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Department of Chemistry & Biomolecular Sciences

Profile for Prof. Ian Paulsen

Research Interests

My research interests have focused on understanding microbial physiology and evolution, in particular in utilizing "big picture" or global approaches such as genome sequencing, bioinformatics, microarray analysis, and high throughput cloning, gene knockout, and phenotypic screening. My research interests have been focused in three broad areas:

  • Genome diversity, metagenomics and lateral gene transfer
  • System biology analysis of membrane transport and metabolism
  • Applying Genomics to Medicine


Selected Publications

  1. Myers, G. S, Parker, D., Al-Hasani, K., Kennan, R. M., Seemann, T., Ren, Q., Badger, J. H., Selengut, J. D., Deboy, R. T., Tettelin, H., Boyce, J. D., McCarl, V. P., Han, X., Nelson, W. C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Khouri, H., Bottomley, S. P., Whittington, R. J., Adler, B., Songer, J. G., Rood, J. I, and Paulsen, I. T. (2007) Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature Biotechnology 25:569-575.
  2. Ren, Q., Chen, K., and Paulsen, I. T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research 35: D274-279.
  3. Palenik, B., Ren, Q., Dupont, C. L., Myers, G. S., Heidelberg, J. F., Badger, J. H., Madupu, R., Nelson, W. C., Brinkac, L. M., Dodson, R. J., Durkin, A. S., Daugherty, S. C., Sullivan, S. A., Khouri, H., Mahamoud, Y., Halpin, R., and Paulsen, I. T. (2006) Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences, USA 103: 13555-13559.
  4. Myers, G. S. A, Rasko, D. A., Cheung, J., Ravel, J., Seshadri, R., DeBoy, R., Varga, J., Awad, M., Brinkac, L., Daugherty, S., Dodson, B., Madupu, R., Nelson, W., Rosovitz, M. J., Sullivan, S., Khouri, H., Dimitrov, G., Watkins, K., Mulligan, S., Benton, J., Fisher, D. J., Atkins, H. S., Hiscox, T., Jost, H., Billington, S., Songer, J. G., McClane, B. A., Titball, R. W., Rood, J. I., Melville, S., and Paulsen, I. T. (2006) Skewed distribution of genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Research 16: 1031-1040.
  5. Ding, X. Z., Paulsen, I. T., Bhattacharjee, A., Nikolich, M. P., Myers, G. and Hoover, D. L. (2006) A high efficiency cloning and expression system for proteomic analysis. Proteomics 6: 4038-4044.
  6. Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., Peralta-Gil, M., and Karp, P. D. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33: D334-337.
  7. Paulsen, I. T., Press, C., Ravel, J., Kobayashi, D.Y., Myers, G.S.A., Mavrodi, D.V., DeBoy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., III, Thomashow, L.S., and Loper, J.E. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5: insights into the biological control of plant disease. Nature Biotechnology 23: 873-878.
  8. Ren, Q. and Paulsen, I. T. (2005) Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. PLOS Computational Biology 1: 190-201
  9. Ren, Q., Kang, K., and Paulsen, I. T. TransportDB: a relational database of cellular membrane transport systems (2004) Nucleic Acids Research 32: 284-288.
  10. Seshadri, R., Myers, G. S., Tettelin. H., Eisen, J. A., Heidelberg, J. F., Dodson, R. J., Davidsen, T. M., DeBoy, R. T., Fouts, D. E., Haft, D. H., Selengut, J., Ren, Q., Brinkac, L. M., Madupu, R., Kolonay, J., Durkin, S. A., Daugherty, S. C., Shetty, J., Shvartsbeyn, A., Gebregeorgis, E., Geer, K., Tsegaye, G., Malek, J., Ayodeji, B., Shatsman, S., McLeod, M. P., Smajs, D., Howell, J. K., Pal, S., Amin, A., Vashisth, P., McNeill, T. Z., Xiang, Q., Sodergren, E., Baca, E., Weinstock, G. M., Norris, S. J., Fraser, C. M., and Paulsen, I. T. (2004) Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences, USA 101: 5646-5651.
  11. Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. H., and Smith, H. O. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
  12. Paulsen, I. T., Banerjei, L., Myers, G. S., Nelson, K. E., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., Tettelin, H., Dodson, R. J., Umayam, L., Brinkac, L., Beanan, M., Daugherty, S., DeBoy, R. T., Durkin, S., Kolonay, J., Madupu, R., Nelson, W., Vamathevan, J., Tran, B., Upton, J., Hansen, T., Shetty, J., Khouri, H., Utterback, T., Radune, D., Ketchum, K. A., Dougherty, B. A., and Fraser, C. M. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. (2003) Science 299: 2071-2074.
  13. Paulsen, I. T. (2003) Multidrug efflux pumps and resistance: regulation and evolution. Current Opinion in Microbiology 6: 446-451.


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Monash University
Monash University