Now showing items 1-12 of 12

  • BioXSD: the common data-exchange format for everyday bioinformatics web services 

    Kalaš, Matúš; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge (Oxford University Press, 2010)
    Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ...
    Journal article
  • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

    Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (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 increased to ∼500 ...
    Peer reviewedJournal article
  • EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats 

    Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter (Oxford University Press, 2013)
    Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore ...
    Journal article
  • Filtering duplicate reads from 454 pyrosequencing data 

    Balzer, Susanne Mignon; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge (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 and metagenomics. Especially ...
    Peer reviewedJournal article
  • Modulation of Transcriptional and Inflammatory Responses in Murine Macrophages by the Mycobacterium tuberculosis Mammalian Cell Entry (Mce) 1 Complex 

    Stavrum, Ruth; Stavrum, Anne-Kristin; Valvatne, Håvard; Riley, Lee W.; Ulvestad, Elling; Jonassen, Inge; Assmus, Jørg; Doherty, Tanya Mark; Grewal, Harleen M. S. (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 ...
    Peer reviewedJournal article
  • Predicting Gene Regulatory Elements in Silico on a Genomic Scale 

    Brazma, Alvis; Jonassen, Inge; Vilo, Jaak; Ukkonen, Esko (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 ...
    Journal article
  • Repeats and EST analysis for new organisms 

    Malde, Ketil; Jonassen, Inge (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 ...
    Journal article
  • 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 (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 ...
    Peer reviewedJournal article
  • Systematic exploration of error sources in pyrosequencing flowgram data 

    Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (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. Although there are ...
    Peer reviewedJournal article
  • TMM@: a web application for the analysis of transmembrane helix mobility 

    Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (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) has ...
    Journal article
  • 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 (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 ...
    Journal article
  • XHM: A system for detection of potential cross hybridizations in DNA microarrays 

    Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge (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 reliability ...
    Journal articlePeer reviewed