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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. 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". Proceedings of the National Academy of Sciences of the United States of America 102, 13950-13955. Nierman, W.C., Pain, A., Anderson, M.J., Wortman, J.R., Kim, H.S., Arroyo, J., Berriman, M., Abe, K., Archer, D.B., Bermejo, C., Bennett, J., Bowyer, P., Chen, D., Collins, M., Coulsen, R., Davies, R., Dyer, P.S., Farman, M., Fedorova, N., Fedorova, N., Feldblyum, T.V., Fischer, R., Fosker, N., Fraser, A., Garcia, J.L., Garcia, M.J., Goble, A., Goldman, G.H., Gomi, K., Griffith-Jones, S., Gwilliam, R., Haas, B., Haas, H., Harris, D., Horiuchi, H., Huang, J., Humphray, S., Jimenez, J., Keller, N., Khouri, H., Kitamoto, K., Kobayashi, T., Konzack, S., Kulkarni, R., Kumagai, T., Lafon, A., Latge, J.P., Li, W., Lord, A., Lu, C., Majoros, W.H., May, G.S., Miller, B.L., Mohamoud, Y., Molina, M., Monod, M., Mouyna, I., Mulligan, S., Murphy, L., O'Neil, S., Paulsen, I., Penalva, M.A., Pertea, M., Price, C., Pritchard, B.L., Quail, M.A., Rabbinowitsch, E., Rawlins, N., Rajandream, M.A., Reichard, U., Renauld, H., Robson, G.D., Rodriguez de Cordoba, S., Rodriguez-Pena, J.M., Ronning, C.M., Rutter, S., Salzberg, S.L., Sanchez, M., Sanchez-Ferrero, J.C., Saunders, D., Seeger, K., Squares, R., Squares, S., Takeuchi, M., Tekaia, F., Turner, G., Vazquez de Aldana, C.R., Weidman, J., White, O., Woodward, J., Yu, J.H.,
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Fraser, C., Galagan, J.E., Asai, K., Machida, M., Hall, N., Barrell, B., Denning, D.W., 2005. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438, 1151-1156. 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. Journal of bacteriology 187, 6488-6498. Haft, D.H., Selengut, J.D., Brinkac, L.M., Zafar, N., White, O., 2005. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (Oxford, England) 21, 293-306. Haas, B.J., Wortman, J.R., Ronning, C.M., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Chan, A.P., Yu, C., Farzad, M., Wu, D., White, O., Town, C.D., 2005. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC biology 3, 7. Gardner, M.J., Bishop, R., Shah, T., de Villiers, E.P., Carlton, J.M., Hall, N., Ren, Q., Paulsen, I.T., Pain, A., Berriman, M., Wilson, R.J., Sato, S., Ralph, S.A., Mann, D.J., Xiong, Z., Shallom, 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., Suh, B., Silva, J.C., Utterback, T.R., Feldblyum, T.V., Pertea, M., Allen, 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., 2005. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309, 134-137. El-Sayed, N.M., Myler, P.J., Blandin, G., Berriman, M., Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E.A., Hertz-Fowler, C., Ghedin, E., Peacock, C., Bartholomeu, D.C., Haas, B.J., Tran, A.N., Wortman, J.R., Alsmark, U.C., Angiuoli, S., Anupama, A., Badger, J., Bringaud, F., Cadag, E., Carlton, J.M., Cerqueira, G.C., Creasy, T., Delcher, A.L., Djikeng, A., Embley, T.M., Hauser, C., Ivens, A.C., Kummerfeld, S.K., Pereira-Leal, J.B., Nilsson, D., Peterson, J., Salzberg, S.L., Shallom, J., Silva, J.C., Sundaram, J., Westenberger, S., White, O., Melville, S.E., Donelson, J.E., Andersson, B., Stuart, K.D., Hall, N., 2005a. Comparative genomics of trypanosomatid parasitic protozoa. Science 309, 404-409. El-Sayed, N.M., Myler, P.J., Bartholomeu, D.C., Nilsson, D., Aggarwal, G., Tran, A.N., Ghedin, E., Worthey, E.A., Delcher, A.L., Blandin, G., Westenberger, S.J.,
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Caler, E., Cerqueira, G.C., Branche, C., Haas, B., Anupama, A., Arner, E., Aslund, L., Attipoe, P., Bontempi, E., Bringaud, F., Burton, P., Cadag, 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., Osoegawa, K., Pai, G., Parsons, M., Pentony, M., Pettersson, U., Pop, M., Ramirez, J.L., Rinta, J., Robertson, L., Salzberg, S.L., Sanchez, D.O., Seyler, A., Sharma, R., Shetty, J., 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., 2005b. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309, 409-415. Buell, C.R., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Maiti, R., Haas, B., Wortman, J., Pertea, M., Jones, K.M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S., Johri, S., Reardon, M., Webb, K., Hill, J., Moffat, K., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A.R., Salzberg, S.L., White, O., Fraser, C., Yu, Y., Kim, H., Rambo, T., Currie, J., Collura, K., Kernodle-Thompson, S., Wei, F., Kudrna, K., Ammiraju, J.S., Luo, M., Goicoechea, J.L., Wing, R.A., Henry, D., Oates, R., Palmer, M., Pries, G., Saski, C., Simmons, J., Soderlund, C., Nelson, W., de la Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'Shaughnessy, A., Dike, S., McCombie, W.R., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H.R., Jiang, J., Jackson, S., 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome research 15, 1284-1291. Ayele, M., Haas, B.J., Kumar, N., Wu, H., Xiao, Y., Van Aken, S., Utterback, T.R., Wortman, J.R., White, O.R., Town, C.D., 2005. Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome research 15, 487-495. 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
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in the Burkholderia mallei genome. Proceedings of the National Academy of Sciences of the United States of America 101, 14246-14251. 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 research 32, 2386-2395. Wortman, J.R., Haas, B.J., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Ronning, C.M., Chan, A.P., Yu, C., Ayele, M., Whitelaw, C.A., White, O.R., Town, C.D., 2003. Annotation of the Arabidopsis genome. Plant physiology 132, 461-468. 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., 2003a. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423, 81-86. 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., 2003b. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic acids research 31, 2134-2147. Methe, B.A., Nelson, K.E., Eisen, J.A., Paulsen, I.T., Nelson, W., 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 302, 1967-1969.
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Haft, D.H., Selengut, J.D., White, O., 2003. The TIGRFAMs database of protein families. Nucleic acids research 31, 371-373. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L., White, O., 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic acids research 31, 5654-5666. El-Sayed, N.M., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., Wanless, D., Peterson, J., Hou, L., Taylor, S., Tweedie, A., Biteau, N., Khalak, H.G., Lin, X., Mason, T., Hannick, L., Caler, E., Blandin, G., Bartholomeu, D., Simpson, A.J., Kaul, S., Zhao, H., Pai, G., Van Aken, S., Utterback, T., Haas, B., Koo, H.L., Umayam, L., Suh, B., Gerrard, C., Leech, V., Qi, R., Zhou, S., Schwartz, D., Feldblyum, T., Salzberg, S., Tait, A., Turner, C.M., Ullu, E., White, O., Melville, S., Adams, M.D., Fraser, C.M., Donelson, J.E., 2003. The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic acids research 31, 4856-4863. 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. Proceedings of the National Academy of Sciences of the United States of America 100, 10181-10186. 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. Proceedings of the National Academy of Sciences of the United States of America 99, 13148-13153. 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., 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
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metabolically versatile Pseudomonas putida KT2440. Environmental microbiology 4, 799-808. 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. Nature biotechnology 20, 1118-1123. Haas, B.J., Volfovsky, N., Town, C.D., Troukhan, M., Alexandrov, N., Feldmann, K.A., Flavell, R.B., White, O., Salzberg, S.L., 2002. Full-length messenger RNA sequences greatly improve genome annotation. Genome biology 3, RESEARCH0029. Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., Salzberg, S.L., Craig, A., Kyes, S., Chan, M.S., Nene, V., Shallom, S.J., Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., Haft, D., Mather, M.W., Vaidya, A.B., Martin, D.M., Fairlamb, A.H., Fraunholz, M.J., Roos, D.S., Ralph, S.A., McFadden, G.I., Cummings, L.M., Subramanian, G.M., Mungall, C., Venter, J.C., Carucci, D.J., Hoffman, S.L., Newbold, C., Davis, R.W., Fraser, C.M., Barrell, B., 2002a. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511. Gardner, M.J., Shallom, S.J., Carlton, J.M., Salzberg, S.L., Nene, V., Shoaibi, A., Ciecko, A., Lynn, J., Rizzo, M., Weaver, B., Jarrahi, B., Brenner, M., Parvizi, B., Tallon, L., Moazzez, A., Granger, D., Fujii, C., Hansen, C., Pederson, J., Feldblyum, T., Peterson, J., Suh, B., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., White, O., Cummings, L.M., Smith, H.O., Adams, M.D., Venter, J.C., Carucci, D.J., Hoffman, S.L., Fraser, C.M., 2002b. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419, 531-534. 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., Jr., Venter, J.C., Fraser, C.M., 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. Journal of bacteriology 184, 5479-5490.
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