Comparative and evolutionary genomics; methods for identification of orthologous and paralogous genes. Physical models of genome evolution. Evolutionary Systems Biology genomics, relationships between the evolution of the genome and of molecular phenotype. neutral and selective processes in the genomic and phenomic evolution. Evolution of viruses and antivirus defense systems, in particular the CRISPR-Cas system of adaptive immunity in bacteria and archaea. Mathematical models of virus-host coevolution. Origin of eukaryotic cells and their molecular innovations. Origin of first cells, replication, translation and the genetic code.