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Research Output 1982 2018

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

Database Management Systems
Systems Biology
Knowledge Bases
Computational Biology

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
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

Computational Biology
Research Personnel
Genome
Databases
RNA
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

Microbial Genome
Databases
Proteins
Genome
Computational Biology
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

Salmonella enteritidis
Salmonella
Salmonella Enteritidis
Pseudogenes
pseudogenes

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

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
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

Agrobacterium
Plasmids
Plant Tumor-Inducing Plasmids
Acyl-Butyrolactones
Genes

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
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

Tenericutes
Mollicutes
Phylogeny
genomics
phylogeny

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

Systematic errors
data analysis
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

Servers
Genes
Genome
genome
Environmental Microbiology
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

codons
Codon
genome
Genome
gene

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
Salmonella enterica
Escherichia coli
Genes
Archaeal Genome
Bacterial Genomes
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

Archaea
DNA replication
Eukaryota
DNA Replication
eukaryotic cells

Modal codon usage: Assessing the typical codon usage of a genome

Davis, J. J. & Olsen, G. J., Apr 1 2010, In : Molecular biology and evolution. 27, 4, p. 800-810 11 p.

Research output: Contribution to journalReview article

codons
Codon
genome
Genome
plasmid
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

Microbiota
Ecosystem
Gene Library
rRNA Genes
Cervix Uteri

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

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
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

Methanocaldococcus
Protein Binding
TATA Box
Transcription Factors
Binding Sites

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

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

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
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

Giardia lamblia
Parasites
Genome
Giardia
Horizontal Gene Transfer

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

Research output: Contribution to journalArticle

Genomics
Genome
Databases
Computational Biology
Research Personnel
2006
computer simulation
Computer Simulation
genome
Genome
phylogenetics
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. J., 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
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

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

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
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

Peptide Mapping
Electrospray Ionization Mass Spectrometry
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Staphylococcal Protein A
Tandem Mass Spectrometry
2002

Comparative genomics of closely related salmonellae

Edwards, R. A., Olsen, G. J. & Maloy, S. R., Feb 1 2002, In : Trends in Microbiology. 10, 2, p. 94-99 6 p.

Research output: Contribution to journalReview article

Genomics
Salmonella
Genome
Horizontal Gene Transfer
DNA

Current Opinion in Microbiology: Editorial Overview

Kurland, C. & Olsen, G. J., Oct 2002, In : Current Opinion in Microbiology. 5, 5, p. 497-498 2 p.

Research output: Contribution to journalEditorial

Microbiology

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. J., 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

Proteome analysis of Methanococcus jannaschii by μLC/MS/MS

Zhu, W., Yates, J. R., Giometti, C. S., Reich, C. I. & Olsen, G. J., Dec 1 2002, p. 233-234. 2 p.

Research output: Contribution to conferencePaper

Proteome
Gels
Proteins
Mass spectrometry
Peptides
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

Methanocaldococcus
Archaea
DNA
Rad51 Recombinase
Proteins

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

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., 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

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

The history of life

Olsen, G. J., Jul 20 2001, In : Nature Genetics. 28, 3, p. 197-198 2 p.

Research output: Contribution to journalShort survey

Molecular Evolution
Protein Sequence Analysis
Phylogeny
Genomics
History

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
2000

Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process

Woese, C. R., Olsen, G. J., Ibba, M. & Söll, D., Mar 2000, In : Microbiology and Molecular Biology Reviews. 64, 1, p. 202-236 35 p.

Research output: Contribution to journalReview article

Genetic Code
Amino Acyl-tRNA Synthetases
Genes
Bacteria
Archaea

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

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

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 RDP (Ribosomal Database Project) continues

Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Saxman, P. R., Stredwick, J. M., Garrity, G. M., Li, B., Olsen, G. J., Pramanik, S., Schmidt, T. M. & Tiedje, J. M., Jan 1 2000, In : Nucleic acids research. 28, 1, p. 173-174 2 p.

Research output: Contribution to journalShort survey

Databases
Sequence Alignment
Restriction Fragment Length Polymorphisms
Japan
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