About

William Cheesman Nelson

Assistant Professor (research) of Biological Sciences

Contact Information
E-mail: wcnelson@usc.edu
Phone: (310) 510-4097
Office: AHF 403

LINKS
Curriculum Vitae
 

Education
B.A. Biology, Bucknell University, 6/1990
B.A. Chemistry, Bucknell University, 6/1990
Ph.D. Biology, University of North Carolina at Chapel Hill, 5/1996
 

Postdoctoral Training
IRTA Fellow, NIH/NIAID/LVD, 06/1996-09/1998  
 

Academic Appointment, Affiliation, and Employment History

Non-Tenure Track Appointments
Research Assistant Professor, University of Southern California, 05/2007-  
 

Other Employment
Bioinformatics Analyst Manager, The Institute for Genomic Research, 08/2004-04/2007  
Bioinformatics Analyst, The Institute for Genomic Research, 10/1998-07/2004  
 

Description of Research

Summary Statement of Research Interests
I am intersted in studying molecular evolution, ecology, and community structure of microbes using genomic and metagenomic techniques. Modern sequencing technologies allow us to explore microbial communities in great detail, discovering which organisms are present in the environment and how they survive. Comparative genomics can be used to study evolution of species, allowing us to examine how life responds to our ever-changing environment.
 

Research Keywords
bioinformatics genomics metagenomics transcriptomics
 

Research Specialties
Whole genome analysis (prokaryotes) Metagenomic analysis
 

Affiliations with Research Centers, Labs, and Other Institutions
Wrigley Institute for Environmental Studies
 

Publications

Journal Article
Heidelberg, J. F., Nelson, W. C., Schoenfeld, T., Bhaya, D. (2009). Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE. Vol. 4 (12009/01/10), pp. e4169.
Morrison, M., Daugherty, S. C., Nelson, W. C., Davidsen, T., Nelson, K. E. (2009). The FibRumBa Database: A Resource for Biologists with Interests in Gastrointestinal Microbial Ecology, Plant Biomass Degradation, and Anaerobic Microbiology. Microb Ecol. (2009/07/18)
Tsolis, R. M., Seshadri, R., Santos, R. L., Sangari, F. J., Lobo, J. M., de Jong, M. F., Ren, Q., Myers, G., Brinkac, L. M., Nelson, W. C., Deboy, R. T., Angiuoli, S., Khouri, H., Dimitrov, G., Robinson, J. R., Mulligan, S., Walker, R. L., Elzer, P. E., Hassan, K. A., Paulsen, I. T. (2009). Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism. PLoS ONE. Vol. 4 (52009/05/14), pp. e5519.
Ward, N. L., Challacombe, J. F., Janssen, P. H., Henrissat, B., Coutinho, P. M., Wu, M., Xie, G., Haft, D. H., Sait, M., Badger, J., Barabote, R. D., Bradley, B., Brettin, T. S., Brinkac, L. M., Bruce, D., Creasy, T., Daugherty, S. C., Davidsen, T. M., DeBoy, R. T., Detter, J. C., Dodson, R. J., Durkin, A. S., Ganapathy, A., Gwinn-Giglio, M., Han, C. S., Khouri, H., Kiss, H., Kothari, S. P., Madupu, R., Nelson, K. E., Nelson, W. C., Paulsen, I., Penn, K., Ren, Q., Rosovitz, M. J., Selengut, J. D., Shrivastava, S., Sullivan, S. A., Tapia, R., Thompson, L. S., Watkins, K. L., Yang, Q., Yu, C., Zafar, N., Zhou, L., Kuske, C. R. (2009). Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol. Vol. 75 (72009/02/10), pp. 2046-56.
Qi, M., Nelson, K. E., Daugherty, S. C., Nelson, W. C., Hance, I. R., Morrison, M., Forsberg, C. W. (2008). Genomic differences between Fibrobacter succinogenes S85 and Fibrobacter intestinalis DR7, identified by suppression subtractive hybridization. Appl Environ Microbiol. Vol. 74 (42007/12/25), pp. 987-93.
Bryant, D. A., Costas, A. M., Maresca, J. A., Chew, A. G., Klatt, C. G., Bateson, M. M., Tallon, L. J., Hostetler, J., Nelson, W. C., Heidelberg, J. F., Ward, D. M. (2007). Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science. Vol. 317 (58372007/07/28), pp. 523-6.
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., Paulsen, I. T. (2007). Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nat Biotechnol. Vol. 25 (52007/05/01), pp. 569-75.
Selengut, J. D., Haft, D. H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M., Nelson, W. C., Richter, A. R., White, O. (2007). TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. Vol. 35 (Database issue2006/12/08), pp. D260-4.
Hotopp, J. C., Lin, M., Madupu, R., Crabtree, J., Angiuoli, S. V., Eisen, J., Seshadri, R., Ren, Q., Wu, M., Utterback, T. R., Smith, S., Lewis, M., Khouri, H., Zhang, C., Niu, H., Lin, Q., Ohashi, N., Zhi, N., Nelson, W. C., Brinkac, L. M., Dodson, R. J., Rosovitz, M. J., Sundaram, J., Daugherty, S. C., Davidsen, T., Durkin, A. S., Gwinn, M., Haft, D. H., Selengut, J. D., Sullivan, S. A., Zafar, N., Zhou, L., Benahmed, F., Forberger, H., Halpin, R., Mulligan, S., Robinson, J., White, O., Rikihisa, Y., Tettelin, H. (2006). Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. Vol. 2 (22006/02/17), pp. e21.
Myers, G. S., Rasko, D. A., Cheung, J. K., Ravel, J., Seshadri, R., DeBoy, R. T., Ren, Q., Varga, J., Awad, M. M., Brinkac, L. M., Daugherty, S. C., Haft, D. H., Dodson, R. J., Madupu, R., Nelson, W. C., Rosovitz, M. J., Sullivan, S. A., Khouri, H., Dimitrov, G. I., Watkins, K. L., Mulligan, S., Benton, J., Radune, D., Fisher, D. J., Atkins, H. S., Hiscox, T., Jost, B. H., Billington, S. J., Songer, J. G., McClane, B. A., Titball, R. W., Rood, J. I., Melville, S. B., Paulsen, I. T. (2006). Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res. Vol. 16 (82006/07/11), pp. 1031-40.
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., Mohamoud, Y., Halpin, R., Paulsen, I. T. (2006). Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A. Vol. 103 (362006/08/30), pp. 13555-9.
Pukatzki, S., Ma, A. T., Sturtevant, D., Krastins, B., Sarracino, D., Nelson, W. C., Heidelberg, J. F., Mekalanos, J. J. (2006). Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci U S A. Vol. 103 (52006/01/25), pp. 1528-33.
Joardar, V., Lindeberg, M., Jackson, R. W., Selengut, J., Dodson, R., Brinkac, L. M., Daugherty, S. C., Deboy, R., Durkin, A. S., Giglio, M. G., Madupu, R., Nelson, W. C., Rosovitz, M. J., Sullivan, S., Crabtree, J., Creasy, T., Davidsen, T., Haft, D. H., Zafar, N., Zhou, L., Halpin, R., Holley, T., Khouri, H., Feldblyum, T., White, O., Fraser, C. M., Chatterjee, A. K., Cartinhour, S., Schneider, D. J., Mansfield, J., Collmer, A., Buell, C. R. (2005). Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol. Vol. 187 (182005/09/15), pp. 6488-98.
Methe, B. A., Nelson, K. E., Deming, J. W., Momen, B., Melamud, E., Zhang, X., Moult, J., Madupu, R., Nelson, W. C., Dodson, R. J., Brinkac, L. M., Daugherty, S. C., Durkin, A. S., DeBoy, R. T., Kolonay, J. F., Sullivan, S. A., Zhou, L., Davidsen, T. M., Wu, M., Huston, A. L., Lewis, M., Weaver, B., Weidman, J. F., Khouri, H., Utterback, T. R., Feldblyum, T. V., Fraser, C. M. (2005). The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci U S A. Vol. 102 (312005/07/27), pp. 10913-8.
Paulsen, I. T., Press, C. M., Ravel, J., Kobayashi, D. Y., Myers, G. S., 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., Schneider, D. J., Cartinhour, S. W., Nelson, W. C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E. A., Pierson, L. S., Thomashow, L. S., Loper, J. E. (2005). Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol. Vol. 23 (72005/06/28), pp. 873-8.
Qi, M., Nelson, K. E., Daugherty, S. C., Nelson, W. C., Hance, I. R., Morrison, M., Forsberg, C. W. (2005). Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization. J Bacteriol. Vol. 187 (112005/05/20), pp. 3739-51.
Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop, M., Smith, D. R., Eisen, M. B., Nelson, W. C. (2005). Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol. Vol. 6 (72005/07/07), pp. 402.
Salzberg, S. L., Hotopp, J. C., Delcher, A. L., Pop, M., Smith, D. R., Eisen, M. B., Nelson, W. C. (2005). Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol. Vol. 6 (32005/03/19), pp. R23.
Seshadri, R., Adrian, L., Fouts, D. E., Eisen, J. A., Phillippy, A. M., Methe, B. A., Ward, N. L., Nelson, W. C., Deboy, R. T., Khouri, H. M., Kolonay, J. F., Dodson, R. J., Daugherty, S. C., Brinkac, L. M., Sullivan, S. A., Madupu, R., Nelson, K. E., Kang, K. H., Impraim, M., Tran, K., Robinson, J. M., Forberger, H. A., Fraser, C. M., Zinder, S. H., Heidelberg, J. F. (2005). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. Vol. 307 (57062005/01/08), pp. 105-8.
Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., Deboy, R. T., Davidsen, T. M., Mora, M., Scarselli, M., Margarit y Ros, I., Peterson, J. D., Hauser, C. R., Sundaram, J. P., Nelson, W. C., Madupu, R., Brinkac, L. M., Dodson, R. J., Rosovitz, M. J., Sullivan, S. A., Daugherty, S. C., Haft, D. H., Selengut, J., Gwinn, M. L., Zhou, L., Zafar, N., Khouri, H., Radune, D., Dimitrov, G., Watkins, K., O'Connor, K. J., Smith, S., Utterback, T. R., White, O., Rubens, C. E., Grandi, G., Madoff, L. C., Kasper, D. L., Telford, J. L., Wessels, M. R., Rappuoli, R., Fraser, C. M. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. Vol. 102 (392005/09/21), pp. 13950-5.
Wu, M., Ren, Q., Durkin, A. S., Daugherty, S. C., Brinkac, L. M., Dodson, R. J., Madupu, R., Sullivan, S. A., Kolonay, J. F., Haft, D. H., Nelson, W. C., Tallon, L. J., Jones, K. M., Ulrich, L. E., Gonzalez, J. M., Zhulin, I. B., Robb, F. T., Eisen, J. A. (2005). Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. Vol. 1 (52005/11/29), pp. e65.
Heidelberg, J. F., Seshadri, R., Haveman, S. A., Hemme, C. L., Paulsen, I. T., Kolonay, J. F., Eisen, J. A., Ward, N., Methe, B., Brinkac, L. M., Daugherty, S. C., Deboy, R. T., Dodson, R. J., Durkin, A. S., Madupu, R., Nelson, W. C., Sullivan, S. A., Fouts, D., Haft, D. H., Selengut, J., Peterson, J. D., Davidsen, T. M., Zafar, N., Zhou, L., Radune, D., Dimitrov, G., Hance, M., Tran, K., Khouri, H., Gill, J., Utterback, T. R., Feldblyum, T. V., Wall, J. D., Voordouw, G., Fraser, C. M. (2004). The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol. Vol. 22 (52004/04/13), pp. 554-9.
Moran, M. A., Buchan, A., Gonzalez, J. M., Heidelberg, J. F., Whitman, W. B., Kiene, R. P., Henriksen, J. R., King, G. M., Belas, R., Fuqua, C., Brinkac, L., Lewis, M., Johri, S., Weaver, B., Pai, G., Eisen, J. A., Rahe, E., Sheldon, W. M., Ye, W., Miller, T. R., Carlton, J., Rasko, D. A., Paulsen, I. T., Ren, Q., Daugherty, S. C., Deboy, R. T., Dodson, R. J., Durkin, A. S., Madupu, R., Nelson, W. C., Sullivan, S. A., Rosovitz, M. J., Haft, D. H., Selengut, J., Ward, N. (2004). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. Vol. 432 (70192004/12/17), pp. 910-3.
Nelson, K. E., Fouts, D. E., Mongodin, E. F., Ravel, J., DeBoy, R. T., Kolonay, J. F., Rasko, D. A., Angiuoli, S. V., Gill, S. R., Paulsen, I. T., Peterson, J., White, O., Nelson, W. C., Nierman, W., Beanan, M. J., Brinkac, L. M., Daugherty, S. C., Dodson, R. J., Durkin, A. S., Madupu, R., Haft, D. H., Selengut, J., Van Aken, S., Khouri, H., Fedorova, N., Forberger, H., Tran, B., Kathariou, S., Wonderling, L. D., Uhlich, G. A., Bayles, D. O., Luchansky, J. B., Fraser, C. M. (2004). Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res. Vol. 32 (82004/04/30), pp. 2386-95.
Nierman, W. C., DeShazer, D., Kim, H. S., Tettelin, H., Nelson, K. E., Feldblyum, T., Ulrich, R. L., Ronning, C. M., Brinkac, L. M., Daugherty, S. C., Davidsen, T. D., Deboy, R. T., Dimitrov, G., Dodson, R. J., Durkin, A. S., Gwinn, M. L., Haft, D. H., Khouri, H., Kolonay, J. F., Madupu, R., Mohammoud, Y., Nelson, W. C., Radune, D., Romero, C. M., Sarria, S., Selengut, J., Shamblin, C., Sullivan, S. A., White, O., Yu, Y., Zafar, N., Zhou, L., Fraser, C. M. (2004). Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A. Vol. 101 (392004/09/21), pp. 14246-51.
Rasko, D. A., Ravel, J., Okstad, O. A., Helgason, E., Cer, R. Z., Jiang, L., Shores, K. A., Fouts, D. E., Tourasse, N. J., Angiuoli, S. V., Kolonay, J., Nelson, W. C., Kolsto, A. B., Fraser, C. M., Read, T. D. (2004). The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. Vol. 32 (32004/02/13), pp. 977-88.
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. C., 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., Smith, H. O. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science. Vol. 304 (56672004/04/07), pp. 66-74.
Ward, N., Larsen, O., Sakwa, J., Bruseth, L., Khouri, H., Durkin, A. S., Dimitrov, G., Jiang, L., Scanlan, D., Kang, K. H., Lewis, M., Nelson, K. E., Methe, B., Wu, M., Heidelberg, J. F., Paulsen, I. T., Fouts, D., Ravel, J., Tettelin, H., Ren, Q., Read, T., DeBoy, R. T., Seshadri, R., Salzberg, S. L., Jensen, H. B., Birkeland, N. K., Nelson, W. C., Dodson, R. J., Grindhaug, S. H., Holt, I., Eidhammer, I., Jonasen, I., Vanaken, S., Utterback, T., Feldblyum, T. V., Fraser, C. M., Lillehaug, J. R., Eisen, J. A. (2004). Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol. Vol. 2 (102004/09/24), pp. e303.
Wu, M., Sun, L. V., Vamathevan, J., Riegler, M., Deboy, R., Brownlie, J. C., McGraw, E. A., Martin, W., Esser, C., Ahmadinejad, N., Wiegand, C., Madupu, R., Beanan, M. J., Brinkac, L. M., Daugherty, S. C., Durkin, A. S., Kolonay, J. F., Nelson, W. C., Mohamoud, Y., Lee, P., Berry, K., Young, M. B., Utterback, T., Weidman, J., Nierman, W. C., Paulsen, I. T., Nelson, K. E., Tettelin, H., O'Neill, S. L., Eisen, J. A. (2004). Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. Vol. 2 (32004/03/17), pp. E69.
Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., Dodson, R. J., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Daugherty, S., Brinkac, L., Beanan, M. J., Haft, D. H., Nelson, W. C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Van Aken, S. E., Feldblyum, T. V., D'Ascenzo, M., Deng, W. L., Ramos, A. R., Alfano, J. R., Cartinhour, S., Chatterjee, A. K., Delaney, T. P., Lazarowitz, S. G., Martin, G. B., Schneider, D. J., Tang, X., Bender, C. L., White, O., Fraser, C. M., Collmer, A. (2003). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A. Vol. 100 (182003/08/21), pp. 10181-6.
Methe, B. A., Nelson, K. E., Eisen, J. A., Paulsen, I. T., Nelson, W. C., Heidelberg, J. F., Wu, D., Wu, M., Ward, N., Beanan, M. J., Dodson, R. J., Madupu, R., Brinkac, L. M., Daugherty, S. C., DeBoy, R. T., Durkin, A. S., Gwinn, M., Kolonay, J. F., Sullivan, S. A., Haft, D. H., Selengut, J., Davidsen, T. M., Zafar, N., White, O., Tran, B., Romero, C., Forberger, H. A., Weidman, J., Khouri, H., Feldblyum, T. V., Utterback, T. R., Van Aken, S. E., Lovley, D. R., Fraser, C. M. (2003). Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science. Vol. 302 (56522003/12/13), pp. 1967-9.
Miller, E. S., Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Durkin, A. S., Ciecko, A., Feldblyum, T. V., White, O., Paulsen, I. T., Nierman, W. C., Lee, J., Szczypinski, B., Fraser, C. M. (2003). Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol. Vol. 185 (172003/08/19), pp. 5220-33.
Nelson, K. E., Fleischmann, R. D., DeBoy, R. T., Paulsen, I. T., Fouts, D. E., Eisen, J. A., Daugherty, S. C., Dodson, R. J., Durkin, A. S., Gwinn, M., Haft, D. H., Kolonay, J. F., Nelson, W. C., Mason, T., Tallon, L., Gray, J., Granger, D., Tettelin, H., Dong, H., Galvin, J. L., Duncan, M. J., Dewhirst, F. E., Fraser, C. M. (2003). Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol. Vol. 185 (182003/09/02), pp. 5591-601.
Read, T. D., Myers, G. S., Brunham, R. C., Nelson, W. C., Paulsen, I. T., Heidelberg, J., Holtzapple, E., Khouri, H., Federova, N. B., Carty, H. A., Umayam, L. A., Haft, D. H., Peterson, J., Beanan, M. J., White, O., Salzberg, S. L., Hsia, R. C., McClarty, G., Rank, R. G., Bavoil, P. M., Fraser, C. M. (2003). Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res. Vol. 31 (82003/04/12), pp. 2134-47.
Read, T. D., Peterson, S. N., Tourasse, N., Baillie, L. W., Paulsen, I. T., Nelson, K. E., Tettelin, H., Fouts, D. E., Eisen, J. A., Gill, S. R., Holtzapple, E. K., Okstad, O. A., Helgason, E., Rilstone, J., Wu, M., Kolonay, J. F., Beanan, M. J., Dodson, R. J., Brinkac, L. M., Gwinn, M., DeBoy, R. T., Madpu, R., Daugherty, S. C., Durkin, A. S., Haft, D. H., Nelson, W. C., Peterson, J. D., Pop, M., Khouri, H. M., Radune, D., Benton, J. L., Mahamoud, Y., Jiang, L., Hance, I. R., Weidman, J. F., Berry, K. J., Plaut, R. D., Wolf, A. M., Watkins, K. L., Nierman, W. C., Hazen, A., Cline, R., Redmond, C., Thwaite, J. E., White, O., Salzberg, S. L., Thomason, B., Friedlander, A. M., Koehler, T. M., Hanna, P. C., Kolsto, A. B., Fraser, C. M. (2003). The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. Vol. 423 (69352003/05/02), pp. 81-6.
Seshadri, R., Paulsen, I. T., Eisen, J. A., Read, T. D., Nelson, K. E., Nelson, W. C., Ward, N. L., Tettelin, H., Davidsen, T. M., Beanan, M. J., Deboy, R. T., Daugherty, S. C., Brinkac, L. M., Madupu, R., Dodson, R. J., Khouri, H. M., Lee, K. H., Carty, H. A., Scanlan, D., Heinzen, R. A., Thompson, H. A., Samuel, J. E., Fraser, C. M., Heidelberg, J. F. (2003). Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A. Vol. 100 (92003/04/22), pp. 5455-60.
Beja, O., Suzuki, M. T., Heidelberg, J. F., Nelson, W. C., Preston, C. M., Hamada, T., Eisen, J. A., Fraser, C. M., DeLong, E. F. (2002). Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature. Vol. 415 (68722002/02/08), pp. 630-3.
Eisen, J. A., Nelson, K. E., Paulsen, I. T., Heidelberg, J. F., Wu, M., Dodson, R. J., Deboy, R., Gwinn, M. L., Nelson, W. C., Haft, D. H., Hickey, E. K., Peterson, J. D., Durkin, A. S., Kolonay, J. L., Yang, F., Holt, I., Umayam, L. A., Mason, T., Brenner, M., Shea, T. P., Parksey, D., Nierman, W. C., Feldblyum, T. V., Hansen, C. L., Craven, M. B., Radune, D., Vamathevan, J., Khouri, H., White, O., Gruber, T. M., Ketchum, K. A., Venter, J. C., Tettelin, H., Bryant, D. A., Fraser, C. M. (2002). The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A. Vol. 99 (142002/07/03), pp. 9509-14.
Fleischmann, R. D., Alland, D., Eisen, J. A., Carpenter, L., White, O., Peterson, J., DeBoy, R., Dodson, R., Gwinn, M., Haft, D., Hickey, E., Kolonay, J. F., Nelson, W. C., Umayam, L. A., Ermolaeva, M., Salzberg, S. L., Delcher, A., Utterback, T., Weidman, J., Khouri, H., Gill, J., Mikula, A., Bishai, W., Jacobs Jr, W. R., Venter, J. C., Fraser, C. M. (2002). Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. Vol. 184 (192002/09/10), pp. 5479-90.
Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., Eisen, J. A., Seshadri, R., Ward, N., Methe, B., Clayton, R. A., Meyer, T., Tsapin, A., Scott, J., Beanan, M., Brinkac, L., Daugherty, S., DeBoy, R. T., Dodson, R. J., Durkin, A. S., Haft, D. H., Kolonay, J. F., Madupu, R., Peterson, J. D., Umayam, L. A., White, O., Wolf, A. M., Vamathevan, J., Weidman, J., Impraim, M., Lee, K., Berry, K., Lee, C., Mueller, J., Khouri, H., Gill, J., Utterback, T. R., McDonald, L. A., Feldblyum, T. V., Smith, H. O., Venter, J. C., Nealson, K. H., Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol. Vol. 20 (112002/10/09), pp. 1118-23.
Nelson, K. E., Weinel, C., Paulsen, I. T., Dodson, R. J., Hilbert, H., Martins dos Santos, V. A., Fouts, D. E., Gill, S. R., Pop, M., Holmes, M., Brinkac, L., Beanan, M., DeBoy, R. T., Daugherty, S., Kolonay, J., Madupu, R., Nelson, W. C., White, O., Peterson, J., Khouri, H., Hance, I., Chris Lee, P., Holtzapple, E., Scanlan, D., Tran, K., Moazzez, A., Utterback, T., Rizzo, M., Lee, K., Kosack, D., Moestl, D., Wedler, H., Lauber, J., Stjepandic, D., Hoheisel, J., Straetz, M., Heim, S., Kiewitz, C., Eisen, J. A., Timmis, K. N., Dusterhoft, A., Tummler, B., Fraser, C. M. (2002). Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol. Vol. 4 (122003/01/22), pp. 799-808.
Paulsen, I. T., Seshadri, R., Nelson, K. E., Eisen, J. A., Heidelberg, J. F., Read, T. D., Dodson, R. J., Umayam, L., Brinkac, L. M., Beanan, M. J., Daugherty, S. C., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Nelson, W. C., Ayodeji, B., Kraul, M., Shetty, J., Malek, J., Van Aken, S. E., Riedmuller, S., Tettelin, H., Gill, S. R., White, O., Salzberg, S. L., Hoover, D. L., Lindler, L. E., Halling, S. M., Boyle, S. M., Fraser, C. M. (2002). The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A. Vol. 99 (202002/09/25), pp. 13148-53.
Nierman, W. C., Feldblyum, T. V., Laub, M. T., Paulsen, I. T., Nelson, K. E., Eisen, J. A., Heidelberg, J. F., Alley, M. R., Ohta, N., Maddock, J. R., Potocka, I., Nelson, W. C., Newton, A., Stephens, C., Phadke, N. D., Ely, B., DeBoy, R. T., Dodson, R. J., Durkin, A. S., Gwinn, M. L., Haft, D. H., Kolonay, J. F., Smit, J., Craven, M. B., Khouri, H., Shetty, J., Berry, K., Utterback, T., Tran, K., Wolf, A., Vamathevan, J., Ermolaeva, M., White, O., Salzberg, S. L., Venter, J. C., Shapiro, L., Fraser, C. M. (2001). Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A. Vol. 98 (72001/03/22), pp. 4136-41.
Tettelin, H., Nelson, K. E., Paulsen, I. T., Eisen, J. A., Read, T. D., Peterson, S., Heidelberg, J., DeBoy, R. T., Haft, D. H., Dodson, R. J., Durkin, A. S., Gwinn, M., Kolonay, J. F., Nelson, W. C., Peterson, J. D., Umayam, L. A., White, O., Salzberg, S. L., Lewis, M. R., Radune, D., Holtzapple, E., Khouri, H., Wolf, A. M., Utterback, T. R., Hansen, C. L., McDonald, L. A., Feldblyum, T. V., Angiuoli, S., Dickinson, T., Hickey, E. K., Holt, I. E., Loftus, B. J., Yang, F., Smith, H. O., Venter, J. C., Dougherty, B. A., Morrison, D. A., Hollingshead, S. K., Fraser, C. M. (2001). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. Vol. 293 (55292001/07/21), pp. 498-506.
Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Clayton, R. A., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Umayam, L., Gill, S. R., Nelson, K. E., Read, T. D., Tettelin, H., Richardson, D., Ermolaeva, M. D., Vamathevan, J., Bass, S., Qin, H., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Fleishmann, R. D., Nierman, W. C., White, O., Salzberg, S. L., Smith, H. O., Colwell, R. R., Mekalanos, J. J., Venter, J. C., Fraser, C. M. (2000). DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. Vol. 406 (67952000/08/22), pp. 477-83.
Read, T. D., Brunham, R. C., Shen, C., Gill, S. R., Heidelberg, J. F., White, O., Hickey, E. K., Peterson, J., Utterback, T., Berry, K., Bass, S., Linher, K., Weidman, J., Khouri, H., Craven, B., Bowman, C., Dodson, R., Gwinn, M., Nelson, W. C., DeBoy, R., Kolonay, J., McClarty, G., Salzberg, S. L., Eisen, J., Fraser, C. M. (2000). Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. Vol. 28 (62000/02/24), pp. 1397-406.
Tettelin, H., Saunders, N. J., Heidelberg, J., Jeffries, A. C., Nelson, K. E., Eisen, J. A., Ketchum, K. A., Hood, D. W., Peden, J. F., Dodson, R. J., Nelson, W. C., Gwinn, M. L., DeBoy, R., Peterson, J. D., Hickey, E. K., Haft, D. H., Salzberg, S. L., White, O., Fleischmann, R. D., Dougherty, B. A., Mason, T., Ciecko, A., Parksey, D. S., Blair, E., Cittone, H., Clark, E. B., Cotton, M. D., Utterback, T. R., Khouri, H., Qin, H., Vamathevan, J., Gill, J., Scarlato, V., Masignani, V., Pizza, M., Grandi, G., Sun, L., Smith, H. O., Fraser, C. M., Moxon, E. R., Rappuoli, R., Venter, J. C. (2000). Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. Vol. 287 (54592000/03/10), pp. 1809-15.
Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., McDonald, L., Utterback, T. R., Malek, J. A., Linher, K. D., Garrett, M. M., Stewart, A. M., Cotton, M. D., Pratt, M. S., Phillips, C. A., Richardson, D., Heidelberg, J., Sutton, G. G., Fleischmann, R. D., Eisen, J. A., White, O., Salzberg, S. L., Smith, H. O., Venter, J. C., Fraser, C. M. (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. Vol. 399 (67341999/06/09), pp. 323-9.
White, O., Eisen, J. A., Heidelberg, J. F., Hickey, E. K., Peterson, J. D., Dodson, R. J., Haft, D. H., Gwinn, M. L., Nelson, W. C., Richardson, D. L., Moffat, K. S., Qin, H., Jiang, L., Pamphile, W., Crosby, M., Shen, M., Vamathevan, J. J., Lam, P., McDonald, L., Utterback, T., Zalewski, C., Makarova, K. S., Aravind, L., Daly, M. J., Minton, K. W., Fleischmann, R. D., Ketchum, K. A., Nelson, K. E., Salzberg, S., Smith, H. O., Venter, J. C., Fraser, C. M. (1999). Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. Vol. 286 (54441999/11/24), pp. 1571-7.
Nelson, W. C., Matson, S. W. (1996). The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications. Mol Microbiol. Vol. 20 (61996/06/01), pp. 1179-87.
Howard, M. T., Nelson, W. C., Matson, S. W. (1995). Stepwise assembly of a relaxosome at the F plasmid origin of transfer. J Biol Chem. Vol. 270 (471995/11/24), pp. 28381-6.
Nelson, W. C., Howard, M. T., Sherman, J. A., Matson, S. W. (1995). The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. Vol. 270 (471995/11/24), pp. 28374-80.
Matson, S. W., Nelson, W. C., Morton, B. S. (1993). Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. Vol. 175 (91993/05/01), pp. 2599-606.
Nelson, W. C., Morton, B. S., Lahue, E. E., Matson, S. W. (1993). Characterization of the Escherichia coli F factor traY gene product and its binding sites. J Bacteriol. Vol. 175 (81993/04/01), pp. 2221-8.
 

Service to the University

Media, Alumni, and Community Relations
Autumn 2009 USC Trojan Family Magazine "Blurring the Lines Between Earth and Life". The article focuses on geobiology research going on in MEB. The genomic work done by John Heidelberg and myself is highlighted., Fall 2009   
Feature in USC News "The Machine That Goes Ping". Article focuses on the 454FLX DNA Sequencer and the research going on in MEB that makes use of it., 2008-2009   
 

Service to the Profession

Professional Memberships
International Society for Microbial Ecology, 01/01/2008-  
American Society for Microbiology, 06/1996-  
 
 
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