Blar i Bergen Open Research Archive på forfatter "Jonassen, Inge"

Viser treff 41-53 av 53

    • ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species 

      Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz; Yadetie, Fekadu; Zielinski, Daniel Craig; Goksøyr, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-11)
      The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ...

    • Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data 

      Xue, Yaxin; Lanzén, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-03-13)
      Motivation Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed ...

    • Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable? 

      Nielsen, Rune; Xue, Yaxin; Jonassen, Inge; Haaland, Ingvild; Kommedal, Øyvind; Wiker, Harald Gotten; Drengenes, Christine; Bakke, Per S.; Eagan, Tomas Mikal Lind (Journal article; Peer reviewed, 2021)
      Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases ...

    • Repeats and EST analysis for new organisms 

      Malde, Ketil; Jonassen, Inge (Journal article, 2008-01-18)
      Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask ...

    • Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis 

      Eichner, Christiane; Frost, Petter; Dysvik, Bjarte; Jonassen, Inge; Kristiansen, Bjørn; Nilsen, Frank (Peer reviewed; Journal article, 2008-03-10)
      Background Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proportion ...

    • The salmon louse genome: Copepod features and parasitic adaptations 

      Skern-Mauritzen, Rasmus; Malde, Ketil; Eichner, Christiane; Dondrup, Michael; Furmanek, Tomasz; Besnier, Francois; Komisarczuk, Anna Zofia; Nuhn, Michael; Dalvin, Sussie; Edvardsen, Rolf Brudvik; Klages, Sven; Huettel, Bruno; Stueber, Kurt; Grotmol, Sindre; Karlsbakk, Egil Erlingsson; Kersey, Paul; Leong, Jong S; Glover, Kevin Alan; Reinhardt, Richard; Lien, Sigbjørn; Jonassen, Inge; Koop, Ben F; Nilsen, Frank (Journal article; Peer reviewed, 2021)
      Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically ...

    • SeeCiTe: a method to assess CNV calls from SNP arrays using trio data 

      Lavrichenko, Ksenia; Helgeland, Øyvind; Njølstad, Pål Rasmus; Jonassen, Inge; Johansson, Stefan (Journal article; Peer reviewed, 2021)
      Motivation Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still ...

    • Systematic exploration of error sources in pyrosequencing flowgram data 

      Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (Peer reviewed; Journal article, 2011)
      Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several ...

    • TMM@: a web application for the analysis of transmembrane helix mobility 

      Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (Peer reviewed; Journal article, 2007-07-02)
      Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ...

    • Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts 

      Leiss, Lina Wik; Mutlu, Ercan; Øyan, Anne Margrete; Yan, Tao; Tsinkalovsky, Oleg; Sleire, Linda; Petersen, Kjell; Rahman, Mohummad Aminur; Johannessen, Mireille Kayitesi; Mitra, Siddharta S.; Jacobsen, Hege; Talasila, Krishna Mukharji; Miletic, Hrvoje; Jonassen, Inge; Li, Xingang; Brons, Nicolas H.C.; Kalland, Karl-Henning; Wang, Jian; Enger, Per Øyvind (Peer reviewed; Journal article, 2017-02-07)
      Background: Little is known about the role of glial host cells in brain tumours. However, supporting stromal cells have been shown to foster tumour growth in other cancers. Methods: We isolated stromal cells from patient-derived ...

    • Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species 

      Malde, Ketil; Seliussen, Bjørghild Breistein; Sanchez, Maria Quintela; Dahle, Geir; Besnier, Francois; Skaug, Hans J.; Øien, Nils Inge; Solvang, Hiroko Kato; Haug, Tore; Skern-Mauritzen, Rasmus; Kanda, Naohisa; Pastene, Luis A.; Jonassen, Inge; Glover, Kevin (Peer reviewed; Journal article, 2017-01-13)
      Background: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An ...

    • Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity 

      Sridhar, Settu; Sharma, Animesh; Kongshaug, Heidi; Nilsen, Frank; Jonassen, Inge (Peer reviewed; Journal article, 2012-11-06)
      Background: Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to ...

    • XHM: A system for detection of potential cross hybridizations in DNA microarrays 

      Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge (Peer reviewed; Journal article, 2004-08-27)
      Background: Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability ...