Bioinformatic Core Unit

General scientific objectives:

The Bioinformatic Core Unit provides support in the bioinformatics assessment of various types of RNA and DNA sequencing data sets. Specifically, the Unit has ample expertise in assessing RNA modifications and splicing, which post-transcriptionally control gene expression (Stellos et al., Nat Medicine 2016¹; John et al., Brief Bioinform. 2016²) and epigenetic mechanisms (Neumann et al, Nat Comm. 2018³). The emergence of single cell RNA sequencing as powerful tool to identify cellular subtypes and transition states requires individualized algorithms as well as adjusted secondary analysis steps. Here we develop new bioinformatic approaches to analyze scRNA-seq data in order to understand the heterogeneity and plasticity of cells in health and diseases using experimental model in combination with lineage tracing.

Dr. David John, Lukas Tombor, in collaboration with Prof. Marcel Schulz

1. Stellos K, Gatsiou A, Stamatelopoulos K, et al. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation. Nat Med. 2016;22(10):1140-1150.
2. John D, Weirick T, Dimmeler S, Uchida S. RNAEditor: easy detection of RNA editing events and the introduction of editing islands. Brief Bioinform. September 2016:bbw087.
3. Neumann P, Jaé N, Knau A, et al. The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2. Nat Commun. 2018;9(1):237.