• 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 (Peer reviewed; Journal article, 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 ...
    • 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 (Peer reviewed; Journal article, 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 ...
    • Gene-methylation interactions: Discovering region-wise DNA methylation levels that modify SNP-associated disease risk 

      Romanowska, Julia; Haaland, Øystein Ariansen; Jugessur, Astanand; Gjerdevik, Miriam; Xu, Zongli; Taylor, Jack A.; Wilcox, Allen J; Jonassen, Inge; Lie, Rolv T.; Gjessing, Håkon K. (Journal article; Peer reviewed, 2020)
      Background Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. ...
    • 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 (Peer reviewed; Journal article, 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 ...
    • The genome sequence of Atlantic cod reveals a unique immune system 

      Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Paulsen, Jonas; Solbakken, Monica Hongrø; Sharma, Animesh; Wetten, Ola Frang; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf; Kirubakaran, G. Tina; Espelund, Mari; Nepal, Chirag; Previti, A. Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul Ragnar; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar Daae; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd (Peer reviewed; Journal article, 2011-09)
      Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex ...
    • 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. (Peer reviewed; Journal article, 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. (Peer reviewed; Journal article, 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 generation. ...
    • High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities 

      Lanzén, Anders; Lekang, Katrine; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer (Peer reviewed; Journal article, 2016-09)
      As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental ...
    • Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod 

      Eide, Marta; Goksøyr, Anders; Yadetie, Fekadu; Gilabert, Alejandra; Bartosova, Zdenka; Frøysa, Håvard Guldbrandsen; Fallahi, Shirin; Zhang, Xiaokang; Blaser, Nello; Jonassen, Inge; Bruheim, Per; Alendal, Guttorm; Brun, Morten; Porte, Cinta; Karlsen, Odd André (Journal article; Peer reviewed, 2023-03-22)
      Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in ...
    • LOCATOR: feature extraction and spatial analysis of the cancer tissue microenvironment using mass cytometry imaging technologies 

      Ehsani, Rezvan; Jonassen, Inge; Akslen, Lars Andreas; Kleftogiannis, Dimitrios (Journal article; Peer reviewed, 2023)
      Motivation Recent advances in highly multiplexed imaging have provided unprecedented insights into the complex cellular organization of tissues, with many applications in translational medicine. However, downstream ...
    • Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data 

      Zhang, Xiaokang; Jonassen, Inge; Goksøyr, Anders (Chapter, 2021)
      Biomarkers are of great importance in many fields, such as cancer research, toxicology, diagnosis and treatment of diseases, and to better understand biological response mechanisms to internal or external intervention. ...
    • Mathematical modelling of nitric oxide/cyclic GMP/cyclic AMP signalling in platelets 

      Kleppe, Rune; Jonassen, Inge; Doskeland, Stein Ove; Selheim, Frode (Peer reviewed; Journal article, 2018-02-19)
      Platelet activation contributes to normal haemostasis but also to pathologic conditions like stroke and cardiac infarction. Signalling by cGMP and cAMP inhibit platelet activation and are therefore attractive targets for ...
    • Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost 

      Xue, Yaxin; Jonassen, Inge; Øvreås, Lise; Tas, Neslihan (Journal article; Peer reviewed, 2020)
      Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing ...
    • 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. (Peer reviewed; Journal article, 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 ...
    • 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 (Peer reviewed; Journal article, 2018)
      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 ...
    • A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis) 

      Zhou, Zhaoran; Eichner, Christiane; Nilsen, Frank; Jonassen, Inge; Dondrup, Michael (Journal article; Peer reviewed, 2021)
      Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and ...
    • Predicting Gene Regulatory Elements in Silico on a Genomic Scale 

      Brazma, Alvis; Jonassen, Inge; Vilo, Jaak; Ukkonen, Esko (Journal article, 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 ...
    • Protected sampling is preferable in bronchoscopic studies of the airway microbiome 

      Grønseth, Rune; Drengenes, Christine; Wiker, Harald G; Tangedal, Solveig; Xue, Yaxin; Husebø, Gunnar; Svanes, Øistein; Lehmann, Sverre; Aardal, Marit Elisabeth; Hoang, Tuyen; Kalananthan, Tharmini; Martinsen, Einar Marius Hjellestad; Leiten, Elise Orvedal; Aanerud, Marianne; Nordeide, Eli; Haaland, Ingvild; Jonassen, Inge; Bakke, Per S.; Eagan, Tomas Mikal (Journal article; Peer reviewed, 2017)
      The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with ...
    • Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site 

      Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Bartosova, Zdenka; Yadetie, Fekadu; Jonassen, Inge; Goksøyr, Anders; Arukwe, Augustine (Journal article; Peer reviewed, 2020)
      In the present study, a previously capped waste disposal site at Kollevåg (Norway) was selected to study the effects of contaminant leakage on biomarkers associated with Atlantic cod (Gadus morhua) reproductive endocrinology ...
    • RASflow: an RNA-Seq analysis workflow with Snakemake 

      Zhang, Xiaokang; Jonassen, Inge (Journal article; Peer reviewed, 2020)
      Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ...