Pastore, S., Wacheul, L., Lehmann, L., Mündnich, S., Lutz, B., Helm, M., Gerber, S., Lafontaine, D. L. J.*, Butto, T*. Mapping human pre‑rRNA processing and modification at single‑nucleotide resolution using long‑read Nanopore sequencing (2025). DOI: 10.1101/2025.03.01.640970. bioRxiv.
Alagna, N., Mündnich, S., Miedema, J., Pastore, S., Lehmann, L., Wierczeiko, A., Friedrich, J., Walz, L., Jörg, M., Butto, T., Friedland, K., Helm, M., Gerber, S. ModiDeC: a multi‑RNA modification classifier for direct nanopore sequencing (2025). Nucleic Acids Research, https://doi.org/10.1093/nar/gkaf673
Butto, T.* †, Pastore, S. †, Müller, M., Iyer, K. V., Jörg, M., Brechtel, J., Mündnich, S., Wierczeiko, A., Friedland, K., Helm, M., Winz, M. L., & Gerber, S*. Real‑time transcriptomic profiling in distinct experimental conditions (2025). eLife 14:e98768. doi:10.7554/eLife.98768
Vincent Dietrich, Nicolò Alagna, Mark Helm, Susanne Gerber* & Tamer Butto*: “Pod5Viewer: a GUI for inspecting raw nanopore sequencing data”. Bioinformatics, https://doi.org/10.1093/bioinformatics/btae665
Müller, M., Tittel, L. S., Petfalski, E., Iyer, K. V., Pastore, S., Butto, T., Winz, M. L. Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no‑go decay (2024). bioRxiv, November 26, 2024. DOI: 10.1101/2024.11.26.625534. bioRxiv.
Hewel, C., Wierczeiko, A., Miedema, J., Hofmann, F., Weißbach, S., Dietrich, V., Friedrich, J., Holthöfer, L., Haug, V., Mündnich, S., Schartel, L., Lehmann, L., Jenson, K., Diederich, S., Sys, S., Butto, T., Paul, N. W., Koch, J., Lyko, F., Kraft, F., Schweiger, S., Lemke, E. A., Helm, M., Linke, M., Gerber, S. Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications (2024). bioRxiv.
Lukas Schartel, Cosimo Jann, Anna Wierczeiko, Tamer Butto, Stefan Mündnich, Virginie Marchand, Yuri Motorin, Mark Helm, Susanne Gerber and Edward A. Lemke. “Selective RNA pseudouridinylation in situ by circular gRNAs in designer organelles”. (2024). Nature communications.
https://doi.org/10.1038/s41467-024-53403-1
Tamer Butto†, Monika Chanu Chongtham†, Kanak Mungikar†, Dewi Hartwich, Matthias Linke, Nicolas Ruffini, Konstantin Radyushkin, Susann Schweiger, Jennifer Winter*, Susanne Gerber*. "Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice". (2024) Molecular Psychiatry. https://doi.org/10.1038/s41380-024-02555-z
Tamer Butto*, Kanak Mungikar, Peter Baumann, Jennifer Winter, Beat Lutz, and Susanne Gerber*. "Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing". (2023) Cells 12, no. 7: 1051. https://doi.org/10.3390/cells12071051
Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Mark Helm, Tamer Butto*, Susanne Gerber*. “NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis” (2022). Bioinformatics. https://doi.org/10.1101/2022.12.13.520220
Tamer Butto. “Epigenetics in Health and Disease: Focus on epigenetic mechanisms as systems of change and adaptability” (2021). Gutenberg Open Science. http://doi.org/10.25358/openscience-6473
Martin Schüle, Tamer Butto, Sri Dewi, Laura Schlichtholz, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter. “mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex” (2021). International Journal of Molecular Sciences. https://doi.org/10.3390/ijms22116034
Monika Chanu Chongtham†, Tamer Butto†, Kanak Mungikar†, Susanne Gerber* and Jennifer Winter*. "INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison" (2021). International Journal of Molecular Sciences. https://doi.org/10.3390/ijms22105335
Alexis Cooper, Tamer Butto, Niklas Hammer, Somanath Jagannath, Junaid Akhtar, Konstantin Radyushkin, Florian Lesage, Jochen Roeper*, Ulrich Zechner*, Susann Schweiger*. "Inhibition of histone deacetylation rescues Birk-Barel intellectual disability dysmorphism syndrome in mice” (2020). Nature communication. https://doi.org/10.1038/s41467-019-13918-4
† Authors contributed equally
* co-corresponding authros