• CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering 

      Valen, Eivind; Labun, Kornel; Montague, Tessa G.; Gagnon, James A.; Thyme, Summer B. (Journal article; Peer reviewed, 2016)
      In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for ...
    • 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 ...
    • 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 ...