We use Oxford Nanopore Long-read sequencing to study RNA regulation.
We do not only apply multiple Nanopore sequencing approaches (for example Native RNA sequencing and custom cDNA approaches), but also develop novel bioinformatics tools to study the impact of specific features of RNA on translational regulation. We have recently published a tool to measure poly(A) tail lengths of the whole transcriptome and aim to apply this approach in early zebrafish development.
- 2020. Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. Cell reports.
- 2019. tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. RNA: A publication of the RNA Society. 1229-1241.
- 2019. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Research. W171-W174.
M Krause, AM Niazi, K Labun, FS Mueller, YN Torres Cleuren, E Valen
„tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing“
07/2019, RNA, doi: 10.1261/rna.071332.119
K Labun, T Montague, M Krause, YN Torres Cleuren, H Tjeldnes, E Valen
„CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing“
02/2019, NAR, doi: 10.1093/nar/gkz365
A Giess, YN Torres Cleuren, H Tjeldnes, M Krause, TT Bizuayehu, S Hiensch, E Valen
„Deconstructing the individual steps of vertebrate translation initiation“
08/2019, bioRxiv, doi: 10.1101/811810