Blar i NTNU Open på forfatter "Sandve, Geir Kjetil"

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    • Assessment of composite motif discovery methods 

      Klepper, Kjetil; Sandve, Geir Kjetil; Abul, Osman; Johansen, Jostein; Drabløs, Finn (Journal article; Peer reviewed, 2008)
      Background: Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have ...

    • Compo: composite motif discovery using discrete models 

      Sandve, Geir Kjetil; Abul, Osman; Drabløs, Finn (Journal article; Peer reviewed, 2008)
      Background: Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent years there ...

    • 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 ...

    • En maskinvareakselerert parallell gibbs-sampler for oppdaging av motiver 

      Eidsheim, Lars Andreas (Master thesis, 2006)
      Store mengder genomisk data er idag tilgjengelig i digital form, og utvikling av teknikker for analyse av dette materialet er et viktig forskningsfelt. Oppdaging av overrepresenterte mønster er et av målene for slik analyse. ...

    • Flexible Discovery of Modules with Distance Constraints 

      Lekang, Øystein (Master thesis, 2006)
      Many authors argue that finding single transcription factor binding sites is not enough to be able to make predictions with regard to regulation in eukaryotic genes, as is the case with simpler prokaryotes. With eukaryotes ...

    • 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 ...

    • 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 ...

    • Metoder for å akselerere MEME 

      Syrstad, Øyvind Bø (Master thesis, 2006)
      MEME er et mye brukt verktøy for å finne nye mønster i biologiske data, og bruker Expectation Maximation på PWM-er for å finne mønster som skiller seg mest mulig fra bakgrunnen. Siden Expectation Maximation er en algoritme ...

    • Motif discovery in biological sequences 

      Sandve, Geir Kjetil (Master thesis, 2005)
      This master thesis is a Ph.D. research plan for motif discovery in biological sequences, and consists of three main parts. Chapter 2 is a survey of methods for motif discovery in DNA regulatory regions, with a special ...

    • The Genomic HyperBrowser: an analysis web server for genome-scale data 

      Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo; Hovig, Johannes Eivind (Journal article; Peer reviewed, 2013)
      The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable ...

    • Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG 

      Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix; Lirussi, Lisa; Sengupta, Tanima; Tekin, Nuriye Basdag; Jobert, Laure; Alexandrov, Ludmil B.; Galashevskaya, Anastasia; Rada, Cristina; Sandve, Geir Kjetil; Rognes, Torbjørn; Krokan, Hans Einar; Nilsen, Hilde Loge (Journal article; Peer reviewed, 2017)
      Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional ...

    • Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease 

      Handel, Adam E; Sandve, Geir Kjetil; Disanto, Giulio; Berlanga-Taylor, Antonio; Gallone, Anna; Hanwell, Heather EC; Drabløs, Finn; Giovannoni, Gavin; Ebers, Georg C; Ramagopalan, Sreeram V (Journal article; Peer reviewed, 2013)
      Background Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated ...

    • Weighted Pattern Matching with PWMs on FPGAs 

      Krutådal, Lars Karsten (Master thesis, 2006)
      This paper has presented a solution to an FPGA-based PWM matcher in the form of the so-called FPWM Prototype, using the hardware facilities on the Cray XD1 Supercomputer. The prototype implementation currently runs as a ...