PhD project of Nina Hofmann: Integrative and comparative analysis of virus-host interactions

Virus infections remain a major threat to human health. Virus-host interactions are often not fully understood resulting in a lack of available treatment and vaccination in many cases. RNA viruses are of particular interest, because their replication machinery introduces a high number of nucleotide substitutions. This leads to high variability among the virus genomes which is an essential factor to adapt to changing environmental conditions or to new hosts.
In my thesis I analyze high-throughput RNA-Seq data taken from human pathogenic RNA viruses from different families covering the respiratory viruses human CoV-229E, MERS-CoV, a highly pathogenic H5N1 IV, a seasonal H1N1 IV and RSV, the hemorrhagic fever causing viruses Ebola virus (EBOV), Marburg virus (MARV), Lassa virus (LASV) and Rift Valley fever virus (RVFV), as well as Nipah virus (NIV), Sandfly fever Sicilian virus (SFSV), and hepatitis C virus (HCV). For this purpose, I am developing a bioinformatics pipeline that is adjusted to evaluate transcriptome changes of virus-host interactions after infection with RNA viruses over time. The RNA-Seq pipeline provides an automated workflow for the joint evaluation of host transcriptome and viral genome data.