Browsing Bergen Open Research Archive by Author "Valen, Eivind Dale"

Now showing items 1-6 of 6

    • CRISPR Genome Editing Made Easy Through the CHOPCHOP Website 

      Labun, Kornel; Krause, Maximilian; Torres Cleuren, Yamila Nicole; Valen, Eivind Dale (Journal article; Peer reviewed, 2021)
      The design of optimal guide RNA (gRNA) sequences for CRISPR systems is challenged by the need to achieve highly efficient editing at the desired location (on-target editing) with minimal editing at unintended locations ...

    • Deep conservation of ribosome stall sites across RNA processing genes 

      Chyzynska, Katarzyna; Labun, Kornel; Jones, Carl Matthew; Grellscheid, Sushma Nagaraja; Valen, Eivind Dale (Journal article; Peer reviewed, 2021)
      The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be ...

    • Long-read single-molecule RNA structure sequencing using nanopore 

      Tilahun Bizuayehu, Teshome; Labun, Kornel; Jakubec, Martin; Jefimov, Kirill; Niazi, Adnan Muhammad; Valen, Eivind Dale (Journal article; Peer reviewed, 2022)
      RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped ...

    • ORFik: a comprehensive R toolkit for the analysis of translation 

      Tjeldnes, Håkon; Labun, Kornel; Torres Cleuren, Yamila Nicole; Chyzynska, Katarzyna; Swirski, Michal; Valen, Eivind Dale (Journal article; Peer reviewed, 2021)
      Background With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, ...

    • Rapid genome editing by CRISPR-Cas9-POLD3 fusion 

      Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri; Mamia, Katariina Aino Inkeri; Tolo, Eero; Szymanska, Monika; Meza-Zepeda, Leonardo A.; Lorenz, Susanne; Cieslar-Pobuda, Artur Grzegorz; Hu, Xian; Bodin, Diana L; Staerk, Judith; Valen, Eivind Dale; Schmierer, Bernhard; Varjosalo, Markku; Taipale, Jussi; Haapaniemi, Emma Maria (Journal article; Peer reviewed, 2021)
      Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the ...

    • Small Open Reading Frames, How to Find Them and Determine Their Function 

      Kute, Preeti; Soukarieh, Omar; Tjeldnes, Håkon; Trégouët, David-Alexandre; Valen, Eivind Dale (Journal article; Peer reviewed, 2022)
      Advances in genomics and molecular biology have revealed an abundance of small open reading frames (sORFs) across all types of transcripts. While these sORFs are often assumed to be non-functional, many have been implicated ...