Browsing Department of Informatics by Author "Labun, Kornel"

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    • Accurate analysis of genuine CRISPR editing events with ampliCan 

      Labun, Kornel; Guo, Xiaoge; Chavez, Alejandro; Church, George M.; Gagnon, James A.; Valen, Eivind (Peer reviewed; Journal article, 2019)
      We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental ...

    • 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 ...

    • CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing 

      Labun, Kornel; Montague, Tessa G.; Krause, Maximilian; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon; Valen, Eivind (Peer reviewed; Journal article, 2019-07-02)
      The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been ...

    • 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 ...

    • In silico design and analysis of targeted genome editing with CRISPR 

      Labun, Kornel (Doctoral thesis, 2020-01-27)
      CRISPR/Cas systems have become a tool of choice for targeted genome engineering in recent years. Scientists around the world want to accelerate their research with the use of CRISPR/Cas systems, but are being slowed down ...

    • 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 ...

    • TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing 

      Krause, Maximilian; Niazi, Adnan Muhammad; Labun, Kornel; Torres Cleuren, Yamila Nicole; Müller, Florian S; Valen, Eivind (Peer reviewed; Journal article, 2019-07-02)
      Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide ...