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Author

  • Gary J Olsen
2017

Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center

Wattam, A. R., Davis, J. J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., Conrad, N., Dietrich, E. M., Disz, T., Gabbard, J. L., Gerdes, S., Henry, C. S., Kenyon, R. W., Machi, D., Mao, C., Nordberg, E. K., Olsen, G. J., Murphy-Olson, D. E., Olson, R., Overbeek, R. & 8 others, Parrello, B., Pusch, G. D., Shukla, M., Vonstein, V., Warren, A., Xia, F., Yoo, H. & Stevens, R. L., Jan 1 2017, In : Nucleic acids research. 45, D1, p. D535-D542

Research output: Contribution to journalArticle

2015

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomason, J. A., Stevens, R., Vonstein, V., Wattam, A. R. & Xia, F., Feb 10 2015, In : Scientific reports. 5, 8365.

Research output: Contribution to journalArticle

2014

Quorum-dependent mannopine-inducible conjugative transfer of an agrobacterium opine-catabolic plasmid

Wetzel, M. E., Kim, K. S., Miller, M., Olsen, G. J. & Farrand, S. K., Mar 1 2014, In : Journal of bacteriology. 196, 5, p. 1031-1044 14 p.

Research output: Contribution to journalArticle

2018

PATRIC as a unique resource for studying antimicrobial resistance

Antonopoulos, D. A., Assaf, R., Aziz, R. K., Brettin, T., Bun, C., Conrad, N., Davis, J. J., Dietrich, E. M., Disz, T., Gerdes, S., Kenyon, R. W., Machi, D., Mao, C., Murphy-Olson, D. E., Nordberg, E. K., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D. & 9 others, Santerre, J., Shukla, M., Stevens, R. L., Vanoeffelen, M., Vonstein, V., Warren, A. S., Wattam, A. R., Xia, F. & Yoo, H., Mar 27 2018, In : Briefings in bioinformatics. 20, 4, p. 1094-1102 9 p.

Research output: Contribution to journalArticle

Open Access
2016

PATtyFams: Protein families for the microbial genomes in the PATRIC database

Davis, J. J., Gerdes, S., Olsen, G. J., Olson, R., Pusch, G. D., Shukla, M., Vonstein, V., Wattam, A. R. & Yoo, H., Feb 8 2016, In : Frontiers in Microbiology. 7, FEB, 118.

Research output: Contribution to journalArticle

2013

Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes

Davis, J. J., Xia, F., Overbeek, R. A. & Olsen, G. J., Jul 1 2013, In : International Journal of Systematic and Evolutionary Microbiology. 63, PART7, p. 2727-2741 15 p.

Research output: Contribution to journalArticle

2020

The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities

Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R., Butler, R. M., Chlenski, P., Conrad, N., Dickerman, A., Dietrich, E. M., Gabbard, J. L., Gerdes, S., Guard, A., Kenyon, R. W., MacHi, D., Mao, C., Murphy-Olson, D., Nguyen, M., Nordberg, E. K., Olsen, G. J. & 14 others, Olson, R. D., Overbeek, J. C., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomas, C., Vanoeffelen, M., Vonstein, V., Warren, A. S., Xia, F., Xie, D., Yoo, H. & Stevens, R., Jan 1 2020, In : Nucleic acids research. 48, D1, p. D606-D612

Research output: Contribution to journalArticle

Open Access
2018

The essential genome of the crenarchaeal model Sulfolobus islandicus

Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J. & Whitaker, R. J., Dec 1 2018, In : Nature communications. 9, 1, 4908.

Research output: Contribution to journalArticle

2013

Parsimony

Olsen, G. J., Feb 27 2013, Brenner's Encyclopedia of Genetics: Second Edition. Elsevier Inc., p. 229-232 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2014

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F. & Stevens, R., Jan 1 2014, In : Nucleic acids research. 42, D1, p. D206-D214

Research output: Contribution to journalArticle

2011

Differences between the normal vaginal bacterial community of baboons and that of humans

Rivera, A. J., Frank, J. A., Stumpf, R., Salyers, A. A., Wilson, B. A., Olsen, G. J. & Leigh, S., Feb 1 2011, In : American journal of primatology. 73, 2, p. 119-126 8 p.

Research output: Contribution to journalArticle

2015

The repABC plasmids with quorum-regulated transfer systems in members of the rhizobiales divide into two structurally and separately evolving groups

Wetzel, M. E., Olsen, G. J., Chakravartty, V. & Farrand, S. K., Jan 1 2015, In : Genome biology and evolution. 7, 12, p. 3337-3357 21 p.

Research output: Contribution to journalArticle

2011

Characterizing the native codon usages of a genome: An axis projection approach

Davis, J. J. & Olsen, G. J., Jan 1 2011, In : Molecular biology and evolution. 28, 1, p. 211-221 11 p.

Research output: Contribution to journalArticle

2015

Genomic comparison of the closely-related Salmonella enterica serovars Enteritidis, Dublin and Gallinarum

Matthews, T. D., Schmieder, R., Silva, G. G. Z., Busch, J., Cassman, N., Dutilh, B. E., Green, D., Matlock, B., Heffernan, B., Olsen, G. J., Hanna, L. F., Schifferli, D. M., Maloy, S., Dinsdale, E. A. & Edwards, R. A., Jun 3 2015, In : PloS one. 10, 6, e0126883.

Research output: Contribution to journalArticle

2011
2018

KBase: The United States department of energy systems biology knowledgebase

Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., Dehal, P., Ware, D., Perez, F., Canon, S., Sneddon, M. W., Henderson, M. L., Riehl, W. J., Murphy-Olson, D., Chan, S. Y., Kamimura, R. T., Kumari, S., Drake, M. M., Brettin, T. S., Glass, E. M. & 61 others, Chivian, D., Gunter, D., Weston, D. J., Allen, B. H., Baumohl, J., Best, A. A., Bowen, B., Brenner, S. E., Bun, C. C., Chandonia, J. M., Chia, J. M., Colasanti, R., Conrad, N., Davis, J. J., Davison, B. H., Dejongh, M., Devoid, S., Dietrich, E., Dubchak, I., Edirisinghe, J. N., Fang, G., Faria, J. P., Frybarger, P. M., Gerlach, W., Gerstein, M., Greiner, A., Gurtowski, J., Haun, H. L., He, F., Jain, R., Joachimiak, M. P., Keegan, K. P., Kondo, S., Kumar, V., Land, M. L., Meyer, F., Mills, M., Novichkov, P. S., Oh, T., Olsen, G. J., Olson, R., Parrello, B., Pasternak, S., Pearson, E., Poon, S. S., Price, G. A., Ramakrishnan, S., Ranjan, P., Ronald, P. C., Schatz, M. C., Seaver, S. M. D., Shukla, M., Sutormin, R. A., Syed, M. H., Thomason, J., Tintle, N. L., Wang, D., Xia, F., Yoo, H., Yoo, S. & Yu, D., Jul 6 2018, In : Nature Biotechnology. 36, 7, p. 566-569 4 p.

Research output: Contribution to journalLetter