IMIB - Institute for Molecular Infection Biology

Implementation and application of bioinformatical tools for the analysis of dual RNA-sequencing data of host and pathogen during infection

In dual RNA-sequencing the transcriptomes of two organisms are sequenced without previous physical separation of the two species. The allocation of the sequenced RNA-fragments only takes place in silico. This approach enables the simultaneous investigation of the transcriptomes of two interacting organisms. Usually researchers apply dual RNA-Seq to study the behavior of eukaryotic host cells and of bacterial pathogens during infection. Comparing the gene expression levels of cells in this process with cells in steady-state can yield information about pathogen genes playing an important role during the infection and a potential internalization into the host cells. Furthermore host genes taking part in the defense of the pathogen can be identified. My doctoral project comprises the bioinformatical analysis of dual RNA-seq data as well as building software for doing so. I will extend the features of READemption (Förstner et al. 2014), a pipeline for the computational evaluation of RNA-seq Data, to make it suitable for Dual RNA-seq. Additionally I will work on enhanced visualization of the data and apply machine learning to it.