Publications
2006 and earlier
Wortman, J.R., Fedorova, N., Crabtree, J., Joardar, V., Maiti, R., Haas, B.J., Amedeo, P.,Lee, E., Angiuoli, S.V., Jiang, B., Anderson, M.J., Denning, D.W., White, O.R., Nierman, W.C., 2006.
Whole genome comparison of the A. fumigatus family. Med Mycol 44 Suppl, 3-7
Donia M., Hathaway B.J., Sudek S., Haygood M.G., Rosovitz M.J., Ravel J., and Schmidt E.W. 2006.
Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nature Chemical Biology. 2(12):729-35.
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., 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 emerginghuman ehrlichiosis agents. PLoS genetics 2, e21.
Wortman, J.R., Fedorova, N., Crabtree, J., Joardar, V., Maiti, R., Haas, B.J., Amedeo, P., Lee, E., Angiuoli, S.V., Jiang, B., Anderson, M.J., Denning, D.W., White, O.R., Nierman, W.C., 2006.
Whole genome comparison of the A. fumigatus family. Med Mycol 44 Suppl, 3-7.
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., 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 genetics 2, e21.
Van Ert MN, Easterday WR, Simonson TS, U'ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB, Beaudry J, Welty-Bernard A, Read T, Fraser CM, Ravel J, Keim P.
2006. Strain-specific single nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology. Nov 8 [Epub ahead of print].
Donia M., Hathaway B.J., Sudek S., Haygood M.G., Rosovitz M.J., Ravel J., and Schmidt E.W.
2006. Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians. Nature Chemical Biology. 2(12):729-35.
Romero CM, DeShazer D, Feldblyum T, Ravel J, Woods D, Kim HS, Yu Y, Ronning CM, Nierman WC.
2006. Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts. BMC Genomics. 2006 7:228-239.
Dempsey MP, Nietfeldt J, Ravel J, Hinrichs S, Crawford R, Benson AK.
2006. Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp. tularensis and Francisella tularensis subsp. holarctica populations. Journal of Bacteriology 188:5904-5914.
Myers G.S.A., Rasko D.A., Cheung J.K., Ravel J., Seshadri R., DeBoy R.T., Ren Q.H., 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. and Paulsen I.T.
2006. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Research 16: 1031-1040.
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.
2006. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5: insights into the biological control of plant disease. Nature Biotechnology. 23:873-878.
Eisen, J.A., Coyne, R.S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J.R., Badger, J.H., Ren, Q., Amedeo, P., Jones, K.M., Tallon, L.J., Delcher, A.L., Salzberg, S.L., Silva, J.C., Haas, B.J., Majoros, W.H., Farzad, M., Carlton, J.M., Smith, R.K., Garg, J., Pearlman, R.E., Karrer, K.M., Sun, L., Manning, G., Elde, N.C., Turkewitz, A.P., Asai, D.J., Wilkes, D.E., Wang, Y., Cai, H., Collins, K., Stewart, B.A., Lee, S.R., Wilamowska, K., Weinberg, Z., Ruzzo, W.L., Wloga, D., Gaertig, J., Frankel, J., Tsao, C.C., Gorovsky, M.A., Keeling, P.J., Waller, R.F., Patron, N.J., Cherry, J.M., Stover, N.A., Krieger, C.J., Del Toro, C., Ryder, H.F., Williamson, S.C., Barbeau, R.A., Hamilton, E.P., Orias, E.
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4 (9):e286, 2006.
Fouts, D.E., Rasko, D.A., Cer, R.Z., Jiang, L., Fedorova, N.B., Shvartsbeyn, A., Vamathevan, J.J., Tallon, L., Althoff, R., Arbogast, T.S., Fadrosh, D.W., Read, T.D., Gill, S.R.
Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry. J Bacteriol 188 (9):3402-3408, 2006.
Goldberg, S.M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., Friedman, R., Halpern, A., Khouri, H., Kravitz, S.A., Lauro, F.M., Li, K., Rogers, Y.H., Strausberg, R., Sutton, G., Tallon, L., Thomas, T., Venter, E., Frazier, M., Venter, J.C.
A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103 (30):11240-11245, 2006.
Lee, S.B., Kaittanis, C., Jansen, R.K., Hostetler, J.B., Tallon, L.J., Town, C.D., Daniell, H.
The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7 (1):61, 2006.
Ruhlman, T., Lee, S.B., Jansen, R.K., Hostetler, J.B., Tallon, L.J., Town, C.D., Daniell, H.
Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7 (1):222, 2006.
Seshadri, R., Joseph, S.W., Chopra, A.K., Sha, J., Shaw, J., Graf, J., Haft, D., Wu, M., Ren, Q., Rosovitz, M.J., Madupu, R., Tallon, L., Kim, M., Jin, S., Vuong, H., Stine, C.O., Ali, A., Horneman, A.J., Heidelberg, J.F.
Genome Sequence of Aeromonas hydrophila ATCC 7966T: The Jack of All Trades. J Bacteriol 186 (23):8272-82, 2006.
Town, C.D., Cheung, F., Maiti, R., Crabtree, J., Haas, B.J., Wortman, J.R., Hine, E.E., Althoff, R., Arbogast, T.S., Tallon, L.J., Vigouroux, M., Trick, M., Bancroft, I.
Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18 (6):1348-1359, 2006.
Wu, D., Daugherty, S.C., Aken, S.E., Pai, G.H., Watkins, K.L., Khouri, H., Tallon, L.J., Zaborsky, J.M., Dunbar, H.E., Tran, P.L., Moran, N.A., Eisen, J.A.
Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 4 (6):e188, 2006.
Lanie J.A., Ng W-L, Kazmierczak K.M., Andrzejewski T.M., Davidsen T.M., Wayne K.J., Tettelin H., Glass J.I., and Winkler M.
(2006) Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J. Bacteriol. 189, 38-51.
Tettelin H., Medini D., Donati C., and Masignani V.
(2006) Towards a universal group B Streptococcus vaccine using multi-strain genome analysis. Expert Rev. Vaccines 5, 687-694. [PubMed]
Dunning Hotopp J.C., Grifantini R., Kumar N., Tzeng Y.L., Fouts D., Frigimelica E., Draghi M., Giuliani M.M., Rappuoli R., Stephens D.S., Grandi G., and Tettelin H.
(2006) Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen specific genes. Microbiology 152, 3733-3749. Featured in Microbiology Today
Savard J., Tautz D., Richards S., Weinstock G.M., Gibbs R.A., Werren J.H., Tettelin H., and Lercher M.J.
(2006) Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of holometabolous insects. Genome Res. 16, 1334-1338.
Baldo L., Dunning Hotopp J.C., Jolley K.A., Bordenstein S.R., Biber S.A., Choudhury R.R., Hayashi C., Maiden M.C.J., Tettelin H., and Werren J.H.
(2006) A multilocus sequence typing system for the endosymbiont Wolbachia. Appl. Environ. Microbiol. 72, 7098-7110.
Ramaswamy S.V., Ferrieri P., Madoff L.C., Flores A.E., Kumar N., Tettelin H., and Paoletti L.C.
(2006) Identification of novel cps locus polymorphisms in nontypeable group B Streptococcus. J. Med. Microbiol. 55, 775-783.
Dunning 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.R., Khouri H., Zhang C., Hua N., Lin Q., Ohashi N., Zhi N., Nelson W., Brinkac L.M., Dodson R.J., Rosovitz M.J., Sundaram J., Daugherty S.C., Davidsen T., Durkin A.S., Gwinn M.L., 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., and Tettelin H.
(2006) Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2, e21. Featured in Nature Reviews Microbiology
Myers G. S. A., 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., and Paulsen I. T.
(2006) Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Research 16: 1031-1040. [PubMed]
Palenik B., Ren Q., Dupont C.L., Myers G. S. A., 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., and Paulsen I.T.
(2006) Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A 103: 13555-13559. [PubMed]
Parker D., Kennan R. M., Myers G. S. A., Paulsen I. T., Songer J. G., and Rood J. I..
(2006) Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus. Journal of Bacteriology 188: 4801-4811. [PubMed]
Ding X.Z., Paulsen I.T., Bhattacharjee A.K., Nikolich M.P., Myers G. S. A., and Hoover D.L.
(2006) A high efficiency cloning and expression system for proteomic analysis. Proteomics 6: 4038-4046. [PubMed]
