashulin, Alexander; Karlsen, Christian; Smalås, Arne O.; Haugen, Peik; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2013-05-31)
      Aims: The aim of this study was to use a sensitive method to screen and quantify 57 Vibrionaceae strains for the production of acyl-homoserine lactones (AHLs) and map the resulting AHL profiles onto a host phylogeny.<p> <p>Methods and Results: We used a high-performance liquid chromatography– tandem mass spectrometry (HPLC-MS/MS) protocol to measure AHLs in spent media after bacterial growth. ...

    • Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi) 

      Assefa, Netsanet Gizaw; Niiranen, Laila; Johnson, Kenneth; Leiros, Hanna-Kirsti S.; Smalås, Arne O.; Willassen, Nils Peder; Moe, Elin (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-07-25)
      Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage ...

    • Transparent Incremental Updates for Genomics Data Analysis Pipelines 

      Pedersen, Edvard; Willassen, Nils Peder; Bongo, Lars Ailo (Chapter; Bokkapittel, 2014)
      A large up-to-date compendium of integrated genomic data is often required for biological data analysis. The compendium can be tens of terabytes in size, and must often be frequently updated with new experimental or meta-data. Manual compendium update is cumbersome, requires a lot of unnecessary computation, and it may result in errors or inconsistencies in the compendium. We propose a transparent ...

    • Transparent Incremental Updates for Genomics Data Analysis Pipelines 

      Pedersen, Edvard; Willassen, Nils Peder; Bongo, Lars Ailo (Chapter; Bokkapittel, 2014)

    • Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation 

      Kahlke, Tim; Goesmann, Alexander; Hjerde, Erik; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes ...