About me
Johannes Miedema
PhD Student
jmiedema@students.uni-mainz.de
Biomedizinisches Forschungszentrum
Duesbergweg 6, 55128 Mainz
5th floor
Room: 05.217
Current project
My current research focuses on characterizing RNA modifications in the human epitranscriptome using Nanopore direct RNA sequencing. By profiling peripheral blood mononuclear cells (PBMCs) from a large human cohort, we aim to establish a comprehensive healthy reference epitranscriptome. A key objective of this work is to identify and characterize age- and sex-specific RNA modification patterns, which may provide insights into biological processes underlying aging and sex-dependent differences in health and disease. To facilitate this research, we develop and implement bioinformatics software tools and pipelines that ensure reproducible and robust data analysis workflows in this field.
Publications
- Johannes Miedema, Beat Lutz, Susanne Gerber, Irina Kovlyagina and Hristo Todorov: Balancing ethics and statistics: Machine learning facilitates highly accurate classification of mice according to their trait anxiety with reduced sample sizes. Translational Psychiatry. 15 (304) (2025)
- 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: a multi-RNA modification classifier for direct nanopore sequencing. Nucleic Acids Research Volume 53, Issue 14, gkaf673, (2025)
- 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)