Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, GA 30602, U.S.A.
BESC BioEnergy Science Center, U.S.A.
College of Computer Science and Technology, Jilin University, Changchun 130012, China

This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage of the rapidly increasing pool of the sequenced bacterial genomes, potentially leading to a much improved understanding of why a bacterial genome is organized in the way it is. This article discusses a number of challenging computational problems in elucidating the genomic structures at multiple levels and the information that is encoded through these genomic structures, gearing towards the ultimate understanding of the governing rules of bacterial genome organization.

The work is supported in part by the NSF of USA (Grant Nos. DBI-0354771, ITR-IIS-0407204, DBI-0542119, CCF0621700), NIH of USA (Grant Nos. 1R01GM075331 and 1R01GM081682) and the grant for the BioEnergy Science Center.