1982 …2018

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Article
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

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

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

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

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

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

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

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

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

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

2012

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

Aziz, R. K., Devoid, S., Disz, T., Edwards, R. A., Henry, C. S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Stevens, R. L., Vonstein, V. & Xia, F., Oct 24 2012, In : PloS one. 7, 10, e48053.

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

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

2010

Evolution of DNA replication protein complexes in Eukaryotes and Archaea

Chia, N., Cann, I. & Olsen, G. J., Aug 9 2010, In : PloS one. 5, 6, e10866.

Research output: Contribution to journalArticle

2009

Heterogeneity of vaginal microbial communities within individuals

Kim, T. K., Thomas, S. M., Ho, M., Sharma, S., Reich, C. I., Frank, J. A., Yeater, K. M., Biggs, D. R., Nakamura, N., Stumpf, R., Leigh, S. R., Tapping, R. I., Blanke, S. R., Slauch, J. M., Gaskins, H. R., Weisbaum, J. S., Olsen, G. J., Hoyer, L. L. & Wilson, B. A., Apr 1 2009, In : Journal of Clinical Microbiology. 47, 4, p. 1181-1189 9 p.

Research output: Contribution to journalArticle

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii

Zhang, J. & Olsen, G. J., Oct 1 2009, In : RNA. 15, 10, p. 1909-1916 8 p.

Research output: Contribution to journalArticle

Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii

Zhang, J., Li, E. & Olsen, G. J., Jul 10 2009, In : Nucleic acids research. 37, 11, p. 3588-3601 14 p.

Research output: Contribution to journalArticle

2008

A whole-genome approach to identifying protein binding sites: Promoters in Methanocaldococcus (Methanococcus) jannaschii

Li, E., Reich, C. I. & Olsen, G. J., Dec 1 2008, In : Nucleic acids research. 36, 22, p. 6948-6958 11 p.

Research output: Contribution to journalArticle

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes

Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A. & Olsen, G. J., Apr 1 2008, In : Applied and environmental microbiology. 74, 8, p. 2461-2470 10 p.

Research output: Contribution to journalArticle

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction

Anderson, I., Rodriguez, J., Susanti, D., Porat, I., Reich, C., Ulrich, L. E., Elkins, J. G., Mavromatis, K., Lykidis, A., Kim, E., Thompson, L. S., Nolan, M., Land, M., Copeland, A., Lapidus, A., Lucas, S., Detter, C., Zhulin, I. B., Olsen, G. J., Whitman, W. & 3 others, Mukhopadhyay, B., Bristow, J. & Kyrpides, N., Apr 1 2008, In : Journal of bacteriology. 190, 8, p. 2957-2965 9 p.

Research output: Contribution to journalArticle

The RAST Server: Rapid annotations using subsystems technology

Aziz, R. K., Bartels, D., Best, A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D. & 6 others, Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A. & Zagnitko, O., Feb 8 2008, In : BMC genomics. 9, 75.

Research output: Contribution to journalArticle

2007

Genomic minimalism in the early diverging intestinal parasite Giardia lamblia

Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A. & 9 others, Nixon, J. E. J., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G. & Sogin, M. L., Sep 28 2007, In : Science. 317, 5846, p. 1921-1926 6 p.

Research output: Contribution to journalArticle

The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation

McNeil, L. K., Reich, C., Aziz, R. K., Bartels, D., Cohoon, M., Disz, T., Edwards, R. A., Gerdes, S., Hwang, K., Kubal, M., Margaryan, G. R., Meyer, F., Mihalo, W., Olsen, G. J., Olson, R., Osterman, A., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D. & 9 others, Rodionov, D. A., Shi, X., Vassieva, O., Vonstein, V., Zagnitko, O., Xia, F., Zinner, J., Overbeek, R. & Stevens, R., Jan 1 2007, In : Nucleic acids research. 35, SUPPL. 1, p. D347-D353

Research output: Contribution to journalArticle

2006
2005

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. Y., Cohoon, M., de Crécy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E. D., Gerdes, S., Glass, E. M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L. & 20 others, Kubal, M., Larsen, N., Linke, B., McHardy, A. C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G. D., Rodionov, D. A., Rül;ckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O. & Vonstein, V., Nov 11 2005, In : Nucleic acids research. 33, 17, p. 5691-5702 12 p.

Research output: Contribution to journalArticle

2004

Evolution of eukaryotic transcription: Insights from the genome of Giardia lamblia

Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L. & Olsen, G. J., Aug 1 2004, In : Genome Research. 14, 8, p. 1537-1547 11 p.

Research output: Contribution to journalArticle

Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis

Zhu, W., Reich, C. I., Olsen, G. J., Giometti, C. S. & Yates, J. R., May 1 2004, In : Journal of Proteome Research. 3, 3, p. 538-548 11 p.

Research output: Contribution to journalArticle

2003

Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to μ LC-ESI tandem mass spectrometry

Lim, H., Eng, J., Yates, J. R., Tollaksen, S. L., Giometti, C. S., Holden, J. F., Adams, M. W. W., Reich, C. I., Olsen, G. J. & Hays, L. G., Sep 2003, In : Journal of the American Society for Mass Spectrometry. 14, 9, p. 957-970 14 p.

Research output: Contribution to journalArticle

2002

Global analysis of a "simple" proteome: Methanococcus jannaschii

Giometti, C. S., Reich, C., Tollaksen, S., Babnigg, G., Lim, H., Zhu, W., Yates, J. & Olsen, G., Dec 25 2002, In : Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences. 782, 1-2, p. 227-243 17 p.

Research output: Contribution to journalArticle

2001

Archaeal RecA homologues: Different response to DNA-damaging agents in mesophilic and thermophilic Archaea

Reich, C. I., McNeil, L. K., Brace, J. L., Brucker, J. K. & Olsen, G. J., Dec 1 2001, In : Extremophiles. 5, 4, p. 265-275 11 p.

Research output: Contribution to journalArticle

Post-transcriptional modification in archaeal tRNAs: Identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales

McCloskey, J. A., Graham, D. E., Zhou, S., Crain, P. F., Ibba, M., Konisky, J., Söll, D. & Olsen, G. J., Nov 15 2001, In : Nucleic acids research. 29, 22, p. 4699-4706 8 p.

Research output: Contribution to journalArticle

Similar subunit architecture of archaeal and eukaryal RNA polymerases

Best, A. A. & Olsen, G. J., Feb 5 2001, In : FEMS microbiology letters. 195, 1, p. 85-90 6 p.

Research output: Contribution to journalArticle

Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis

Giometti, C. S., Tollaksen, S. L., Babnigg, G., Reich, C. I., Olsen, G. J., Lim, H. & Yates, J. R., Jan 1 2001, In : European Journal of Mass Spectrometry. 7, 2, p. 207-217 11 p.

Research output: Contribution to journalArticle

Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis

Giometti, C. S., Reich, C. I., Tollaksen, S. L., Babnigg, G., Lim, H., Yates, J. R. & Olsen, G. J., Aug 1 2001, In : Proteomics. 1, 8, p. 1033-1042 10 p.

Research output: Contribution to journalArticle

The RDP-II (Ribosomal Database Project)

Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Saxman, P. R., Farris, R. J., Garrity, G. M., Olsen, G. J., Schmidt, T. M. & Tiedje, J. M., Jan 1 2001, In : Nucleic acids research. 29, 1, p. 173-174 2 p.

Research output: Contribution to journalArticle

2000

An archaeal genomic signature

Graham, D. E., Overbeek, R., Olsen, G. J. & Woese, C. R., Mar 28 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 7, p. 3304-3308 5 p.

Research output: Contribution to journalArticle

Phylogenomic analysis of the α proteasome gene family from early-diverging eukaryotes

Bouzatrid, J. L., McNeilrid, L. K., Robertson, H. M., Solter, L. F., Nixon, J. E., Beever, J. E., Gaskins, H. R., Olsen, G. J., Subramaniam, S., Sogin, M. L. & Lewinid, H. A., 2000, In : Journal of Molecular Evolution. 51, 6, p. 532-543 12 p.

Research output: Contribution to journalArticle

The Giardia genome project database

McArthur, A. G., Morrison, H. G., Nixon, J. E. J., Passamaneck, N. Q. E., Kim, U., Hinkle, G., Crocker, M. K., Holder, M. E., Farr, R., Reich, C. I., Olsen, G. J., Aley, S. B., Adam, R. D., Gillin, F. D. & Sogin, M. L., Aug 15 2000, In : FEMS microbiology letters. 189, 2, p. 271-273 3 p.

Research output: Contribution to journalArticle

1999

Archaeal and bacterial hyperthermophiles horizontal gene exchange or common ancestry?

Kyrpides, N. C. & Olsen, G. J., Aug 1 1999, In : Trends in Genetics. 15, 8, p. 298-299 2 p.

Research output: Contribution to journalArticle

CRITICA: Coding region identification tool invoking comparative analysis

Badger, J. H. & Olsen, G. J., Apr 1999, In : Molecular biology and evolution. 16, 4, p. 512-524 13 p.

Research output: Contribution to journalArticle

Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

Haney, P. J., Badger, J. H., Buldak, G. L., Reich, C. I., Woese, C. R. & Olsen, G. J., Mar 30 1999, In : Proceedings of the National Academy of Sciences of the United States of America. 96, 7, p. 3578-3583 6 p.

Research output: Contribution to journalArticle

1998

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R. A., Short, J. M., Olsen, G. J. & Swanson, R. V., Mar 26 1998, In : Nature. 392, 6674, p. 353-358 6 p.

Research output: Contribution to journalArticle

1997

A reconstruction of the metabolism of Methanococcus jannaschii from sequence data

Selkov, E., Maltsev, N., Olsen, G. J., Overbeek, R. & Whitman, W. B., Sep 15 1997, In : Gene. 197, 1-2, p. GC11-GC26

Research output: Contribution to journalArticle

Biochemical characterization of archaeal transcription factors

Coldn Gonzalez, G. M., McNeil, L. K., Reich, C. I. & Olsen, G. J., Dec 1 1997, In : FASEB Journal. 11, 9, p. A943

Research output: Contribution to journalArticle

Compilation and analysis of intein sequences

Perler, F. B., Olsen, G. J. & Adam, E., Mar 15 1997, In : Nucleic acids research. 25, 6, p. 1087-1093 7 p.

Research output: Contribution to journalArticle

Majority-rule consensus of phylogenetic trees obtained by maximum- likelihood analysis

Jermiin, L. S., Olsen, G. J., Mengersen, K. L. & Easteal, S., Jan 1 1997, In : Molecular biology and evolution. 14, 12, p. 1296-1302 7 p.

Research output: Contribution to journalArticle

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Klenk, H. P., Clayton, R. A., Tomb, J. F., White, O., Nelson, K. E., Ketchum, K. A., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D., Richardson, D. L., Kerlavage, A. R., Graham, D. E., Krypides, N. C., Fleischmann, R. D., Quackenbush, J., Lee, N. H., Sutton, G. G., Gill, S., Kirkness, E. F. & 31 others, Dougherty, B. A., McKenney, K., Adams, M. D., Loftus, B., Peterson, S., Reich, C. I., McNeil, L. K., Badger, J. H., Glodek, A., Zhou, L., Overbeek, R., Gocayne, J. D., Wiedman, J. F., McDonald, L., Utterback, T., Cotton, M. D., Spriggs, T., Artiach, P., Kaine, B. P., Sykes, S. M., Sadow, P. W., D'Andrea, K. P., Bowman, C., Fujii, C., Garland, S. A., Mason, T. M., Olsen, G. J., Fraser, C. M., Smith, H. O., Woese, C. R. & Craig Venter, J., Nov 27 1997, In : Nature. 390, 6658, p. 364-370 7 p.

Research output: Contribution to journalArticle

The RDP (Ribosomal Database Project)

Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R., Jan 1 1997, In : Nucleic acids research. 25, 1, p. 109-110 2 p.

Research output: Contribution to journalArticle

1996

Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus

Collart, F. R., Osipiuk, J., Trent, J., Olsen, G. J. & Huberman, E., Jan 1 1996, In : Gene. 174, 2, p. 209-216 8 p.

Research output: Contribution to journalArticle