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Defense transcriptional responses of mammalian cells are vital for the maintenance of organisms’ homeostasis and substantially rely on stimulus-specific inducible gene expression programs. We address these phenomena on basic-research and disease-oriented model-systems, with emphasis on Viral-infections-related autoimmune human diseases. Currently, the scientific mission of the laboratory is centered on elucidating the role of the (epi)genome architecture in the establishment of the virus-stimulated gene expression programs in mammalian cells. This is achieved by the application of cutting-edge functional genomics technologies, DNA evolution investigations, and computational biology tools.  We utilize an advanced rationale composed of gene expression investigations (RNA-seq), chromatin states accessibility and epigenomics profiling (DNaseI-seq & ChIP-seq), and in vivo massive in parallel functional validation (ChIP-STARR-seq & synthetic STARR-seq). These are coupled with computational methodologies (Galaxy platform, Python scripts, R studio), ideal for conducting conservational comparisons (phylogenomics footprinting) and alignment to GWAS studies (SNPs centered), and to generate topographic maps and genomics databases of the findings. The accomplishment of our aims is anticipated to benefit both basic and applied biomedical research.