Publications
Fraser, C.M. A genomics-based approach to biodefense preparedness. Nature Reviews Genetics 5:23-33, 2004.
Ghedin, E., Bringaud, F., Peterson J., Myler, P., Berriman, M., Ivens, A., Andersson B., Bontempi, E., Eisen, J., Angiuoli, S., Wanless, D., von arx, A., Murphy, L., Lennard, N., Salzberg, S., Adams, M.D., White, O., Hall, N. Stuart, K., Fraser, C.M. and El-Sayed, N.M. Gene synteny and evolution of genome architecture in trypanosomatids. Mol. Biochem. Parasitol. 134(2): 183-91, 2004.
Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521, 2004.
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., Federova, N., Forberger, H., Tran, B., Kathariou, S., Wonderling, L.D., Uhlich, G.A., Bayles, D.O., Luchansky, J.C. and Fraser, C.M. 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. Nucl. Acids Res. 32(8): 2386-2395, 2004.
Seshadri, R., Myers, G.S., Tettelin, H., Eisen, J.A., Hedelberg, 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., Dolonay, 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., Smajis, D., Howell, J.K., Pal, S., Amin, A., Vashisth, P., McNeill, T.Z., Xian, Q., Sodergren, E., Baca, E., Weinstock, G.M., Norris, S.J., Fraser, C.M. and Paulsen, I.T. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc. Natl. Acad. Sci. USA 101 (15): 5646-51. 2004.
Hoffmaster, A.R., Ravel, J., Rasko, D.A., Chapman, G.D., Chute, M.D., Marston, C.K., De, B.K., Sacchi, C.T., Fitzgerald, C., Mayer, L.W., Maiden, M.C., Priest, F.G., Barker, M., Jian, L., Cer, R.Z., Rilstone, J., Peterson, S.N., Weyant, R.S., Galloway, D.R., Read, T.D., Popovic, T. and Fraser, C.M. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc. Natl. Acad. Sci. USA 101 (22): 8449-54. 2004.
Budowle, B., Schutzer, S.E., Ascher, M.S., Atlas, R.M., Burans, J.P., Chakraborty, R., Dunn, J.J., Franz, D.R., Fraser, C.M., Leighton, T.J., Morse, S.A., Murch, R.S., Ravel, J., Rock, D.L., Slezak, T.R., Velsko, S.P., Walsh, A.C., Walters, R.A. Toward a System of Microbial Forensics; from Sample Collection to Interpretation of Evidence. ASM Journal Applied and Environmental Microbiology, 2004.
Person, T., Busch J.D., Ravel, J., Read, T.D., Rhoton S.D., U'Ren, J.M., Simonson, T.S., Kachur, S.M., Leadem, R.R., Cardon, M.L., Van Ert, M.N., Huynh, L.Y., Fraser, C.M., Keim, P. Phylogentic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. USA 101(37): 13536-41, 2004.
Qiu, W.G., Schutzer, S.E., Bruno, J.F., Attie, O., Xu, Y., Dunn, J.J., Fraser, C.M., Casjens, S.R., Luft. B.J. Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu strictu revealed by three-way genome comparisons and multilocus sequence typing. Proc. Natl. Acad. Sci. USA 101(39):14150-5, 2004.
Nierman, W.C., DeShazer, D., Kim, H.S., Tettelin, H., Nelson, K.E., Feldblyum, T., Ulrich, R.L., Ronning, C.M., Brinkac, L.M., Daughterty, 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. Structural flexibility in the Burkholderia mallei genome. Proc. Natl. Acad. Sci. USA 101(39):14246-51, 2004.
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, B.T., Seshadri, R., Salzberg, S.L., Jensen, H.B., Birkeland, N.K., Nelson, W.C., Dodson, R.J., Grindhaug, S.H., Holt, J., Eidhammer, I., Jonasen, I., Vanaken, S., Utterback, T., Feldblyum, T.V., Fraser, C.M., Lillehaug, J.R., Eisen, J.A. Genomic insights into methanotrophy; the complete genome sequence of Methylococcus capsulatus (Bath). PloS Biol. 2(10):e303, 2004.
Loftus, B.J., Fung E., Roncagila, P., Rowley, D., Amedeo, P., Bruno, D., Vamathevan, J., Miranda, M., Anderson, I.J., Fraser, J.A., Allen, J.E., Bosdet, I.E., Brent, M.R., Chiu, R., Doering, T.L., Donlin, M.J., D'Souza, C.A., Fox, D.S., Grinberg, V., Fu, J., Fukushima, M., Haas, B.J., Huang, J.C., Janbon, G., Jones, S.J., Koo, H.L., Krzywinski, M.I., Kwon-Chung, J.K., Lengeler, K.B., Maiti, R., Marra, M.A., Marra, R.E., Matthewson, C.A., Mitchell, T.G., Pertea, M., Riggs, F.R., Salzberg, S.L., Schein, J.E., Shvartsbeyn, A. , Jin, H., Shumway, M., Specht, C.A., Suh, B.B., Tenney, A., Utterback, T.R., Wickes, B.L., Wortman, J.R., Wye, N.H., Kronstad, J.W., Lodge, J.K., Heitman, J., David, R.W., Fraser, C.M., Hyman, R.W. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307(5713): 1321-1324, 2005.
Ghedin, E., Sengamaly, N.A., Shumway, M., Zaborsky, J., Feldblum, T., Subbu, V., Spiro, D.J., Sitz, J., Koo, H., Bolotov, P., Dernovoy, D., Tatusova, T., Bao, Y., St. George, K., Taylor, J., Lipman, D.J., Fraser, C.M., Taubenberger, J.K., Salzberg, S.L. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature, 437(7062): 1162-6, 2005.
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. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'opan-genome'. Proc. Natl. Acad. Sci 102(30):13950-5, 2005.
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. Whole-genome sequence analysis of Pseudomonas syringae pv. Phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J. Bacteriol. 187(18):64888-98, 2005.
Methe, B.A., Nelson, K.E., Deming, J.W., Momen, B., Melamud, E., Zhang, X., Moult, J., Madapu, 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. The psychrophilic lifestyle as revealed by the genome sequent of Colwellia psychreerthraeca 34H through genomic and proteomic analysis. Proc. Natl. Acad. Sci. 102(31): 10913-8, 2005.
Holmes, E.C., Ghedin, E., Miller, N., Taylor, J., Bao, Y., St. George, K., Grenfell, B.T., Salzberg, S.L., Fraser, C.M., Lipman, D.J., Taubenberger, J.K. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 3(9):e300, 2005.
Berriman, M., Ghedin, E., Hertz-Fowler, C., Blandin, G., Renauld, H., Bartholomeu, D.C., Lennard, N.J., Caler, E., Hamlin, N.E., Haas, B., Bohme, U., Hannick, L., Aslett, M.A., Shallom, J., Marcell, L., Hou, L., Wickstead, B., Alsmark, U.C., Arrowsmith, C., Atkin, R.J., Barron, A.J., Bringaud, F., Brooks, K., Carrington, M., Cherevach, I., Chillingworth, T.J., Churcher, C., Clark, L.N., Corton, C.H., Cronin, A., Davies, R.M., Doggett, J., Djikeng, A., Feldblyum, T., Field, M.C., Fraser, A., Goodhead, I., Hance Z., Harper, D., Harris, B.R., Hauser, H., Hostetler, J., Ivens, A., Jagels, K., Johnson, D., Johnson, J., Jones, K., Keerhornou, A.X., Koo, H., Larke, N., Landfear S., Larkin, C., Leech, V., Line, A., Lord, A., Macleod, A., Mooney, P.J., Moule, S., Martin, D.M., Morgan, G.W., Mungall, K., Norbertczak, H., Ormand, D., Pai, G., Peacock, C.S., Peterson, J., Quail, M.A., Rabbinowitsch, E., Rajandream, M.A., Reitter, C., Salzburg, S.L., Sanders, M., Scholbel. S., Sharp, S., Simmonds, M., Simpson, A.J., Tallon, L., Turner, C.M., Tait, A., Tivy, A.R., Van Aken, S., Walker, D., Wanless, D., Wang, S., White, B., White, O., Whitehead, S., Woodward, J., Wortman, J., Adams, M.D., Embley, T.M., Gull, K., Ullu, E., Barry, J.D., Fairlam, A.H., Opperdoes, F., Barrell, B.G., Donelson, J.E., Hall, N., Fraser, C.M., Melveille, S.E., El-Sayed, N.M. The genome of the African trypanosome Trypansomoa brucei. Science 309(5733): 416-22, 2005.
El-Sayed, N.M., Myler, P.J., Bartholomeu, D.C., Nilsson, D., Aggarwal, G. Tran, A.N., Ghedin, E., Wrothy, E.A., Delcher, A.L., Blandin, G., Westenberger, S.J., Caler, E., Cerqueira, G.C., Branche, C., Haas, B., Anupama, A., Arner E., Aslund, L., Attipoe, P., Bontempi, E., Bringaud, F., Burton, P., Cada, E., Campbell, D.A., Carrington, M., Crabtree, J., Darban, H., da Silveira, J.F., de Jong, P., Edwards, K., Englund, P.T., Fazelina, G., Feldblyum, T., Ferella, M., Frasch, A.C., Gull, K., Horn, D., Hou, L., Huang, Y., Kindlund, E., Klingbeil, M., Kluge, S., Koo, H., Lacerda, D., Levin, M.J., Lorenzi, H., Louie, T., Machado, C.R., McCulloch R., McKenna, A., Mizuno, Y., Mottram, J.C., Nelson, S., Ochaya, S., Oseogawa, K., Pai, G., Parson, M., Pentony, M., Pettersson, U., Pop, M., Ramirez, J.L., Rinta, J., Robertson, Simpson, A.J., Sisk, E., Tammi, M.T., Tarleton, R., Teixeira, S., Van Aken, S., Vogt, C., Ward, P.N., Wickstead, B., Wortman, J., White, O., Fraser, C.M., Stuart, K.D., Andersson, B. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309(5733):409-15, 2005.
Gardner, M.J., Bishop, R., Shah, T., de Villiers, E.P., Carlton, J.M., Hall, N., Ren, Q., Paulesn, I.T., Pain, A., Berriman, M., Wilson, R.J., Sato, S., Ralph, S.A., Mann, D.J., Xiong, Z., Shallon, S.J., Weidman, J., Jiang, L., Lynn, J., Weaver, B., Shoaibi, A., Domingo, A.R., Wasawo, D., Crabtree, J., Wortman, J.R., Haas, B., Angiuoli, S.V., Creasy, T.H., Lu, C.J., Nierman, W.C., Taracha, E.L., Salzberg, S.L., White, O.R., Fitzhugh, H.A., Morzaria, S., Venter, J.C., Fraser, C.M., Nene, V. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309(5731):134-7, 2005.
Budowle, B., Schutzer, S.E., Ascher, M.S., Atlas, R.M., Burans, J.P., Chakraborty, R., Dunn, J.J., Fraser, C.M., Franz, D.R., Leighton, T.J., Morese, S.A., Murch, R.S., Ravel, J., Rock, D.L., Slezak, T.R., Velsko, S.P. Walsh, A.C., Walters, R.A. Toward a system of microbial forensics: from sample collection to interpretation of evidence. Appl. Environ. Microbiol. 71(5):2209-13, 2005.
Wang, R., Arevalo-Herrara, M., Gardner, M.J., Bonelo, A., Carlton, J.M., Gomez, A., Vera, O., Soto, L., Vergara, J., Bidwell, S.L., Domingo, A., Fraser, C.M., Herrera, S. Immune responses to Plasmodium vivax pre-erythrocytic stage antigens in naturally exposed Duffy-negative humans: a potential model for identification of liver-state antigens. Eur. J. Immunol. 35(6):1859-68, 2005.
Gill, S.R., Fouts, D.E., Archer, G.L., Mongodin, E.F., Deboy, R.T., Ravel, J., Paulsen, I.T., Kolonay, J.F., Brinkac, L., Beanan, M., Dodson, R.J., Daugherty, S.C., Madupu, R., Angiuoli, S.V., Durkin, A.S., Haft, D.H., Vamathevan, J., Khouri, H., Utterback, T., Lee, C., Dimitrov, G., Jiang, L., Qin, H., Weidman, J., Tran, K., Kang, K., Hance, I.R., Nelson, K.E., Fraser, C.M. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureau strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J. Bacteriol. 187(7):2426-38, 2005.
Loftus, B., Anderson, I., Davies, R., Alsmark, U.C., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R.P., Mann, B.J., Nozaki, T., Suh, B., Pop, M., Duchene, M., Ackers, J., Tannich, E., Leippie, M., Hofer, M., Bruchhaus, I., Willhoeft, U., Bhattacharya, A., Jagelss, K., Moule, S., Mungall, K., Ormond, D., Squares, R., Whitehead, S., Quail, MA., Rabbinowitsch, E., Norbertczak, H., Price, C., Wang, Z., Guillen, N., Gilchrist, C., Stroup, S.E., Bhattacharya, S., Lohia, A., Foster, P.G., Sicheritz-Ponten, T., Weber, C., Singh, U., Mukherjee, C., El-Sayed, N.M., Petri, W.A.Jr., Clark, C.G., Embley, T.M., Barrell, B., Fraser, C.M., Hall, N. The genome of the protest parasite Entamoeba histolytica. Nature 433(7028):865-8, 2005.
Fouts, D.E., Mongodin, E.F., Mandress, R.E., Miller, W.G., Rasko, D.A., Ravel, J., Brinkac, L.M., Deboy, R.T., Parker, C.T., Daugherty, S.C., Dodson, R.J., Durkin, A.S., Madupu, R., Sullivan, S.A., Shetty, J.U., Ayodegi, M.A., Shvartsbeyn, A., Schatz, M.C., Badger, J.H., Fraser, C.M., Nelson, K.E. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 3(1):e15, 2005.
Graham, S.P., Pelle, R., Honda, Y., Mwangi, D.M., Tonukari, N.J., Yamage, M., Glew, E.J., de Villiers, E.P., Shah, T., Bishop, R., Abuya, E., Awino, E., Gachanja, J., Luyai, A.E., Mbwika, F., Muthiani, A.M., Ndegwa, D.M., Njahira, M., Nyanjui, J.K., Onono, F.O., Osaso, J., Saya, R.M., Wildmann, C., Fraser, C.M., Maudlin, I., Gardner, M.J., Morzaria, S.P., Loosmore, S., Gilbert, S.C., Audonnet, J.C., van der Bruggen, P., Nene, V., Taracha, E.L. Theileria parva candidate vaccine antigens recognized by immune bovine cytotoxic T lymphocytes. Proc Natl Acad Sci USA. Feb 21 [Epub ahead of print] 2006.
Gill, S. R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., Gordon, J.I., Relman, D.A., Fraser-Liggett, C.M., Nelson, K.E. Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355, 2006.
Carlton, J.M., Hirt, R.P., Silva, J.C., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark, U.C., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van de Peer, Y., Miranda-Saavedra, D., Barton, G.J., Westrop, G.D., Muller, S., Dessi, D., Fiori, P.L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F.D., Simoes-Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, R., Smith, A.J., Vanacova, S., Villalvazo, M., Haas, B.J., Pertea, M., Feldblyum, T.V., Utterback, T.R., Shu, C.L., Osoegawa, K., deJong, P.J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S.B., Logsdon, J.M., Henze, K., Gupta, A., Wang, C.C., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tang, P., Chiu, C.H., Lee, Y.S., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., and Johnson, P.J. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315: 207-212, 2007.
VanErt, M.N., Easterday, W.R., Simonson, T.S., U'Ren, J.M., Pearson, T., Kenefic, L.J., Busch, J.D., Huynh, L.Y., Dukerich, M., Trim, C.B., Beaudry, J., Welty-Bernard, A., Read, T., Fraser, C.M., Ravel, J., and Keim, P. Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. J. Clin. Microbiol. 45: 47-53, 2007.
