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2007

Multidimensional annotation of the Escherichia coli K-12 genome

Karp, P. D., Keseler, I. M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S. M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spínola, M. I., Bonavides-martinez, C. & Ingraham, J., Dec 2007, In : Nucleic Acids Research. 35, 22, p. 7577-7590 14 p.

Research output: Contribution to journalArticle

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132 Citations (Scopus)
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The Chlamydomonas genome reveals the evolution of key animal and plant functions

Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., Terry, A., Salamov, A., Fritz-Laylin, L. K., Maréchal-Drouard, L., Marshall, W. F., Qu, L. H., Nelson, D. R., Sanderfoot, A. A., Spalding, M. H., Kapitonov, V. V., Ren, Q., Ferris, P., Lindquist, E., Shapiro, H. & 97 others, Lucas, S. M., Grimwood, J., Schmutz, J., Grigoriev, I. V., Rokhsar, D. S., Grossman, A. R., Cardol, P., Cerutti, H., Chanfreau, G., Chen, C. L., Cognat, V., Croft, M. T., Dent, R., Dutcher, S., Fernández, E., Fukuzawa, H., González-Ballester, D., González-Halphen, D., Hallmann, A., Hanikenne, M., Hippler, M., Inwood, W., Jabbari, K., Kalanon, M., Kuras, R., Lefebvre, P. A., Lemaire, S. D., Lobanov, A. V., Lohr, M., Manuell, A., Meier, I., Mets, L., Mittag, M., Mittelmeier, T., Moroney, J. V., Moseley, J., Napoli, C., Nedelcu, A. M., Niyogi, K., Novoselov, S. V., Paulsen, I. T., Pazour, G., Purton, S., Ral, J. P., Riaño-Pachón, D. M., Riekhof, W., Rymarquis, L., Schroda, M., Stern, D., Umen, J., Willows, R., Wilson, N., Zimmer, S. L., Allmer, J., Balk, J., Bisova, K., Chen, C. J., Elias, M., Gendler, K., Hauser, C., Lamb, M. R., Ledford, H., Long, J. C., Minagawa, J., Page, M. D., Pan, J., Pootakham, W., Roje, S., Rose, A., Stahlberg, E., Terauchi, A. M., Yang, P., Ball, S., Bowler, C., Dieckmann, C. L., Gladyshev, V. N., Green, P., Jorgensen, R., Mayfield, S., Mueller-Roeber, B., Rajamani, S., Sayre, R. T., Brokstein, P., Dubchak, I., Goodstein, D., Hornick, L., Huang, Y. W., Jhaveri, J., Luo, Y., Martínez, D., Ngau, W. C. A., Otillar, B., Poliakov, A., Porter, A., Szajkowski, L., Werner, G. & Zhou, K., 12 Oct 2007, In : Science. 318, 5848, p. 245-251 7 p.

Research output: Contribution to journalArticle

1597 Citations (Scopus)

The genomic sequence of Pseudomonas fluorescens Pf-5: insights into biological control

Loper, J. E., Kobayashi, D. Y. & Paulsen, I. T., Feb 2007, In : Phytopathology. 97, 2, p. 233-238 6 p.

Research output: Contribution to journalArticle

79 Citations (Scopus)

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Palenik, B., Grimwood, J., Aerts, A., Rouzé, P., Salamov, A., Putnam, N., Dupont, C., Jorgensen, R., Derelle, E., Rombauts, S., Zhou, K., Otillar, R., Merchant, S. S., Podell, S., Gaasterland, T., Napoli, C., Gendler, K., Manuell, A., Tai, V., Vallon, O. & 18 others, Piganeau, G., Jancek, S., Heijde, M., Jabbari, K., Bowler, C., Lohr, M., Robbens, S., Werner, G., Dubchak, I., Pazour, G. J., Ren, Q., Paulsen, I., Delwiche, C., Schmutz, J., Rokhsar, D., Van De Peer, Y., Moreau, H. & Grigoriev, I. V., 1 May 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 18, p. 7705-7710 6 p.

Research output: Contribution to journalArticle

404 Citations (Scopus)

TransportDB: A comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels

Ren, Q., Chen, K. & Paulsen, I. T., Jan 2007, In : Nucleic Acids Research. 35, SUPPL. 1, p. D274-D279 6 p.

Research output: Contribution to journalArticle

259 Citations (Scopus)
2006

Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

Khan, A., Böhme, U., Kelly, K. A., Adlem, E., Brooks, K., Simmonds, M., Mungall, K., Quail, M. A., Arrowsmith, C., Chillingworth, T., Churcher, C., Harris, D., Collins, M., Fosker, N., Fraser, A., Hance, Z., Jagels, K., Moule, S., Murphy, L., O'Neil, S. & 19 others, Rajandream, M. A., Saunders, D., Seeger, K., Whitehead, S., Mayr, T., Xuan, X., Watanabe, J., Suzuki, Y., Wakaguri, H., Sugano, S., Sugimoto, C., Paulsen, I., Mackey, A. J., Roos, D. S., Hall, N., Berriman, M., Barrell, B., Sibley, L. D. & Ajioka, J. W., 2006, In : Genome Research. 16, 9, p. 1119-1125 7 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

Badger, J. H., Hoover, T. R., Brun, Y. V., Weiner, R. M., Laub, M. T., Alexandre, G., Mrázek, J., Ren, Q., Paulsen, I. T., Nelson, K. E., Khouri, H. M., Radune, D., Sosa, J., Dodson, R. J., Sullivan, S. A., Rosovitz, M. J., Madupu, R., Brinkac, L. M., Durkin, A. S., Daugherty, S. C. & 9 others, Kothari, S. P., Giglio, M. G., Zhou, L., Haft, D. H., Selengut, J. D., Davidsen, T. M., Yang, Q., Zafar, N. & Ward, N. L., Oct 2006, In : Journal of Bacteriology. 188, 19, p. 6841-6850 10 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102

Su, Z., Mao, F., Dam, P., Wu, H., Olman, V., Paulsen, I. T., Palenik, B. & Xu, Y., 2006, In : Nucleic Acids Research. 34, 3, p. 1050-1065 16 p.

Research output: Contribution to journalArticle

49 Citations (Scopus)

Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/SpsH system. Application of a novel phylogenetic profiling heuristic

Haft, D. H., Paulsen, I. T., Ward, N. & Selengut, J. D., 24 Aug 2006, In : BMC Biology. 4, p. 1-16 16 p., 29.

Research output: Contribution to journalArticle

48 Citations (Scopus)

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment

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., 5 Sep 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 36, p. 13555-13559 5 p.

Research output: Contribution to journalArticle

174 Citations (Scopus)

Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii

Boyle, J. P., Rajasekar, B., Saeij, J. P. J., Ajioka, J. W., Berriman, M., Paulsen, I., Roos, D. S., Sibley, L. D., White, M. W. & Boothroyd, J. C., 4 Jul 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 27, p. 10514-10519 6 p.

Research output: Contribution to journalArticle

98 Citations (Scopus)

Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus

Parker, D., Kennan, R. M., Myers, G. S., Paulsen, I. T., Songer, J. G. & Rood, J. I., Jul 2006, In : Journal of Bacteriology. 188, 13, p. 4801-4811 11 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens

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. & 14 others, 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, In : Genome Research. 16, 8, p. 1031-1040 10 p.

Research output: Contribution to journalArticle

184 Citations (Scopus)

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

Scott, K. M., Sievert, S. M., Abril, F. N., Ball, L. A., Barrett, C. J., Blake, R. A., Boller, A. J., Chain, P. S. G., Clark, J. A., Davis, C. R., Detter, C., Do, K. F., Dobrinski, K. P., Faza, B. I., Fitzpatrick, K. A., Freyermuth, S. K., Harmer, T. L., Hauser, L. J., Hügler, M., Kerfeld, C. A. & 23 others, Klotz, M. G., Kong, W. W., Land, M., Lapidus, A., Larimer, F. W., Longo, D. L., Lucas, S., Malfatti, S. A., Massey, S. E., Martin, D. D., McCuddin, Z., Meyer, F., Moore, J. L., Ocampo, L. H., Paul, J. H., Paulsen, I. T., Reep, D. K., Ren, Q., Ross, R. L., Sato, P. Y., Thomas, P., Tinkham, L. E. & Zeruth, G. T., Nov 2006, In : PLoS Biology. 4, 12, p. 2196-2212 17 p.

Research output: Contribution to journalArticle

94 Citations (Scopus)
2005

Cloning, expression, and purification of Brucella suis outer membrane proteins

Ding, X. Z., Bhattacharjee, A., Nikolich, M. P., Paulsen, I. T., Myers, G., Seshadri, R. & Hoover, D. L., Mar 2005, In : Protein Expression and Purification. 40, 1, p. 134-141 8 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
93 Citations (Scopus)

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Paulsen, I. T., Press, C. M., 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., Schneider, D. J., Cartinhour, S. W. & 9 others, Nelson, W. C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E. A., Pierson, L. S., Thomashow, L. S. & Loper, J. E., 2005, In : Nature Biotechnology. 23, 7, p. 873-878 6 p.

Research output: Contribution to journalArticle

410 Citations (Scopus)

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

Khan, A., Taylor, S., Su, C., Mackey, A. J., Boyle, J., Cole, R., Glover, D., Tang, K., Paulsen, I. T., Berriman, M., Boothroyd, J. C., Pfefferkorn, E. R., Dubey, J. P., Ajioka, J. W., Roos, D. S., Wootton, J. C. & Sibley, L. D., 2005, In : Nucleic Acids Research. 33, 9, p. 2980-2992 13 p.

Research output: Contribution to journalArticle

124 Citations (Scopus)

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., Peralta-Gil, M. & Karp, P. D., 1 Jan 2005, In : Nucleic Acids Research. 33, DATABASE ISS., p. D334-D337 4 p.

Research output: Contribution to journalArticle

524 Citations (Scopus)

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes

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. M., Sato, S., Ralph, S. A., Mann, D. J., Xiong, Z., Shallom, S. J., Weidman, J., Jiang, L., Lynn, J., Weaver, B. & 24 others, 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. N., Salzberg, S. L., White, O. R., Fitzhugh, H. A., Morzaria, S., Venter, J. C., Fraser, C. M. & Nene, V., 1 Jul 2005, In : Science. 309, 5731, p. 134-137 4 p.

Research output: Contribution to journalArticle

238 Citations (Scopus)

Genome sequencing and analysis of Aspergillus oryzae

Machida, M., Asai, K., Sano, M., Tanaka, T., Kumagai, T., Terai, G., Kusumoto, K. I., Arima, T., Akita, O., Kashiwagi, Y., Abe, K., Gomi, K., Horiuchi, H., Kitamoto, K., Kobayashi, T., Takeuchi, M., Denning, D. W., Galagan, J. E., Nierman, W. C., Yu, J. & 44 others, Archer, D. B., Bennett, J. W., Bhatnagar, D., Cleveland, T. E., Fedorova, N. D., Gotoh, O., Horikawa, H., Hosoyama, A., Ichinomiya, M., Igarashi, R., Iwashita, K., Juvvadi, P. R., Kato, M., Kato, Y., Kin, T., Kokubun, A., Maeda, H., Maeyama, N., Maruyama, J. I., Nagasaki, H., Nakajima, T., Oda, K., Okada, K., Paulsen, I., Sakamoto, K., Sawano, T., Takahashi, M., Takase, K., Terabayashi, Y., Wortman, J. R., Yamada, O., Yamagata, Y., Anazawa, H., Hata, Y., Koide, Y., Komori, T., Koyama, Y., Minetoki, T., Suharnan, S., Tanaka, A., Isono, K., Kuhara, S., Ogasawara, N. & Kikuchi, H., 22 Dec 2005, In : Nature. 438, 7071, p. 1157-1161 5 p.

Research output: Contribution to journalArticle

817 Citations (Scopus)

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

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. & 78 others, Feldblyum, T. V., Fischer, R., Fosker, N., Fraser, A., García, J. L., García, 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., Jiménez, J., Keller, N., Khouri, H., Kitamoto, K., Kobayashi, T., Konzack, S., Kulkarni, R., Kumagai, T., Lafon, A., Latgé, 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., Peñalva, 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., Rodríguez-Peña, J. M., Ronning, C. M., Rutter, S., Salzberg, S. L., Sanchez, M., Sánchez-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., Fraser, C., Galagan, J. E., Asai, K., Machida, M., Hall, N., Barrell, B. & Denning, D. W., 22 Dec 2005, In : Nature. 438, 7071, p. 1151-1156 6 p.

Research output: Contribution to journalArticle

902 Citations (Scopus)

Identification of a Dichelobacter nodosus ferric uptake regulator and determination of its regulatory targets

Parker, D., Kennan, R. M., Myers, G. S., Paulsen, I. T. & Rood, J. I., Jan 2005, In : Journal of Bacteriology. 187, 1, p. 366-375 10 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain

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. & 9 others, Dimitrov, G., Jiang, L., Qin, H., Weidman, J., Tran, K., Kang, K., Hance, I. R., Nelson, K. E. & Fraser, C. M., Apr 2005, In : Journal of Bacteriology. 187, 7, p. 2426-2438 13 p.

Research output: Contribution to journalArticle

667 Citations (Scopus)

Reciprocal regulation of pyoluteorin production with membrane transporter gene expression in Pseudomonas fluorescens Pf-5

Brodhagen, M., Paulsen, I. & Loper, J. E., Nov 2005, In : Applied and Environmental Microbiology. 71, 11, p. 6900-6909 10 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

The ergosterol biosynthesis pathway, transporter genes, and azole resistance in Aspergillus fumigatus

Da Silva Ferreira, M. E., Colombo, A. L., Paulsen, I., Ren, Q., Wortman, J., Huang, J., Goldman, M. H. S. & Goldman, G. H., 2005, In : Medical Mycology. 43, SUPPL.1, p. S313-S319 7 p.

Research output: Contribution to journalArticle

99 Citations (Scopus)
2004

Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes

Seshadri, R., Myers, G. S. A., Tettelin, H., Eisen, J. A., Heidelberg, 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., Kolonay, J., Durkin, S. A., Daugherty, S. C., Shetty, J., Shvartsbeyn, A., Gebregeorgis, E. & 19 others, Geer, K., Tsegaye, G., Malek, J., Ayodeji, B., Shatsman, S., McLeod, M. P., Šmajs, D., Howell, J. K., Pal, S., Amin, A., Vashisth, P., McNeill, T. Z., Xiang, Q., Sodergren, E., Baca, E., Weinstock, G. M., Norris, S. J., Fraser, C. M. & Paulsen, I. T., 13 Apr 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, 15, p. 5646-5651 6 p.

Research output: Contribution to journalArticle

174 Citations (Scopus)

Environmental Genome Shotgun Sequencing of the Sargasso Sea

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. & 3 others, Pfannkoch, C., Rogers, Y. H. & Smith, H. O., 2 Apr 2004, In : Science. 304, 5667, p. 66-74 9 p.

Research output: Contribution to journalArticle

2766 Citations (Scopus)

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Moran, M. A., Buchan, A., González, J. M., Heidelberg, J. F., Whitman, W. B., Klene, R. P., Henriksen, J. R., King, G. M., Belas, R., Fuqua, C., Brinkac, L., Lewis, M., Johri, S., Weaver, B., Pai, G., Elsen, J. A., Rahe, E., Sheldon, W. M., Ye, W., Miller, T. R. & 15 others, 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., 16 Dec 2004, In : Nature. 432, 7019, p. 910-913 4 p.

Research output: Contribution to journalArticle

313 Citations (Scopus)

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Ward, N., Larsen, Ø., Sakwa, J., Bruseth, L., Khouri, H., Durkin, A. S., Dimitrov, G., Jiang, L., Scanlan, D., Kang, K. H., Lewis, M., Nelson, K. E., Methé, B., Wu, M., Heidelberg, J. F., Paulsen, I. T., Fouts, D., Ravel, J., Tettelin, H., Ren, Q. & 18 others, 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., Oct 2004, In : PLoS Biology. 2, 10, p. 1616-1628 13 p.

Research output: Contribution to journalArticle

219 Citations (Scopus)

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements

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. & 10 others, 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, In : PLoS Biology. 2, 3, p. 0327-0341 15 p.

Research output: Contribution to journalArticle

528 Citations (Scopus)

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

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. & 15 others, 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., May 2004, In : Nature Biotechnology. 22, 5, p. 554-559 6 p.

Research output: Contribution to journalArticle

392 Citations (Scopus)

TransportDB: a relational database of cellular membrane transport systems

Ren, Q., Kang, K. H. & Paulsen, I. T., 1 Jan 2004, In : Nucleic Acids Research. 32, Database issue, p. D284-D288 5 p.

Research output: Contribution to journalArticle

160 Citations (Scopus)

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

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. & 13 others, 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, In : Nucleic Acids Research. 32, 8, p. 2386-2395 10 p.

Research output: Contribution to journalArticle

336 Citations (Scopus)
2003

Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage

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., Sep 2003, In : Journal of Bacteriology. 185, 17, p. 5220-5233 14 p.

Research output: Contribution to journalArticle

169 Citations (Scopus)

Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83

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. & 3 others, Duncan, M. J., Dewhirst, F. E. & Fraser, C. M., Sep 2003, In : Journal of Bacteriology. 185, 18, p. 5591-5601 11 p.

Research output: Contribution to journalArticle

279 Citations (Scopus)

Complete genome sequence of the Q-fever pathogen Coxiella burnetii

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. & 4 others, Thompson, H. A., Samuel, J. E., Fraser, C. M. & Heidelberg, J. F., 29 Apr 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 9, p. 5455-5460 6 p.

Research output: Contribution to journalArticle

371 Citations (Scopus)

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

Methé, 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. & 15 others, Selengut, J., Davidsen, T. M., Zafar, N., White, O., Tran, B., Romero, C., Forberger, H. A., Weidman, J., Khouri, H., Khouri, H., Feldblyum, T. V., Utterback, T. R., Van Aken, S. E., Lovley, D. R. & Fraser, C. M., 12 Dec 2003, In : Science. 302, 5652, p. 1967-1969 3 p.

Research output: Contribution to journalArticle

501 Citations (Scopus)

Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae

Read, T. D., Myers, G. S. A., 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. & 1 others, Fraser, C. M., 15 Apr 2003, In : Nucleic Acids Research. 31, 8, p. 2134-2147 14 p.

Research output: Contribution to journalArticle

231 Citations (Scopus)

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis

Paulsen, I. T., Banerjei, L., Hyers, G. S. A., 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. & 12 others, Nelson, W., Vamathevan, J., Tran, B., Upton, J., Hansen, T., Shetty, J., Khouri, H., Utterback, T., Radune, D., Ketchum, K. A., Dougherty, B. A. & Fraser, C. M., 28 Mar 2003, In : Science. 299, 5615, p. 2071-2074 4 p.

Research output: Contribution to journalArticle

612 Citations (Scopus)

The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

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. & 24 others, 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., 2 Sep 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 18, p. 10181-10186 6 p.

Research output: Contribution to journalArticle

563 Citations (Scopus)

The genome of a motile marine Synechococcus

Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P., Lamerdin, J., Regala, W., Allen, E. E., McCarren, J., Paulsen, I., Dufresne, A., Partensky, F., Webb, E. A. & Waterbury, J., 28 Aug 2003, In : Nature. 424, 6952, p. 1037-1042 6 p.

Research output: Contribution to journalArticle

476 Citations (Scopus)

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

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., Økstad, O. A., Helgason, E., Rilstone, J., Wu, M., Kolonay, J. F., Beanan, M. J., Dodson, R. J., Brinkac, L. M., Gwinn, M. & 32 others, 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., Kolstø, A. B. & Fraser, C. M., 2003, In : Nature. 423, 6935, p. 81-86 6 p.

Research output: Contribution to journalArticle

606 Citations (Scopus)

The genome sequence of the filamentous fungus Neurospora crassa

Galagan, J. E., Calvo, S. E., Borkovich, K. A., Selker, E. U., Read, N. O., Jaffe, D., FitzHugh, W., Ma, L. J., Smirnov, S., Purcell, S., Rehman, B., Elkins, T., Engels, R., Wang, S., Nielsen, C. B., Butler, J., Endrizzi, M., Qui, D., Ianakiev, P., Bell-Pedersen, D. & 57 others, Nelson, M. A., Werner-Washburne, M., Selitrennikoff, C. P., Kinsey, J. A., Braun, E. L., Zelter, A., Schulte, U., Kothe, G. O., Jedd, G., Mewes, W., Staben, C., Marcotte, E., Greenberg, D., Roy, A., Foley, K., Naylor, J., Stange-Thomann, N., Barrett, R., Gnerre, S., Kamal, M., Kamvysselis, M., Mauceli, E., Bielke, C., Rudd, S., Frishman, D., Krystofova, S., Rasmussen, C., Metzenberg, R. L., Perkins, D. D., Kroken, S., Cogoni, C., Macino, G., Catcheside, D., Li, W., Pratt, R. J., Osmani, S. A., DeSouza, C. P. C., Glass, L., Orbach, M. J., Berglund, J. A., Voelker, R., Yarden, O., Plamann, M., Seiler, S., Dunlap, J., Radford, A., Aramayo, R., Natvig, D. O., Alex, L. A., Mannhaupt, G., Ebbole, D. J., Freitag, M., Paulsen, I., Sachs, M. S., Lander, E. S., Nusbaum, C. & Birren, B., 24 Apr 2003, In : Nature. 422, 6934, p. 859-868 10 p.

Research output: Contribution to journalArticle

1110 Citations (Scopus)
2002

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

Nelson, K. E., Weinel, C., Paulsen, I. T., Dodson, R. J., Hilbert, H., Martins dos Santos, V. A. P., 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. & 23 others, 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., Timmis, K. N., Düsterhöft, A., Tümmler, B. & Fraser, C. M., 1 Dec 2002, In : Environmental microbiology. 4, 12, p. 799-808 10 p.

Research output: Contribution to journalArticle

889 Citations (Scopus)

Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae

Tettelin, H., Masignani, V., Cieslewicz, M. J., Eisen, J. A., Peterson, S., Wessels, M. R., Paulsen, I. T., Nelson, K. E., Margarit, I., Read, T. D., Madoff, L. C., Wolf, A. M., Beanan, M. J., Brinkac, L. M., Daugherty, S. C., DeBoy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Lewis, M. R. & 23 others, Radune, D., Fedorova, N. B., Scanlan, D., Khouri, H., Mulligan, S., Carty, H. A., Cline, R. T., Van Aken, S. E., Gill, J., Scarselli, M., Mora, M., Iacobini, E. T., Brettoni, C., Galli, G., Mariani, M., Vegni, F., Maione, D., Rinaudo, D., Rappuoli, R., Telford, J. L., Kasper, D. L., Grandi, G. & Fraser, C. M., 17 Sep 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 19, p. 12391-12396 6 p.

Research output: Contribution to journalArticle

356 Citations (Scopus)

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis

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. & 23 others, 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, In : Nature Biotechnology. 20, 11, p. 1118-1123 6 p.

Research output: Contribution to journalArticle

571 Citations (Scopus)

Genome sequence of the human malaria parasite Plasmodium falciparum

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. & 24 others, Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., Haft, D., Mather, M. W., Vaidya, A. B., Martin, D. M. A., 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., Davis, R. W., Fraser, C. M. & Barrell, B., 2002, In : Nature. 419, 6906, p. 498-511 14 p.

Research output: Contribution to journalArticle

3031 Citations (Scopus)

Regulation of carbon utilization by sulfur availability in Escherichia coli and Salmonella typhimurium

Quan, J. A., Schneider, B. L., Paulsen, I. T., Yamada, M., Kredich, N. M. & Saier, M. H., 2002, In : Microbiology. 148, 1, p. 123-131 9 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts

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. & 11 others, 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., 1 Oct 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 20, p. 13148-13153 6 p.

Research output: Contribution to journalArticle

338 Citations (Scopus)