• Discovery of approximate composite motifs in biological sequences 

      Valebjørg, Vetle Søraas (Master thesis, 2006)
      Mapping the regulatory system in living organisms is a great challenge, and many methods have been created during the last 15 years to solve this problem. The biological processes are however more flexible and complex than ...
    • DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation 

      Rauluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2020)
      Background Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional ...
    • DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis 

      Rauluseviciute, Ieva; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2019)
      Sequencing technologies have changed not only our approaches to classical genetics, but also the field of epigenetics. Specific methods allow scientists to identify novel genome-wide epigenetic patterns of DNA methylation ...
    • Enhanced efficacy of bleomycin in bladder cancer cells by photochemical internalization 

      Baglo, Yan; Hagen, Lars; Høgset, Anders; Drabløs, Finn; Otterlei, Marit; Gederaas, Odrun Arna (Journal article; Peer reviewed, 2014)
      Bleomycin is a cytotoxic chemotherapeutic agent widely used in cancer treatment. However, its efficacy in different cancers is low, possibly due to limited cellular internalization. In this study, a novel approach known ...
    • Enhanced identification of significant regulators of gene expression 

      Ehsani, Rezvan; Drabløs, Finn (Peer reviewed; Journal article, 2020)
      Background Diseases like cancer will lead to changes in gene expression, and it is relevant to identify key regulatory genes that can be linked directly to these changes. This can be done by computing a Regulatory Impact ...
    • EpiFactors: A comprehensive database of human epigenetic factors and complexes 

      Medvedeva, Yulia; Lennartsson, Andreas; Ehsani, Rezvan; Kulakovskiy, Ivan; Vorontsov, Ilya E; Panahandeh, Pouda; Khimulya, Grigory; Kasukawa, Takeya; Drabløs, Finn (Peer reviewed; Journal article, 2015)
      Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se . Rather, covalent modifications of DNA and histones affect gene expression and genome ...
    • FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer 

      Rise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck (Peer reviewed; Journal article, 2022)
      Mitochondrial activity in cancer cells has been central to cancer research since Otto Warburg first published his thesis on the topic in 1956. Although Warburg proposed that oxidative phosphorylation in the tricarboxylic ...
    • FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks 

      Rise, Kjersti; Tessem, May-Britt; Drabløs, Finn; Rye, Morten Beck (Journal article; Peer reviewed, 2021)
      Cytoscape is often used for visualization and analysis of metabolic pathways. For example, based on KEGG data, a reader for KEGG Markup Language (KGML) is used to load files into Cytoscape. However, although multiple genes ...
    • GAPGOM—an R package for gene annotation prediction using GO metrics 

      van Mourik, Casper; Ehsani, Rezvan; Drabløs, Finn (Peer reviewed; Journal article, 2021)
      Objective Properties of gene products can be described or annotated with Gene Ontology (GO) terms. But for many genes we have limited information about their products, for example with respect to function. This is ...
    • Gene regulation in three dimensions 

      Wittek, Kristian Thoresen (Master thesis, 2016)
      Gene regulation has traditionally mainly been viewed as a 1D and possibly 2D process. In the 1D view the genome is seen as a linear string of nucleotides, where one or more transcription factors (TFs) bind to transcription ...
    • Gene signatures ESC, MYC and ERG-fusion are early markers of a potentially dangerous subtype of prostate cancer 

      Rye, Morten Beck; Bertilsson, Helena; Drabløs, Finn; Angelsen, Anders; Bathen, Tone Frost; Tessem, May-Britt (Journal article; Peer reviewed, 2014)
      Background Good prognostic tools for predicting disease progression in early stage prostate cancer (PCa) are still missing. Detection of molecular subtypes, for instance by using microarray gene technology, can give new ...
    • The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems 

      Rye, Morten Beck; Krossa, Sebastian; Hall, Martina; van Mourik, Casper; Bathen, Tone Frost; Drabløs, Finn; Tessem, May-Britt; Bertilsson, Helena (Peer reviewed; Journal article, 2022)
      High secretion of the metabolites citrate and spermine is a unique hallmark for normal prostate epithelial cells, and is reduced in aggressive prostate cancer. However, the identity of the genes controlling this biological ...
    • Improved benchmarks for computational motif discovery 

      Sandve, Geir Kjetil; Abul, Osman; Walseng, Vegard; Drabløs, Finn (Journal article; Peer reviewed, 2007-06-08)
      Background An important step in annotation of sequenced genomes is the identification of transcription factor binding sites. More than a hundred different computational methods have been proposed, and it is difficult ...
    • Investigation of properties and classification of human transcription factors 

      Bahrami, Shahram (Doctoral theses at NTNU;2016:243, Doctoral thesis, 2016)
      Studier av egenskaper og klassifisering av humane transkripsjonsfaktorer Egenskaper og funksjonen av ulike celler bestemmes gjennom regulering av genuttrykket, og en rekke ulike mekanismer er aktive i den enkelte ...
    • Learning pattern models from examples 

      Walseng, Vegard (Master thesis, 2006)
      The aim of this thesis is twofold. Firstly, it is a survey of some of the most prevalent pattern models used in motif discovery algorithms. The main goal of the survey is to see how well these models with all their ...
    • LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium 

      Zwiggelaar, Rosalie; Lindholm, Håvard Takle; Fosslie, Madeleine Lystad; Pedersen, Marianne Terndrup; Ohta, Yuki; Díez-Sánchez, Alberto; Martín-Alonso, Mara; Ostrop, Jenny; Matono, Mami; Parmar, Naveen; Kvaløy, Emilie; Spanjers, Roos; Nazmi, Kamran; Rye, Morten Beck; Drabløs, Finn; Arrowsmith, Cheryl H; Dahl, John Arne; Jensen, Kim B.; Sato, Toshiro; Oudhoff, Menno (Journal article; Peer reviewed, 2020)
      Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify regulators of neonatal intestinal epithelial ...
    • MACPET: model-based analysis for ChIA-PET 

      Vardaxis, Ioannis; Drabløs, Finn; Rye, Morten Beck; Lindqvist, Bo Henry (Journal article; Peer reviewed, 2019)
      We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET ...
    • Making substitution matrices metric 

      Anfinsen, Jarle (Master thesis, 2005)
      With the emergence and growth of large databases of information, efficient methods for storage and processing are becoming increasingly important. The existence of a metric distance measure between data entities enables ...
    • Measures of co-expression for improved function prediction of long non-coding RNAs 

      Ehsani, Rezvan; Drabløs, Finn (Journal article; Peer reviewed, 2018)
      Background Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes ...