We refer to our lab as Computational Microbiology Laboratory and our research centers on comparative analyses of microbial (mainly prokaryotic) genomes. However, unlike standard comparative genomic studies, which compare gene contents among different genomes, our analyses focus mainly on genome properties other than protein- and RNA-coding genes. For example, different genomes often have distinct nucleotide and oligonucleotide compositions, repeat structures, and/or sequence patterns that affect structures of DNA or RNA molecules and physical organization of the chromosomes. Our goal is to understand how these genome features evolve and what physiological roles they play in the organisms. Our research relies to a large extent on statistics and computer science, and includes development of new methods, algorithms and software for sequence analysis. Our web site features a number of programs developed in our lab that we not only use in our research but also offer for use by other researchers.
Our most recent project involved analyses of simple sequence repeats (SSRs), that is, uninterrupted tandem repeats of a single nucleotide or a short oligonucleotide like AAAAAAAA… or ATCCGATCCGATCCG… Such repeats are hypervariable due to slipped-strand mutations and a common source of phase variation, including antigenic variation in pathogens. By comparative analysis among hundreds of genomes, we found that repeats of mono-, di-, tri-, and tetranucleotides occur in different types of genomes (mostly host-adapted pathogens) than repeats of pentanucleotides and longer oligonucleotides (environmental organisms and opportunistic pathogens), and probably have different functions. Further investigation revealed that the function of SSRs is not limited to phase variation, and extends to genome reduction in host adapted pathogens, influence on DNA structure, and possibly expression of adjacent genes.