Blar i Bergen Open Research Archive på forfatter "Torres Cleuren, Yamila Nicole"

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    • 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 ...

    • Evolution and developmental system drift in the endoderm gene regulatory network of Caenorhabditis and other nematodes 

      Ewe, Chee Kiang; Torres Cleuren, Yamila Nicole; Rothman, Joel H (Journal article; Peer reviewed, 2020)
      Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis ...

    • Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network 

      Torres Cleuren, Yamila Nicole; Ewe, Chee Kiang; Chipman, Kyle C; Mears, Emily R; Wood, Cricket G; Al-Alami, Coco Emma Alma; Alcorn, Melissa R; Turner, Thomas L; Joshi, Pradeep M; Snell, Russell G; Rothman, Joel H (Peer reviewed; Journal article, 2019-08-15)
      Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, ...

    • 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, ...

    • Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation 

      Giess, Adam; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon; Krause, Maximilian; Bizuayehu, Teshome Tilahun; Hiensch, Senna; Okon, Aniekan; Wagner, Carlston; Valen, Eivind (Journal article; Peer reviewed, 2020)
      Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly ...

    • 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 ...

    • Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR 

      Danks, Gemma Barbara; Galbiati, Heloisa; Raasholm, Martina; Torres Cleuren, Yamila Nicole; Valen, Eivind; Navratilova, Pavla; Thompson, Eric (Journal article; Peer reviewed, 2019)
      Background: In phylogenetically diverse organisms, the 5′ ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Results: We ...