Announcements:

• Eivind Valen named NCMM Associate Investigator

Press (mostly Norwegian):

• Nye metoder for lesing av DNA gir bedre utsikter
• Discovery of Apela/Toddler
• Rekruttering til Bergen
• Kartleggingen av menneskets promotere

Interviews (mostly Norwegian):

• Forskerforum - Her er forskernes beste tips for å holde seg faglig oppdatert
• Forskning.no - Så langt har forskere kommet med å bruke gensaksen CRISPR på mennesker
• Forskning.no - Dataprogram avdekker fusk i cellene dine
• Forskningsetikk og Teknisk Ukeblad - Frykt og håp rundt ny genteknologi

Panel debates (mostly Norwegian):

• Bergen Film Festival - Alt du vil vite om CRISPR (men ikke våger å spørre om)
• Arendalsuka - KUNSTIG INTELLIGENS I HELSESEKTOREN: NØKKELEN TIL ET LENGRE LIV, MEN…?

Video:

• Study bioinformatics at UiB (Norwegian)

I teach BINF201: Introduction to Omics

Academic article

• Eivind Valen; Kornel Labun; Tessa G. Montague et al. (2016). CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. (external link)
• Robin Andersson; Peter Refsing Andersen; Eivind Valen et al. (2014). Nuclear stability and transcriptional directionality separate functionally distinct RNA species. (external link)
• Elvis Ndah; Veronique Jonckheere; Adam Giess et al. (2017). REPARATION: ribosome profiling assisted (re-) annotation of bacterial genomes. (external link)
• Katarzyna Chyzynska; Kornel Labun; Carl Matthew Jones et al. (2021). Deep conservation of ribosome stall sites across RNA processing genes. (external link)
• Jack A.S. Tierney; Michał Sẃirski; Håkon Tjeldnes et al. (2024). Ribosome decision graphs for the representation of eukaryotic RNA translation complexity. (external link)
• Oguzhan Begik; Gregor Diensthuber; Huanle Liu et al. (2022). Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. (external link)
• Máté Pálfy; Gunnar Schulze; Eivind Valen et al. (2020). Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. (external link)
• Melanie Lianne Engelfriet; Yanwu Guo; Andreas Arnold et al. (2025). Reprograming gene expression in ‘hibernating’ C. elegans involves the IRE-1/XBP-1 pathway. (external link)
• Teshome Tilahun Bizuayehu; Kornel Labun; Martin Jakubec et al. (2022). Long-read single-molecule RNA structure sequencing using nanopore. (external link)
• Pernille Svalastoga; Åsta Nordsveen Sulen; Jarle Røneid Fehn et al. (2020). Intellectual disability in KATP channel neonatal diabetes. (external link)
• Åsmund Birkeland; Katarzyna Chyzynska; Eivind Valen (2018). Shoelaces: An interactive tool for ribosome profiling processing and visualization. (external link)
• Summer B. Thyme; Laila Akhmetova; Tessa G. Montague et al. (2016). Internal guide RNA interactions interfere with Cas9-mediated cleavage. (external link)
• Adam Giess; Yamila Nicole Torres Cleuren; Håkon Tjeldnes et al. (2020). Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. (external link)
• Kornel Labun; Tessa G. Montague; Maximilian Krause et al. (2019). CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. (external link)
• Jack A.S. Tierney; Michał I. Świrski; Håkon Tjeldnes et al. (2025). RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. (external link)
• Jamie Auxillos; Arnaud Stigliani; Christian Skov Vaagensø et al. (2025). True length of diverse capped RNA sequencing (TLDR-seq): 5′–3′-end sequencing of capped RNAs regardless of 3′-end status. (external link)
• Oguzhan Begik; Leszek P. Pryszcz; Adnan Muhammad Niazi et al. (2025). Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution. (external link)
• Deepak Poduval; Elisabet Ognedal Berge; Zuzana Sichmanovà et al. (2020). Assessment of tumor suppressor promoter methylation in healthy individuals. (external link)
• Audun Sivertsen; Nicolay Mortensen; Unni Solem et al. (2024). Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected. (external link)
• Kornel Labun; Maximilian Krause; Yamila Nicole Torres Cleuren et al. (2021). CRISPR Genome Editing Made Easy Through the CHOPCHOP Website. (external link)
• Ganna Reint; Zhuokun Li; Kornel Labun et al. (2021). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. (external link)
• Eric W Deutsch; Leron W Kok; Jonathan M Mudge et al. (2024). High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. (external link)
• Kornel Labun; Oline Eriksen Rio; Håkon Tjeldnes et al. (2025). CHOPOFF: symbolic alignments enable fast and sensitive CRISPR off-target detection. (external link)
• Katariina Aino Inkeri Mamia; Solrun Kolbeinsdottir; Kornel Labun et al. (2025). Precision T cell correction platform for Inborn Errors of Immunity. (external link)
• Gemma Barbara Danks; Heloisa Galbiati; Martina Raasholm et al. (2019). Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. (external link)
• Maximilian Krause; Adnan Muhammad Niazi; Kornel Labun et al. (2019). tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. (external link)
• Adam Giess; Veronique Jonckheere; Elvis Ndah et al. (2017). Ribosome signatures aid bacterial translation initiation site identification. (external link)
• Håkon Tjeldnes; Kornel Labun; Yamila Nicole Torres Cleuren et al. (2021). ORFik: a comprehensive R toolkit for the analysis of translation. (external link)
• Leanne H. Kelley; Ian V. Caldas; Matthew T. Sullenberger et al. (2024). Poly(U) polymerase activity in Caenorhabditis elegans regulates abundance and tailing of sRNA and mRNA. (external link)
• Florian T. Merkle; Werner M. Neuhausser; David Santos et al. (2015). Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. (external link)
• Mathys Grapotte; Manu Saraswat; Chloé Bessière et al. (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. (external link)
• Sonia Chothani; Jorge Ruiz-Orera; Jack A. S. Tierney et al. (2025). An expanded reference catalog of translated open reading frames for biomedical research. (external link)
• Preeti Kute; Francois Philippe Pauzin; Kornel Labun et al. (2025). Transcriptome-wide mapping of small ribosomal subunits elucidates scanning mechanisms of translation initiation in the mammalian brain. (external link)
• Pernille Svalastoga; Alba Kaci; Janne Molnes et al. (2023). Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes. (external link)
• Kornel Labun; Xiaoge Guo; Alejandro Chavez et al. (2019). Accurate analysis of genuine CRISPR editing events with ampliCan. (external link)

Doctoral thesis (PhD)

• Adam Giess; Eivind Valen (2019). Understanding translational landscapes through the footprints of ribosomes. (external link)

Academic literature review

• Adnan Muhammad Niazi; Maximilian Krause; Eivind Dale Valen (2021). Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA. (external link)
• Preeti Kute; Omar Soukarieh; Håkon Tjeldnes et al. (2022). Small Open Reading Frames, How to Find Them and Determine Their Function. (external link)

Master’s thesis

• Eric Holt; Nils Henrik Halberg; Eivind Valen (2024). The pancreas remembers: epigenetic memory of obesity as subtle, coordinated changes in promoter accessibility. (external link)

Conference poster

• Frida Loe Haugen; Katariina Aino Inkeri Mamia; Oline Eriksen Rio et al. (2025). CRISPR-Cas9 pipeline for custom editing in autologous T cells. (external link)
• Katariina Aino Inkeri Mamia; Janna Saija Saarela; Zhuokun Li et al. (2022). CRISPR-Cas9 T cell editing pipeline for Finnish founder diseases. (external link)
• Katariina Aino Inkeri Mamia; Solrun Kolbeinsdottir; Zhuokun Li et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)
• Frida Loe Haugen; Katariina Aino Inkeri Mamia; Oline Eriksen Rio et al. (2025). CRISPR/Cas9-based pipeline to introduce custom edits in autologous T cells. (external link)
• Katariina Aino Inkeri Mamia; Solrun Kolbeinsdottir; Zhuokun Li et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)
• Katariina Aino Inkeri Mamia; Solrun Kolbeinsdottir; Zhuokun Li et al. (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. (external link)

Lecture

• Ganna Reint; Zhuokun Li; Kornel Labun et al. (2022). Rapid genome editing by CRISPR-Cas9-POLD3 fusion.. (external link)

Journal corrigendum

• Mathys Grapotte; Manu Saraswat; Chloé Bessière et al. (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). (external link)

Editorial/Leader article

• Eivind Valen (2022). Nye CRISPR-metoder og mer presis presisjonsmedisin. (external link)

Professional article

• Michał I. Świrski; Jack A. S. Tierney; M. Mar Albà et al. (2025). Translon: a single term for translated regions. (external link)

See a complete overview of publications in Cristin.

CRISPR genome engineering

RNA Biology

Nanopore sequencing

Regulation of Translation