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Comparative Microbial Genomics

Guest member: Shinny Leekitcharoenphon

Catalog of previous student projects.

Link to publications from the Comparative Microbial Genomics group

Today, hundreds of bacterial genome sequences are available in the public databases and several more genomes are being sequenced every month. Many of these genomes are known to be human pathogens. The sequence data represent a vast amount of information and comparison and analysis is important for a deeper understanding of virulence factors and if/how new organisms constitute a potential food safety problem. Comparison of completely sequenced bacterial genomes is a challenging task which can require sophisticated bioinformatics techniques.

The Comparative Microbial Genomics Group at CBS uses a combination of computational predictions and experiments to explore the relationships between the hundreds of sequenced bacterial genomes. The approach is "DNA-centric" in that the DNA sequence is used to predict DNA structures which can in turn be indicators of useful biology (for example, localization of a promoter based on DNA curvature and melting profiles). Currently, the four major focus areas of the group are:
  • prediction of transcripts, including promoters, operons (containing genes coding for proteins, rRNAs, tRNAs or other ncRNAs), and terminators
  • prediction of highly expressed genes (based on chromatin properties of the genomic DNA sequence, as well as CAI (codon adaption index) values for genes encoding proteins)
  • developing models of gene interaction networks involved in bacterial pathogenesis
  • developing novel methods for comparison of bacterial genomes
The analysis of a single genome can contain much information, and coupled with experimental data, such as transcriptomic, proteomic, and metabolomic results, the information for even one organism can be overwhelming. To handle and maintain this large amount of data for hundreds of organisms sequenced requires a structured database system. For this purpose, the GenomeAtlas database ( has been developed including a web interface for presenting much of this information from a genomic perspective. The GenomeAtlas database also includes visualisation methods for viewing and comparison of genomic properties for all the sequenced microbial genomes.

The group also designs high-density microarrays for bacterial genomes, and perform laboratory experiments to test the predictions, as well as generate new data for models and making new predictions, in an iterative manner. The microarrays are designed to test predictions of transcriptional start sites, non-coding RNA and conserved and unique coding regions within a bacterial species.

Online services
CBS Genome Atlas Database   -   a method used to visualize structural features within large regions of DNA. It was originally designed for analysis of complete genomes, but can also be used quite readily for analysis of regions of DNA as small as a few thousand bp in length. The basic idea is to plot the values for six different mechanical-structural properties of the DNA helix in a circle (or arc) representing the complete genome (or chromosome).
Read more about the Genome Atlas.

Read more about the Comparative Microbial Genomics Group

Selected Publications:
  • Structual features of fungal genomes, Wanchanthuek P, Hallin PF, Gouveia- Oliveira R, Ussery DW, Topics in Current Genetics 15:47-77, 2006.
  • Ten years of bacterial genome sequencing: comparative-genomics-based discoveries, Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW, Functional and Integrative Genomics 6, 2006.
    PMID: 16628440
  • The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis, Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, Tummler B, Hum Genet 119(3):331-43, 2006.
    PMID: 16463024
  • Extracytoplasmic function sigma factors in Pseudomona syringae, Oguiza JA, Kiil K, Ussery DW, Trends Microbiology 13(12):565-8, 2005.
    PMID: 16257528
  • Crystal ball. Systems biology: in the broadest sense of the word, Ussery DW, de Lichtenberg U, Jensen LJ, Environmental Microbiology, 7, 482-83, 2005.
    PMID: 15816924
  • CBS Genome Atlas Database: A dynamic storage for bioinformatic results and sequence data, PF Hallin and DW Ussery, Bioinformatics 12, 3682-6, 2004.
    PMID: 15256401
  • Chromatin architecture and gene expression in Escherichia coli, H Willenbrock, DW Ussery, Genome Biology, 5, 252, 2004.
    PMID: 15575978
  • The genome sequence of Schizosaccharomyces pombe, V. Wood, R. Gwilliam, M-A. Rajandream, M. Lyne, R. Lyne, A. Stewart, J. Sgouros, N. Peat, J Hayles, S. Baker, D. Basham, S. Bowman, K. Brooks, D. Brown, S. Brown, T. Chillingworth, C. Churcher, M. Collins, R. Connor, A. Cronin, P. Davis, T. Feltwell, A. Fraser, S. Gentles, A. Goble, N. Hamlin, D. Harris, J. Hidalgo, G. Hodgson, S. Holroyd, T. Hornsby, S. Howarth, E. J. Huckle, S. Hunt, K. Jagels, K. James, L. Jones, M. Jones, S. Leather, S. McDonald, J. McLean, S. Moule, K. Mungall, L. Murphy, D. Niblett, C. Odell, K. Oliver, S. O'Neil, D. Pearson, M. A. Quail, E. Rabbinowitsch, K. Rutherford, S. Rutter, D. Saunders, K. Seeger, S. Sharp, J. Skelton, M. Simmonds, R. Squares, S. Squares, K. Stevens, K. Taylor, R. G. Taylor, S. Walsh, T. Warren, S. Whitehead, J. Woodward, G. Volckaert?, R. Aert?, J. Robben, B. Grymonprez, I. Weltjens?, E. Vanstreels, M. Rieger, M. Sch?fer, S. Muller-Auer, C. Gabel, M. Fuchs, C. Fritzc, E. Holzer, D. Moestl, H. Hilbert, K. Borzym, I. Langer, A. Beck, H. Lehrach, R. Reinhardt, T. M. Pohl, P. Eger, W. Zimmermann, H. Wedler, R. Wambutt, B. Purnelle, A. Goffeau, E. Cadieu, S. Dr?ano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, S. J. Aves, Z. Xiang, C. Hunt, K. Moore, S. M. Hurst, M. Lucas, M. Rochet, C. Gaillardin, V. A. Tallada, A. Garzon, G. Thode, R. R. Daga, L. Cruzado, J. Jimenez, M. Sanchez, F. del Rey, A. Dominguez, J. L. Revuelta, S. Moreno, J. Armstrong, S. Forsburg?,L. Cerrutti, T. Lowe, W. R. McCombie, I. Paulsen, J. Potashkin, G.V. Shpakovski, D. Ussery, B. G. Barrell and P. Nurse, Nature, 415, 871-880, 2002.
    PMID: 11859360
Full list of CBS publications