About me
Vincent Dietrich
PhD-student
dietricv@uni-mainz.de
Current project
Nanopore sequencing measures changes in ionic current across a membrane as a polynucleotide strand translocates through a pore. The resulting raw signal traces ("squiggles") encode not only the underlying base sequence but also signatures of chemical base modifications. While current base-calling frameworks can detect selected modified nucleotides at single-base resolution, widespread detection - particularly for RNA - remains challenging due to high structural and chemical variability. My work focuses on simplifying and standardizing signal-level nanopore data analysis by developing open, accessible tools for processing, inspection, and downstream interpretation.
The pod5Viewer is a graphical interface for exploring POD5 files, enabling users to quickly inspect raw signal data and associated metadata without requiring custom scripts or command-line workflows.
Fishnet is designed to accelerate and streamline signal-to-sequence alignment ("resquiggling"), assigning signal segments to their corresponding base calls. This mapping step is a core prerequisite for robust signal-level analysis and downstream modification detection in nanopore sequencing datasets.
Publications
- Vincent Dietrich, Lioba Lehmann, Stefan Pastore, Stefan Mündnich, Lukas Walz, Mark Helm, Kristina Friedland, Susanne Gerber: Fishnet simplifies and accelerates signal-to-sequence alignment in Nanopore sequencing. Preprint (2026)
- Charlotte Hewel, Anna Wierczeiko, Johannes Miedema, Felix Hofmann, Stephan Weissbach, Vincent Dietrich, Johannes Friedrich, Laura Holthoefer, Verena Haug, Stefan Muendnich, Lukas Schartel, Kristi Jenson, Stefan Diederich, Stanislav Sys, Tamer Butto, Norbert Paul, Jonas Koch, Frank Lyko, Florian Kraft, Susann Schweiger, Edward A Lemke, Mark Helm, Matthias Linke, Susanne Gerber: Direct RNA sequencing (RNA004) allows for improved transcriptome assessment and near real-time tracking of methylation for medical applications. Nucleic Acids Research, 53(22), gkaf1314 (2025)
- Jannes Spangenberg, Stefan Mündnich, Anne Busch, Stefan Pastore, Anna Wierczeiko, Winfried Goettsch, Vincent Dietrich, Leszek Pryszcz, Sonia Cruciani, Eva Maria Novoa, Kandarp Joshi, Ranjan Perera, Salvatore Di Giorgio, Paola Arrubarrena, Irem Tellioglu, Chi-Lam Poon, Yuk Wan, Jonathan Göke, Andreas Hildebrand*, Christoph Dieterich*, Mark Helm*, Manja Marz*, Susanne Gerber* and Nicolò Alagna*: Predicting RNA modifications by nanopore sequencing: The RMaP challenge. Communications Chemistry 8, 115 (2025)
- Vincent Dietrich, Nicolò Alagna, Mark Helm, Susanne Gerber* & Tamer Butto* : Pod5Viewer: a GUI for inspecting raw nanopore sequencing data. Bioinformatics, btae665 (2024)
- Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne Busch, Vincent Dietrich, Mark Helm, Tamer Butto* and Susanne Gerber*: NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. Bioinformatics, btad492, https://doi.org/10.1093/bioinformatics/btad492 (2023).