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Bergen Open Research Archive

Browsing by Author "Jonassen, Inge"

Bergen Open Research Archive

Browsing by Author "Jonassen, Inge"

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  • Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, Oxford University Press, 2010)
    Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have ...
  • Hadziavdic, Kenan; Lekang, Katrine; Lanzén, Anders; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer (Journal article, PLOS, 2014-02-07)
    High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of ...
  • Lanzén, Anders; Jørgensen, Steffen L.; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; Øvreås, Lise; Urich, Tim (Peer reviewed; Journal article, Public Library of Science, 2012-11-08)
    Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably ...
  • Johansson, Stefan; Irgens, Henrik; Chudasama, Kishan K.; Molnes, Janne; Aerts, Jan; Knappskog, Per; Njølstad, Pål Rasmus; Roque, Francisco S.; Jonassen, Inge; Molven, Anders (Peer reviewed; Journal article, Public Library of Science, 2012-05-25)
    Context: Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when ...
  • Balzer, Susanne Mignon; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge (Peer reviewed; Journal article, Oxford University Press, 2013)
    Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing ...
  • Lunde, Mai Lill Suhr; Dysvik, Bjarte; Bruland, Ove; Warnakulasuriya, K. A. A. Saman; Amaratunga, Asoka N.; Jonassen, Inge; Vasstrand, Endre N.; Ibrahim, Salah Osman (Peer reviewed; Journal article, Spandidos Publications, 2007-11)
    Oral squamous cell carcinoma (OSCC) is one of the major health problems in Sri Lanka and the disease is associated with the habit of Betel Quid (BQ) chewing. Using 35k oligo microarrays, we analyzed the gene expression profile ...
  • Stansberg, Christine; Vik-Mo, Audun O.; Holdhus, Rita; Breilid, Harald; Srebro, Boleslaw; Petersen, Kjell; Jørgensen, Hugo A.; Jonassen, Inge; Steen, Vidar Martin (Journal article, BioMed Central, 2007-04-04)
    Background: The mammalian brain is divided into distinct regions with structural and neurophysiological differences. As a result, gene expression is likely to vary between regions in relation to their cellular composition ...
  • Øyan, Anne Margrete; Ånensen, Nina; Bø, Trond Hellem; Stordrange, Laila; Jonassen, Inge; Bruserud, Øystein; Kalland, Karl-Henning; Gjertsen, Bjørn Tore (Journal article, BioMed Central, 2009-03-05)
    Background: The molecular changes in vivo in acute myeloid leukemia cells early after start of conventional genotoxic chemotherapy are incompletely understood, and it is not known if early molecular modulations reflect ...
  • 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. (Journal article; Peer reviewed, Public Library of Science, 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 ...
  • De Souza, Gustavo A.; Målen, Hiwa; Søfteland, Tina; Sælensminde, Gisle; Prasad, Swati; Jonassen, Inge; Wiker, Harald G. (Journal article; Peer reviewed, BioMed Central, 2008-07-02)
    Background: While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset ...
  • Stavrum, Ruth; Stavrum, Anne-Kristin; Valvatne, Håvard; Riley, Lee W.; Ulvestad, Elling; Jonassen, Inge; Assmus, Jørg; Doherty, Tanya Mark; Grewal, Harleen M. S. (Peer reviewed; Journal article, Public Library of Science, 2011-10-24)
    The outcome of many infections depends on the initial interactions between agent and host. Aiming at elucidating the effect of the M. tuberculosis Mce1 protein complex on host transcriptional and immunological responses ...
  • Brazma, Alvis; Jonassen, Inge; Vilo, Jaak; Ukkonen, Esko (Journal article, Cold Spring Harbor Laboratory Press, 1998-05-18)
    We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have ...
  • Malde, Ketil; Jonassen, Inge (Journal article, BioMed Central, 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 ...
  • Eichner, Christiane; Frost, Petter; Dysvik, Bjarte; Jonassen, Inge; Kristiansen, Bjørn; Nilsen, Frank (Peer reviewed; Journal article, BioMed Central, 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 ...
  • Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (Peer reviewed; Journal article, Oxford University Press, 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. ...
  • Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (Journal article, BioMed Central, 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) ...
  • Sridhar, Settu; Sharma, Animesh; Kongshaug, Heidi; Nilsen, Frank; Jonassen, Inge (Journal article, BioMed Central, 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 ...
  • Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge (Journal article; Peer reviewed, BioMed Central, 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 ...

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