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Research Output 1982 2018

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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

Microbial Genome
Databases
Proteins
Genome
Computational Biology

Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences

Lane, D. J., Stahl, D. A., Olsen, G. J., Heller, D. J. & Pace, N. R., Nov 6 1985, In : Journal of bacteriology. 163, 1, p. 75-81 7 p.

Research output: Contribution to journalArticle

Phylogenetic Analysis Using Ribosomal RNA

Olsen, G. J., Jan 1988, In : Methods in enzymology. 164, C, p. 793-812 20 p.

Research output: Contribution to journalArticle

Ribosomal RNA
Phylogeny
Sequence Homology
Sequence Analysis
RNA

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA - a review

Pace, N. R., Smith, D. K., Olsen, G. J. & James, B. D., Oct 15 1989, In : Gene. 82, 1, p. 65-75 11 p.

Research output: Contribution to journalArticle

Ribonuclease P
RNA
Guidelines
Bacteria

Phylogenetic comparative analysis of RNA secondary structure

James, B. D., Olsen, G. J. & Pace, N. R., Jan 1 1989, In : Methods in enzymology. 180, C, p. 227-239 13 p.

Research output: Contribution to journalArticle

Ribonuclease P
Ribosomal RNA
Sequence Homology
Ribonucleoproteins
Endonucleases

Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells.

Giovannoni, S. J., DeLong, E. F., Olsen, G. J. & Pace, N. R., Feb 1988, In : Journal of bacteriology. 170, 2, p. 720-726 7 p.

Research output: Contribution to journalArticle

Oligodeoxyribonucleotides
Conserved Sequence
Nylons
Archaea
Bacteria

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

proteasome endopeptidase complex
eukaryote
Proteasome Endopeptidase Complex
Eukaryota
eukaryotic cells

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

Methanococcales
Methanococcus
Transfer RNA
Nucleosides
Nucleotides

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

Position-Specific Scoring Matrices
Methanocaldococcus
Transcription Initiation Site
Proteins
General Transcription Factors

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

Agrobacterium
Plasmids
Plant Tumor-Inducing Plasmids
Acyl-Butyrolactones
Genes

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

Lane, D. J., Pace, B., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R., Dec 1 1985, In : Proceedings of the National Academy of Sciences of the United States of America. 82, 20, p. 6955-6959 5 p.

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

Genome
Technology
Software
Archaeal Genome
Bacterial Genomes

Reverse Transcriptase Sequencing of Ribosomal RNA for Phylogenetic Analysis

Lane, D. J., Field, K. G., Olsen, G. J. & Pace, N. R., Jan 1988, In : Methods in enzymology. 167, C, p. 138-144 7 p.

Research output: Contribution to journalArticle

Ribosomal RNA
RNA-Directed DNA Polymerase
Dideoxynucleotides
RNA
Centrifugation

Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme

Reich, C., Olsen, G. J., Pace, B. & Pace, N. R., Jan 1 1988, In : Science. 239, 4836, p. 178-181 4 p.

Research output: Contribution to journalArticle

Ribonuclease P
Ribonucleoproteins
RNA
Enzymes
Proteins

Secondary structure of tbe Dictyostelium discoideum small subunit ribosomal RNA

Olsen, G. J., Mccarroll, R. & Sogin, M. L., Nov 25 1983, In : Nucleic acids research. 11, 22, p. 8037-8049 13 p.

Research output: Contribution to journalArticle

Nucleic Acid Conformation
Species Specificity
Dictyostelium
Ribosomal RNA
Phylogeny

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

Servers
Genes
Genome
genome
Environmental Microbiology

Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications

Olsen, G. J., Pace, N. R., Nuell, M., Kaine, B. P., Gupta, R. & Woese, C. R., Dec 1 1985, In : Journal of Molecular Evolution. 22, 4, p. 301-307 7 p.

Research output: Contribution to journalArticle

Sulfolobus solfataricus
secondary structure
Archaea
eukaryote
rRNA Genes

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

Methanocaldococcus
Firearms
Proteomics
Proteins
water dikinase pyruvate
Salmonella enterica
Escherichia coli
Genes
Archaeal Genome
Bacterial Genomes

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

Archaeal RNA
DNA-Directed RNA Polymerases
Proteins
Methanocaldococcus
RNA Polymerase II

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

proteome
Flagellin
Proteome
proteins
Proteins

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

Methanocaldococcus
Flagellin
Proteome
Proteins
Isoelectric Point

Structure and catalytic function in ribonuclease P

Pace, N. R., Reich, C., James, B. D., Olsen, G. J., Pace, B. & Waugh, D. S., Jan 1 1987, In : Cold Spring Harbor symposia on quantitative biology. 52, p. 239-248 10 p.

Research output: Contribution to journalArticle

ribonucleases

Structure detection through automated covariance search

Winker, S., Overbeek, R., Woese, C. R., Oisen, G. J. & Pfluger, N., Oct 1 1990, In : Bioinformatics. 6, 4, p. 365-371 7 p.

Research output: Contribution to journalArticle

23S Ribosomal RNA
16S Ribosomal RNA
RNA
Ribosomal RNA
Molecules

Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences.

Distel, D. L., Lane, D. J., Olsen, G. J., Giovannoni, S. J., Pace, B., Pace, N. R., Stahl, D. A. & Felbeck, H., Jun 1988, In : Journal of bacteriology. 170, 6, p. 2506-2510 5 p.

Research output: Contribution to journalArticle

Symbiosis
Phylogeny
Sulfur
Hydrothermal Vents
Proteobacteria
position effect (genetics)
operator regions
Lakes
substitution
lakes

The agent of tyzzer's disease is a clostridium species

Wilson, K. H., Duncan, A. J., Carman, R. J. & Olsen, G. J., Jun 1 1993, In : Clinical Infectious Diseases. 16, p. S422-S422

Research output: Contribution to journalArticle

Rodent Diseases
Bacterial RNA
16S Ribosomal RNA
Clostridium Infections
Clostridium

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

Inorganic Chemicals
Extreme Heat
Genome
Oxygen
Bacteria

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

Archaeoglobus fulgidus
Archaea
Sulfates
Methanocaldococcus
Genome

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

Sulfolobus
genome
Essential Genes
genes
Genes

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

Giardia
Genome
Databases
Giardia lamblia
Access to Information

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

Genomics
Genome
Databases
Computational Biology
Research Personnel

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

Genome
Technology
Archaeal Genome
Bacterial Genomes
Transfer RNA

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

Ribosomal RNA
Sequence Alignment
Gophers
Software
Databases

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

Sequence Alignment
Nucleic Acids
Japan
Databases

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

Rhizobiales
plasmid
plasmids
Plasmids
protein

The ribosomal database project

Maidak, B. L., Larsen, N., McCaughey, M. J., Overbeek, R., Olsen, G. J., Fogel, K., Blandy, J. & Woese, C. R., Sep 1994, In : Nucleic acids research. 22, 17, p. 3485-3487 3 p.

Research output: Contribution to journalArticle

Gophers
Software
Databases
Ribosomal RNA
Sequence Alignment

The ribosomal database project

Larsen, N., Olsen, G. J., Maidak, B. L., Mccaughey, M. J., Overbeek, R., Macke, T. J., Marsh, T. L. & Woese, C. R., Jul 1 1993, In : Nucleic acids research. 21, 13, p. 3021-3023 3 p.

Research output: Contribution to journalArticle

Databases
Ribosomal RNA
Sequence Alignment
Ribosomes
Software

The ribosomal rna database project

Oisen, G. J., Larsen, N. & Woese, C. R., Apr 25 1991, In : Nucleic acids research. 19, p. 2017-2018 2 p.

Research output: Contribution to journalArticle

Bibliographic Databases
Ribosomal RNA
Nucleic Acid Databases
Bacteria

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

Methanococcus
Methanocaldococcus
Proteins
Amino Acids
Temperature

The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure

Reich, C., Gardiner, K. J., Olsen, G. J., Pace, B., Marsh, T. L. & Pace, N. R., Dec 1 1986, In : Journal of Biological Chemistry. 261, 17, p. 7888-7893 6 p.

Research output: Contribution to journalArticle

Ribonuclease P
Bacilli
Bacillus subtilis
RNA
Genes

The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme

James, B. D., Olsen, G. J., Liu, J. & Pace, N. R., Jan 15 1988, In : Cell. 52, 1, p. 19-26 8 p.

Research output: Contribution to journalArticle

Ribonuclease P
Catalytic RNA
Ribonucleoproteins
Bacilli
RNA

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

Microbial Genome
Genome
Technology
Databases
Proteins

The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata

Elwood, H. J., Olsen, G. J. & Sogin, M. L., 1985, In : Molecular Biology and Evolution. 2, 5, p. 399-410 12 p.

Research output: Contribution to journalArticle

Oxytricha
Ribosomal RNA
ciliate
Fungi
rRNA Genes

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

Genome
Microbial Genome
Genes
Libraries
Technology
Archaeal Proteins
Thermococcus
Transcription Factor TFIID
TATA-Box Binding Protein
Archaea