Whole-genome shotgun sequencing of bacterial genomes have enabled large-scale comparative genomics studies to learn more about phylogeography, pathogenicity, host specificity, antibiotics resistance, and several other aspects of bacterial biology. We are studying a number of different bacterial species in terms of these different aspects, with the focus on Helicobacter pylori, but also Enterotoxigenic E. coli, Clostridium sp, Shewanella algae and other bacteria. In these projects we are working with 1000s of bacterial genomes, many sequenced in house, and are performing both basic bioinformatics such as de novo assembly and annotation and different kinds of large-scale comparative genomic methods such as GWAS, epistasis analyses and different kinds of functional genomics approaches.