Our main interest is in developing mathematical & computational methods that allow studying the (epi-)transcriptome and particularly its role in viral infection.
Since the ENCODE project, it is well established that the majority of RNAs within human cells is non-coding, but at the same time under strong selective pressure. Since then, research into the diverse roles of non-coding RNA (ncRNA) in various biological processes has intensified, since a better understanding of ncRNA not only aids our fundamental understanding of biological principles, but because it may also be important for drug development, i.e. to target disease processes.
Together with experimental partners, we develop methods that allow studying the structure & function of RNA. We make heavy use of novel sequencing methods, such as illumina- or ONT-based next-generation sequencing, which we merely use as powerful read-outs when designing experiments that provide us with information on RNA structure & function. We hereby focus on mutational interference mapping experiments (MIME), as well as chemical probing using ONT-based sequencing. Our role in these collaborative efforts includes data analytics, as well as the development of mathematical and computational tools to extract biophysical information from the complex assay read-outs.
R.P. Smyth et al. Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function, Nature Methods, 12 (2015), 866
Ye L, et al. Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging. Nat Struct Mol Biol. 2022;29(4):306-319
Liu-Wei W, et al. Sequencing accuracy and systematic errors of nanopore direct RNA sequencing, 2023. preprint
This work is supported by funding from the EU and the BMBF.