• 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 ...
    • Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation 

      Pálfy, Máté; Schulze, Gunnar; Valen, Eivind; Vastenhouw, Nadine L. (Journal article; Peer reviewed, 2020-01)
      In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its ...
    • Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus 

      Merkle, Florian T.; Neuhausser, Werner M.; Santos, David; Valen, Eivind; Gagnon, James A.; Maas, Kristi; Sandoe, Jackson; Schier, Alexander F.; Eggan, Kevin (Peer reviewed; Journal article, 2015-05)
      The CRISPR-Cas9 system has the potential to revolutionize genome editing in human pluripotent stem cells (hPSCs), but its advantages and pitfalls are still poorly understood. We systematically tested the ability of CRISPR-Cas9 ...
    • Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing 

      Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra; Niazi, Adnan Muhammad; Valen, Eivind; Giraldez, Antonio J.; Beaudoin, Jean-Denis; Mattick, John S.; Novoa, Eva Maria (Journal article; Peer reviewed, 2022)
      RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop ...
    • 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 ...
    • Shoelaces: An interactive tool for ribosome profiling processing and visualization 

      Birkeland, Åsmund; Chyzynska, Katarzyna; Valen, Eivind (Peer reviewed; Journal article, 2018-07-18)
      Background: The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this ...
    • 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 ...