Our current focus is to bridge the gap between cell biology and bioinformatics by advising the group on the utilization of high-throughput techniques such as next generation sequencing (NGS) as well as to provide bioinformatics support for various NGS-related projects in yeast and mammalian cells.
Some of our typical analyses include differential gene expression and splicing based on RNA-seq, identification of protein-RNA interactions from RIP/CLIP-seq and protein-DNA interactions found by ChIP-seq.
Besides these standard procedures, our current main project revolves around the integration of multiple NGS-based experimental procedures to assess the contribution of multiple factors on overall RNA abundance / gene expression in stress conditions. To do so, we are working on an integrative analysis of PolII ChIP-seq and RNA-seq data, which will be supplemented by data on DNA-DNA interactions obtained from HiC as well as nucleosome positioning by MNase-seq to provide a comprehensive view of the cellular transcriptional response to stress.
In addition, we are also involved in the identification of genes essential for stress adaptation by genome-wide CRISPR screenings and collaborative projects utilzing ribosome profiling.
Particular research interests:
- epigenetic regulation of gene expression
- discovery of novel context-specific RNAs
- exploration of long non-coding RNA functions