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Chronic viral infections are still a major challenge for our society and our healthcare system. Based on our work in the field of hepatitis virus infections (HBV, HCV, and HEV), we will present the challenges we face in analyzing our heterogeneous ‘wet lab’ datasets (e.g. different OMICs and flow cytometry measurements) as well as with clinical dataset to gain new insights for new treatment approaches and to stratify patients for more individualized medicine.