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Research Output 1982 2018

Article

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
computer simulation
Computer Simulation
genome
Genome
phylogenetics

A microbiological study of Guaymas Basin high temperature hydrothermal vents

Karl, D. M., Taylor, G. T., Novitsky, J. A., Jannasch, H. W., Wirsen, C. O., Pace, N. R., Lane, D. J., Olsen, G. J. & Giovannoni, S. J., May 1988, In : Deep Sea Research Part A, Oceanographic Research Papers. 35, 5, p. 777-791 15 p.

Research output: Contribution to journalArticle

black smoker
hydrothermal vent
hydrothermal plume
bacterium
basin

Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences

Stahl, D. A., Lane, D. J., Olsen, G. J. & Pace, N. R., Jan 1 1984, In : Science. 224, 4647, p. 407-408 2 p.

Research output: Contribution to journalArticle

symbionts
ribosomal RNA
Solemya velum
Bivalvia
phylogeny

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

Proteins
Archaea
Genome
Archaeal Proteins
Euryarchaeota

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

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

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

Methanocaldococcus
Archaea
DNA
Rad51 Recombinase
Proteins

Are arguments against archaebacteria valid?

Woese, C. R., Pace, N. R. & Olsen, G. J., Dec 1 1986, In : Nature. 320, 6061, p. 401-402 2 p.

Research output: Contribution to journalArticle

Archaea

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

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

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

Methanocaldococcus
Protein Binding
TATA Box
Transcription Factors
Binding Sites

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

Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp.

Romaniuk, P. J., Zoltowska, B., Trust, T. J., Lane, D. J., Olsen, G. J., Pace, N. R. & Stahl, D. A., Jan 1 1987, In : Journal of bacteriology. 169, 5, p. 2137-2141 5 p.

Research output: Contribution to journalArticle

Campylobacter
Gastritis
Helicobacter pylori
Bacteria
Wolinella

Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences.

Stahl, D. A., Lane, D. J., Olsen, G. J. & Pace, N. R., Jun 1 1985, In : Applied and environmental microbiology. 49, 6, p. 1379-1384 6 p.

Research output: Contribution to journalArticle

Hot Springs
hot springs
Archaea
thermal spring
microbial communities

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

codons
Codon
genome
Genome
gene

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

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

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

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data

Rogers, M. J., Simmons, J., Walker, R. T., Weisburg, W. G., Woese, C. R., Tanner, R. S., Robinson, I. M., Stahl, D. A., Olsen, G. & Leach, R. H., Jun 13 1985, In : Proceedings of the National Academy of Sciences of the United States of America. 82, 4, p. 1160-1164 5 p.

Research output: Contribution to journalArticle

Mycoplasma
Acholeplasma
Spiroplasma
Genome
Mycoplasma mycoides

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

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

rRNA Genes
amplification
ribosomal RNA
gene
Gardnerella

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

Papio
bacterial communities
bacterium
primate
phylogenetics
branching
ribosomal RNA
phylogeny
methodology

Enzymatic and Chemical Structure Mapping of Mouse 28S Ribosomal Ribonucleic Acid Contacts in 5.8S Ribosomal Ribonucleic Acid

Walker, T. A., Johnson, K. D., Olsen, G. J., Peters, M. A. & Pace, N. R., May 1982, In : Biochemistry. 21, 10, p. 2320-2329 10 p.

Research output: Contribution to journalArticle

Ribonucleases
Nucleotides
Diethyl Pyrocarbonate
RNA
Molecules

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 cyanobacteria and green chloroplasts

Giovannoni, S. J., Turner, S., Olsen, G. J., Barns, S., Lane, D. J. & Pace, N. R., Jan 1 1988, In : Journal of bacteriology. 170, 8, p. 3584-3592 9 p.

Research output: Contribution to journalArticle

Cyanobacteria
Chloroplasts
Cyanophora
Dideoxynucleotides
Chlorophyta

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

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

Archaea
DNA replication
Eukaryota
DNA Replication
eukaryotic cells

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

Giardia
Giardia lamblia
DNA-Directed RNA Polymerases
Peptide Initiation Factors
Genome

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

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

Thermofilaceae
formic acid
Biosynthetic Pathways
Sulfur
Genome

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

Tenericutes
Mollicutes
Phylogeny
genomics
phylogeny

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

Salmonella enteritidis
Salmonella
Salmonella Enteritidis
Pseudogenes
pseudogenes

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

Giardia lamblia
Parasites
Genome
Giardia
Horizontal Gene Transfer

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

Methanocaldococcus
Proteome
Proteins
Genes
Genome

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

Microbiota
Ecosystem
Gene Library
rRNA Genes
Cervix Uteri

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

Peptide Mapping
Electrospray Ionization Mass Spectrometry
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Staphylococcal Protein A
Tandem Mass Spectrometry

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

Computational Biology
Research Personnel
Genome
Databases
RNA

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

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

Methanocaldococcus
RNA
Messenger RNA
RNA Cleavage
Initiator Codon

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

Mitochondrial origins

Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G. J. & Woese, C. R., Dec 1 1985, In : Proceedings of the National Academy of Sciences of the United States of America. 82, 13, p. 4443-4447 5 p.

Research output: Contribution to journalArticle

Mitochondria
Comamonas testosteroni
16S Ribosomal RNA
Rickettsia
Proteobacteria

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

Molecular phylogeny of the animal kingdom

Field, K. G., Olsen, G. J., Lane, D. J., Giovannoni, S. J., Ghiselin, M. T., Raff, E. C., Pace, N. R. & Raff, R. A., Jan 1 1988, In : Science. 239, 4841, p. 748-753 6 p.

Research output: Contribution to journalArticle

Phylogeny
18S Ribosomal RNA
Platyhelminths
Cnidaria
Chordata

Nucleotide Sequence of Dictyostelium discoideum 5.8S Ribosomal Ribonucleic Acid: Evolutionary and Secondary Structural Implications

Olsen, G. J. & Sogin, M. L., May 1982, In : Biochemistry. 21, 10, p. 2335-2343 9 p.

Research output: Contribution to journalArticle

Dictyostelium
Nucleotides
RNA
Phylogeny

Nucleotide Sequence of the Dictyostelium discoideum Small-Subunit Ribosomal Ribonucleic Acid Inferred from the Gene Sequence: Evolutionary Implications

McCarroll, R., Olsen, G. J., Stahl, Y. D., Woese, C. R., Sogin, M. L., McCarroll, R., Olsen, G. J., Stahl, Y. D., Woese, C. R., Sogin, M. L. & Woese, C. R., Jan 1 1983, In : Biochemistry. 22, 25, p. 5858-5868 11 p.

Research output: Contribution to journalArticle

Small Ribosome Subunits
Dictyostelium
Nucleotides
Genes
RNA

Paramecium mitochondrial genes. I. Small subunit rRNA gene sequence and microevolution

Seilhamer, J. J., Olsen, G. J. & Cummings, D. J., 1984, In : Journal of Biological Chemistry. 259, 8, p. 5167-5172 6 p.

Research output: Contribution to journalArticle

Paramecium
Mitochondrial Genes
rRNA Genes
Genes
Ribosomal DNA

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
Genes
Genome
Molecular Sequence Annotation
Proteins
Research Personnel