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Research Output 1982 2018

1999

A new version of the RDP (Ribosomal Database Project)

Maidak, B. L., Cole, J. R., Parker, C. T., Garrity, G. M., Larsen, N., Li, B., Lilburn, T. G., McCaughey, M. J., Olsen, G. J., Overbeek, R., Pramanik, S., Schmidt, T. M., Tiedje, J. M. & Woese, C. R., Jan 1 1999, In : Nucleic acids research. 27, 1, p. 171-173 3 p.

Research output: Contribution to journalShort survey

Databases
Ribosomal RNA
Software
Sequence Alignment
Ecology

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

Archaea
Phylogeny
Bacteria
Genes

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

nucleotide sequences
DNA
Databases
Nucleic Acid Databases
Salmonella typhimurium

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

What's eating the free lunch?

Olsen, G. J., Jul 29 1999, In : Nature. 400, 6743

Research output: Contribution to journalShort survey

Quaternary Ammonium Compounds
Lunch
Anaerobic Bacteria
Nitrites
Oxidation-Reduction
1998

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon archaeoglobus fulgidus (Nature (1997) 390 (364- 370))

Klenk, H. P., Clayton, R. A., Tomb, J. F., White, O., Nelson, K. E., Ketchum, K. A., Dodaon, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D., Richardson, D. L., Kerlavage, A. R., Graham, D. E., Kyrpides, 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., Weldman, 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., Fujli, C., Garland, S. A., Mason, T. M., Olsen, G. J., Fraser, C. M., Smith, H. O., Woese, C. R. & Venter, J. C., Jul 2 1998, In : Nature. 394, 6688, 1 p.

Research output: Contribution to journalComment/debate

Archaeoglobus fulgidus
Archaea
Sulfates
Genome

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
1997

Archaeal genomics: An overview

Olsen, G. J. & Woese, C. R., Jan 1 1997, In : Cell. 89, 7, p. 991-994 4 p.

Research output: Contribution to journalReview article

Bacterial Genomes
Archaea
Genomics

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

Factual Databases
Methanococcus
Methanocaldococcus
Chemical Models
Genetic Models

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

TATA-Box Binding Protein
Transcription Factor TFIIB
thermophilic microorganisms
binding proteins
Transcription Factors

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

Inteins
Sequence Analysis
Alleles
Protein Splicing
Matched-Pair Analysis

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

maximum likelihood analysis
probability analysis
phylogenetics
Likelihood Functions
phylogeny

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 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
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

IMP Dehydrogenase
Pyrococcus furiosus
Inosine Monophosphate
Organism Cloning
Oxidoreductases

Cloning and characterization of the gene encoding IMP dehydrogenase from Arabidopsis thaliana

Collart, F. R., Osipiuk, J., Trent, J., Olsen, G. J. & Huberman, E., Jan 1 1996, In : Gene. 174, 2, p. 217-220 4 p.

Research output: Contribution to journalArticle

IMP Dehydrogenase
Inosine Monophosphate
Arabidopsis
Organism Cloning
Oxidoreductases

Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii

Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M., Clayton, R. A., Gocayne, J. D., Kerlavage, A. R., Dougherty, B. A., Tomb, J. F., Adams, M. D., Reich, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodek, A. & 20 others, Scott, J. L., Geoghagen, N. S. M., Weidman, J. F., Fuhrmann, J. L., Nguyen, D., Utterback, T. R., Kelley, J. M., Peterson, J. D., Sadow, P. W., Hanna, M. C., Cotton, M. D., Roberts, K. M., Hurst, M. A., Kaine, B. P., Borodovsky, M., Klenk, H. P., Fraser, C. M., Smith, H. O., Woese, C. R. & Venter, J. C., Aug 23 1996, In : Science. 273, 5278, p. 1058-1073 16 p.

Research output: Contribution to journalArticle

Methanocaldococcus
Archaea
Genome
Eukaryota
Cell Division

Lessons from an Archaeal genome: What are we learning from Methanococcus jannaschii?

Olsen, G. J. & Woese, C. R., Jan 1 1996, In : Trends in Genetics. 12, 10, p. 377-379 3 p.

Research output: Contribution to journalComment/debate

Archaeal Genome
Methanocaldococcus
Learning

Methanococcus genome [1]

Lake, J. A., Rivera, M., Haselkorn, R., Buikema, W. J., Golomb, S. W., Olsen, G. J., Woese, C. R., White, O. & Venter, J. C., Jan 1 1996, In : Science. 274, 5289, p. 901-903 3 p.

Research output: Contribution to journalLetter

Methanococcus
Bacterial Genomes
Nitrogenase
Nitrogen Fixation
Molecular Evolution

Methanococcus jannaschii genome: revisited.

Kyrpides, N. C., Olsen, G. J., Klenk, H. P., White, O. & Woese, C. R., 1996, In : Microbial & comparative genomics. 1, 4, p. 329-338 10 p.

Research output: Contribution to journalArticle

Methanocaldococcus
Genes
Genome
Sequence Analysis
Pattern matching

The Ribosomal Database Project (RDP)

Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R., Mar 27 1996, In : Nucleic acids research. 24, 1, p. 82-85 4 p.

Research output: Contribution to journalShort survey

Ribosomal RNA
Sequence Alignment
Internet
Gophers
Software
1994

Acquired thermotolerance and heat shock proteins in thermophiles from the three phylogenetic domains

Trent, J. D., Gabrielsen, M., Jensen, B., Neuhard, J. & Olsen, J., Jan 1 1994, In : Journal of bacteriology. 176, 19, p. 6148-6152 5 p.

Research output: Contribution to journalComment/debate

Heat-Shock Proteins
Hot Temperature
Shock
Proteins
Sulfolobus

Archaea, Archaea, every where

Olsen, G. J., Jan 1 1994, In : Nature. 371, 6499, p. 657-658 2 p.

Research output: Contribution to journalShort survey

Plankton
Archaea
Phylogeny

FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

Olsen, G. J., Matsuda, H., Hagstrom, R. & Overbeek, R., Feb 1 1994, In : Bioinformatics. 10, 1, p. 41-48 8 p.

Research output: Contribution to journalArticle

Phylogenetic Tree
DNA sequences
DNA Sequence
Maximum likelihood
Maximum Likelihood

Fast phylogenetic analysis on a massively parallel machine

Matsuda, H., Olsen, G. J., Overbeek, R. & Kaneda, Y., Jul 16 1994, Proceedings of the 8th International Conference on Supercomputing, ICS 1994. Association for Computing Machinery, p. 297-302 6 p. (Proceedings of the International Conference on Supercomputing; vol. Part F129421).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Maximum likelihood
DNA sequences
Parallel processing systems
Microorganisms
Costs

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 winds of (evolutionary) change: Breathing new life into microbiology

Olsen, G. J., Woese, C. R. & Overbeek, R., Jan 1 1994, In : Journal of bacteriology. 176, 1, p. 1-6 6 p.

Research output: Contribution to journalReview article

Prokaryotic Cells
16S Ribosomal RNA
Microbiology
Respiration
Bacteria
Archaeal Proteins
Thermococcus
Transcription Factor TFIID
TATA-Box Binding Protein
Archaea
1993

Assignment of the agent of Tyzzer's disease to Clostridium piliforme comb. nov. on the basis of 16S rRNA sequence analysis

Duncan, A. J., Carman, R. J., Olsen, G. J. & Wilson, K. H., Jan 1 1993, In : International Journal of Systematic Bacteriology. 43, 2, p. 314-318 5 p.

Research output: Contribution to journalArticle

Clostridium piliforme
maximum likelihood analysis
Comb and Wattles
Clostridium
nucleic acid

Implementation of a parallel processing system for inference of phylogenetic trees

Matsuda, H., Olsen, G. J., Hagstrom, R., Overbeek, R. & Kaneda, Y., 1993, IEEE Pac Rim Conf Commun Comput Signal Process. Publ by IEEE, p. 280-283 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Parallel processing systems
DNA sequences
Stochastic models
Maximum likelihood
Costs

Ribosomal RNA: A key to phylogeny

Olsen, G. J. & Woese, C. R., Jan 1 1993, In : FASEB Journal. 7, 1, p. 113-123 11 p.

Research output: Contribution to journalReview article

Ribosomal RNA
Phylogeny
ribosomal RNA
Molecules
phylogeny

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 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
1992

A Phylogenetic Analysis of Aquifex pyrophilus

Burggraf, S., Olsen, G. J., Stetter, K. O. & Woese, C. R., Jan 1 1992, In : Systematic and Applied Microbiology. 15, 3, p. 352-356 5 p.

Research output: Contribution to journalArticle

Aquifex
phylogenetics
phylogeny
ancestry
branching

Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods

Ballard, J. W. O., Olsen, G. J., Faith, D. P., Odgers, W. A., Rowell, D. M. & Atkinson, P. W., Jan 1 1992, In : Science. 258, 5086, p. 1345-1348 4 p.

Research output: Contribution to journalArticle

Arthropods
Scorpions
Spiders
Insects

Evolutionary relationships among sulfur- and iron-oxidizing eubacteria

Lane, D. J., Harrison, A. P., Stahl, D., Pace, B., Giovannoni, S. J., Olsen, G. J. & Pace, N. R., Jan 1 1992, In : Journal of bacteriology. 174, 1, p. 269-278 10 p.

Research output: Contribution to journalArticle

Sulfur
Iron
Bacteria
Proteobacteria
Piscirickettsiaceae

The ribosomal database project

Olsen, G. J., Overbeek, R., Larsen, N., Marsh, T. L., McCaughey, M. J., Maciukenas, M. A., Kuan, W. M., Macke, T. J., Xing, Y. & Woese, C. R., Jan 1 1992, In : Nucleic acids research. 20, SUPPL., p. 2199-2200 2 p.

Research output: Contribution to journalComment/debate

Databases
Software
1991

Corrigendum: The ribosomal database project: Updated description (Nucleic Acids Research (1991) 19 (2017-2021))

Olsen, G. J., Overbeek, R., Larsen, N. & Woese, C. R., Oct 9 1991, In : Nucleic acids research. 19, 17, 1 p.

Research output: Contribution to journalComment/debate

Nucleic Acids
Databases
Research
corrigendum
position effect (genetics)
operator regions
Lakes
substitution
lakes

The ribosomal database project: Updated description

Olsen, G. J., Overbeek, R., Larsen, N. & Woese, C. R., Sep 11 1991, In : Nucleic acids research. 19, 17, 1 p.

Research output: Contribution to journalComment/debate

Databases
Data base

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
1990

Molecular and genetic organization of the antennapedia gene complex of drosophila melanogaster

Kaufman, T. C., Seeger, M. A. & Olsen, G. J., Jan 1 1990, In : Advances in Genetics. 27, C, p. 309-362 54 p.

Research output: Contribution to journalArticle

Drosophila melanogaster
Molecular Biology
Homeobox Genes
Genes
Drosophila

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

The halophillc archaebacteria Hb. lacusprofundi and Hb. saccharovorum are closely related: 16S rRNA sequence comparison

Holmes, M. L., Olsen, G. J. & Dyall-Smith, M. L., Aug 11 1990, In : Nucleic acids research. 18, 15, 1 p.

Research output: Contribution to journalComment/debate

Nucleic Acid Sequence Homology
Molecular Sequence Data
Halobacterium
Bacterial RNA
16S Ribosomal RNA

Variation among the masses

Olsen, G. J., Jan 1 1990, In : Nature. 345, 6270, 1 p.

Research output: Contribution to journalShort survey

1989

A brief note concerning archaebacterial phylogeny

Olsen, G. J. & Woese, C. R., 1989, In : Canadian Journal of Microbiology. 35, 1, p. 119-123 5 p.

Research output: Contribution to journalArticle

Phylogeny
Topology
Chemical analysis
Eukaryota
Artifacts

Metazoan phylogeny based on analysis of 18S ribosomal RNA

Raff, R. A., Field, K. G., Olsen, G. J., Giovannoni, S. J., Lane, D. J., Ghiselin, M. T., Pace, N. R. & Raff, E. C., Jan 1 1989, The hierarchy of life. Molecules and Morphology in phylogenetic analysis: proceedings from Nobel Symposium 70. ICS824. Fernholm, B., Bremer, K. & Jornvall, H. (eds.). Elsevier Science Publishers B.V., p. 247-260 14 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Phylogeny and molecular data

Nielsen, C., Walker, W. F., Bode, H. R., Steele, R. E., Field, K. G., Olsen, G. J., Giovannoni, S. J., Raff, E. C., Pace, N. R. & Raff, R. A., Jan 1 1989, In : Science. 243, 4890, p. 548-551 4 p.

Research output: Contribution to journalComment/debate

5S Ribosomal RNA
18S Ribosomal RNA
Cnidaria
Ribosomal RNA
Phylogeny