Now showing items 1-18 of 18

  • 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 ...
  • Characterization of the 18s rRNA gene for designing universal eukaryote specific primers 

    Hadziavdic, Kenan; Lekang, Katrine; Lanzén, Anders; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer (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 ...
  • CREST – Classification Resources for Environmental Sequence Tags 

    Lanzén, Anders; Jørgensen, Steffen L.; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; Øvreås, Lise; Urich, Tim (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 ...
  • Exome Sequencing and Genetic Testing for MODY 

    Johansson, Stefan; Irgens, Henrik; Chudasama, Kishan K.; Molnes, Janne; Aerts, Jan; Knappskog, Per; Njølstad, Pål Rasmus; Roque, Francisco S.; Jonassen, Inge; Molven, Anders (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 standard ...
  • 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 ...
  • Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users 

    Lunde, Mai Lill Suhr; Dysvik, Bjarte; Bruland, Ove; Warnakulasuriya, K. A. A. Saman; Amaratunga, Asoka N.; Jonassen, Inge; Vasstrand, Endre N.; Ibrahim, Salah Osman (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 ...
  • Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation 

    Stansberg, Christine; Vik-Mo, Audun O.; Holdhus, Rita; Breilid, Harald; Srebro, Boleslaw; Petersen, Kjell; Jørgensen, Hugo A.; Jonassen, Inge; Steen, Vidar Martin (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 ...
  • Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia 

    Øyan, Anne Margrete; Ånensen, Nina; Bø, Trond Hellem; Stordrange, Laila; Jonassen, Inge; Bruserud, Øystein; Kalland, Karl-Henning; Gjertsen, Bjørn Tore (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 ...
  • 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. (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 ...
  • High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example 

    De Souza, Gustavo A.; Målen, Hiwa; Søfteland, Tina; Sælensminde, Gisle; Prasad, Swati; Jonassen, Inge; Wiker, Harald G. (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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...