Author
Johannes Gutenberg University Mainz
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
Johannes Miedema, Stefan Pastore, Luca Drescher, Alexander Haehnel, Anna Wierczeiko, Nicolò Alagna, Lioba Lehmann, Mark Helm, Tamer Butto, Susanne Gerber
DModE provides an end-to-end framework for analyzing Nanopore DRS data, enabling integrated differential expression and modification analysis with automated reporting.
bioRxiv · Jun 11, 2026 · PreprintBioinformatics
Stefan Pastore, Ludivine Wacheul, Lioba Lehmann, Stefan Mündnich, Beat Lutz, Mark Helm, Susanne Gerber, Denis L. J. Lafontaine, Tamer Butto
This study introduces NanoRibolyzer, a long-read nanopore sequencing method to map pre-rRNA processing and modification at single-nucleotide resolution, revealing cleavage sites and modification patterns.
Nature Communications · Mar 31, 2026Peer-reviewedCell Biology
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer, Marko Jörg, Julia Brechtel, Stefan Mündnich, Anna Wierczeiko, Kristina Friedland, Mark Helm, Marie‐Luise Winz, Susanne Gerber
This paper demonstrates real-time transcriptomic analysis using nanopore sequencing for quality control and differential expression in various experimental conditions.
eLife · Mar 19, 2026Peer-reviewedBioinformatics
Max Müller, Lena Sophie Tittel, Elisabeth Petfalski, Kaushik Viswanathan Iyer, Alina-Andrea Kraft, Stefan Pastore, Tamer Butto, Marie‐Luise Winz
The paper shows that New1 prevents ribosomal collisions and subsequent mRNA degradation in yeast by no-go decay, protecting essential genes from downregulation.
Nucleic Acids Research · Jan 14, 2026Peer-reviewedMolecular Biology
Nicolò Alagna, Stefan Mündnich, Johannes Miedema, Stefan Pastore, Lioba Lehmann, Anna Wierczeiko, Johannes Friedrich, Lukas Walz, Marko Jörg, Tamer Butto, Kristina Friedland, Mark Helm, Susanne Gerber
ModiDeC is a deep-learning classifier that identifies multiple RNA modifications from direct nanopore sequencing, validated on synthetic data and biological samples.
Nucleic Acids Research · Jul 19, 2025Peer-reviewedBioinformatics
Stefan Pastore, Philipp Hillenbrand, Nils Molnar, Irina Kovlyagina, Monika Chanu Chongtham, Stanislav Sys, Beat Lutz, Margaryta Tevosian, Susanne Gerber
ClearFinder provides a Python GUI for cell annotation in cleared mouse brains, improving accessibility and enabling statistical analysis and visualization.
BMC Bioinformatics · Jan 21, 2025Peer-reviewedBioinformatics
Stephan Weißbach, Jonas Milkovits, Stefan Pastore, Martin Heine, Susanne Gerber, Hristo Todorov
Cortexa provides a web-portal with standardized RNA-sequencing data and tools for analyzing gene expression and alternative splicing in the mouse brain.
BMC Bioinformatics · Sep 5, 2024Peer-reviewedGenomics
Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber
NanopoReaTA provides a user-friendly tool for real-time RNA-seq analysis of nanopore sequencing data, enabling interactive decision-making during sequencing.
Bioinformatics · Aug 1, 2023Peer-reviewedBioinformatics