Publications
From Paulsen Laboratory
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Ian Paulsen currently has more than 170 publications in the fields of microbial genomics, bioinformatics, membrane transport and multidrug export. He is an ISI Highly Cited Researcher, with a current H index of 70, and more than 20,000 total citations. In the last ten years, he has published 32 Highly Cited papers, and 82 papers that rank within the top 10% of cited papers in their respective fields. Approximately half of these 82 papers are genome sequence papers, the remainder are focused on functional genomic, molecular biology or bioinformatic analyses.
Current publications
Check out our current publications through pubmed
Selected Publications
- Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LD, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A. (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnology; Epub ahead of print.
- Hassan KA, Brzoska AJ, Wilson NL, Eijkelkamp BA, Brown MH, Paulsen IT. Roles of DHA2 family transporters in drug resistance and iron homeostasis in Acinetobacter spp. (2011) J Mol Microbiol Biotechnol. 2011 20(2):116-24
- Roy PH, Tetu SG, Larouche A, Elbourne L, Tremblay S, Ren Q, Dodson R, Harkins D, Shay R, Watkins K, Mahamoud Y, Paulsen IT (2010). Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7. PLoS One. 22;5(1):e8842.
- Thomas EV, Phillippy KH, Brahamsha B, Haaland DM, Timlin JA, Elbourne LD, Palenik B, Paulsen IT.(2009) Statistical analysis of microarray data with replicated spots: a case study with synechococcus WH8102. Comp Funct Genomics. 2009:950171
- 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.
- 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.
- 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.
- 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
- Ren, Q., Kang, K., and Paulsen, I. T. TransportDB: a relational database of cellular membrane transport systems (2004) Nucleic Acids Research 32: 284-288.
- 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.
- 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.
- Paulsen, I. T. (2003) Multidrug efflux pumps and resistance: regulation and evolution. Current Opinion in Microbiology 6: 446-451.
Press Releases and News Articles
- Genomic technology provides footrot breakthrough
- Surf's Up-And One Coastal Microbe Has Adapted
- Cell Scenario: A New Look at Microarrays
- Genome Study of Beneficial Microbe May Help Boost Plant Health
- A New Spin on Spirochetes
- Scientists Finish Sequencing Genome of Oral Pathogen
- Thomson Scientific Names "Hottest" Researchers 2004
- The Hottest Research of 2003-2004
- Aliens Inside Us: A (Mostly Friendly) Nation
- Genome Analysis Sheds Light on Mobile DNA's Role in Pathogen's Resistance to Vancomycin
- Deciphering the "Bugs" in Human Intestines
- Microbial Multidrug Efflux
- Genome of Potential Bioterror Agent Sequenced; Highlights Similarities Between Animal, Plant Pathogens
- U.S. - German Research Consortium Sequences Genome of Versatile Soil Microbe
- Biolog Phenotype Microarrays
- The Genome of Agrobacterium tumefaciens A plant pathogen with a talent for transferring genes
Web Sites
- TransportDB: A database of genomic analysis of transporters in all sequenced genomes which my group developed and maintains.
- EcoCyc: A comprehensive database of E. coli genes and biology, on which I have been a long term collaborator with Peter Karp at SRI International.
- Microbial Lifestyles: The Paulsen Lab Blog
