R. Overbeek

Most-cited papers

The RAST Server: Rapid Annotations using Subsystems Technology
R. Aziz, D. Bartels, Aaron A. Best, M. DeJongh +22 more
2008BMC Genomics12K citations Open access
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
R. Overbeek, Robert Olson, G. Pusch, G. Olsen +10 more
2013Nucleic Acids Res.4,375 citations Open access
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RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
T. Brettin, James J. Davis, T. Disz, R. Edwards +12 more
2015Scientific Reports2,641 citations Open access
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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
R. Overbeek, T. Begley, R. Butler, J. Choudhuri +36 more
2005Nucleic Acids Research2,040 citations Open access
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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
A. Wattam, James J. Davis, Rida Assaf, S. Boisvert +24 more
2016Nucleic Acids Res.1,561 citations Open access
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Insights into social insects from the genome of the honeybee Apis mellifera
G. Weinstock, G. Robinson, R. Gibbs, K. Worley +225 more
2006Nature1,462 citations Open access
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The use of gene clusters to infer functional coupling.
R. Overbeek, M. Fonstein, M. D'Souza, G. Pusch +1 more
1999Proceedings of the National Academy of Sciences of the United States of America1,340 citations Open access
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PATRIC, the bacterial bioinformatics database and analysis resource
A. Wattam, David Abraham, O. Dalay, T. Disz +24 more
2013Nucleic Acids Res.1,198 citations Open access
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The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
G. Deckert, P. Warren, T. Gaasterland, William G. Young +11 more
1998Nature1,130 citations Open access
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The RDP (Ribosomal Database Project)
B. Maidak, G. Olsen, N. Larsen, R. Overbeek +2 more
1997Nucleic Acids Res.980 citations Open access
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A new version of the RDP (Ribosomal Database Project)
B. Maidak, J. Cole, C. Parker, G. Garrity +10 more
1999Nucleic Acids Res.943 citations Open access
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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
James J. Davis, A. Wattam, R. Aziz, T. Brettin +30 more
2019Nucleic Acids Res.872 citations Open access
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Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
Natalia N. Ivanova, A. Sorokin, I. Anderson, N. Galleron +19 more
2003Nature871 citations Open access
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Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
S. Gerdes, M. Scholle, J. Campbell, G. Balázsi +17 more
2003Journal of Bacteriology780 citations Open access
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The genome sequence of the facultative intracellular pathogen Brucella melitensis
V. Delvecchio, V. Kapatral, R. Redkar, G. Patra +21 more
2001Proceedings of the National Academy of Sciences of the United States of America566 citations Open access
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Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus
A. Bolotin, B. Quinquis, P. Renault, A. Sorokin +19 more
2004Nature Biotechnology534 citations Open access
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The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.
U. Deppenmeier, André Johann, Thomas Hartsch, R. Merkl +18 more
2002Journal of Molecular Microbiology and Biotechnology463 citations
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WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
R. Overbeek, N. Larsen, G. Pusch, M. D'Souza +4 more
2000Nucleic Acids Res.413 citations Open access
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Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586
V. Kapatral, I. Anderson, Natalia N. Ivanova, G. Reznik +21 more
2002Journal of Bacteriology348 citations Open access
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Missing genes in metabolic pathways: a comparative genomics approach.
A. Osterman, R. Overbeek
2003Current Opinion in Chemical Biology326 citations
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Searching for patterns in genomic data.
Mark D'Souza, Niels Larsen, R. Overbeek
1997Trends in Genetics318 citations
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Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover
K. Anderson, C. Roberts, T. Disz, V. Vonstein +5 more
2006Journal of Bacteriology291 citations Open access
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The ERGOTM genome analysis and discovery system
R. Overbeek, N. Larsen, Theresa Walunas, M. D'Souza +18 more
2003Nucleic Acids Res.265 citations Open access
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Discovering lactic acid bacteria by genomics
T. Klaenhammer, E. Altermann, F. Arigoni, A. Bolotin +32 more
2002Antonie van Leeuwenhoek261 citations Open access
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Antimicrobial Resistance Prediction in PATRIC and RAST
James J. Davis, S. Boisvert, T. Brettin, R. Kenyon +9 more
2016Scientific Reports219 citations Open access
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SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
R. Aziz, Scott Devoid, T. Disz, R. Edwards +9 more
2012PLoS ONE205 citations Open access
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Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter
C. Jenkins, R. Samudrala, I. Anderson, B. Hedlund +6 more
2002Proceedings of the National Academy of Sciences of the United States of America184 citations Open access
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FIGfams: yet another set of protein families
Folker Meyer, R. Overbeek, Alex C Rodriguez
2009Nucleic Acids Research154 citations Open access
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Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.
Scott Devoid, R. Overbeek, M. DeJongh, V. Vonstein +2 more
2013Methods in molecular biology146 citations
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Use of Contiguity on the Chromosome to Predict Functional Coupling
R. Overbeek, M. Fonstein, M. D'Souza, G. Pusch +1 more
1999Silico Biol.143 citations Open access
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An archaeal genomic signature.
D. Graham, R. Overbeek, G. Olsen, C. Woese
2000Proceedings of the National Academy of Sciences of the United States of America134 citations Open access
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Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
T. Disz, Sajia Akhter, Daniel Cuevas, Robert Olson +4 more
2010BMC Bioinformatics130 citations Open access
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Characterizing the Effect of the Staphylococcus aureus Virulence Factor Regulator, SarA, on Log-Phase mRNA Half-Lives
C. Roberts, K. Anderson, E. Murphy, S. Projan +6 more
2006Journal of Bacteriology118 citations Open access
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Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains
A. Bhattacharyya, S. Stilwagen, Natalia N. Ivanova, M. D'Souza +18 more
2002Proceedings of the National Academy of Sciences of the United States of America116 citations Open access
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Universal Protein Families and the Functional Content of the Last Universal Common Ancestor
N. Kyrpides, R. Overbeek, C. Ouzounis
1999Journal of Molecular Evolution115 citations Open access
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PATRIC as a unique resource for studying antimicrobial resistance
D. Antonopoulos, Rida Assaf, R. Aziz, T. Brettin +25 more
2017Briefings Bioinform.109 citations Open access
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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
L. K. McNeil, C. Reich, R. Aziz, D. Bartels +25 more
2006Nucleic Acids Res.108 citations Open access
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Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase Family
M. Daugherty, V. Vonstein, R. Overbeek, A. Osterman
2001Journal of Bacteriology97 citations Open access
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Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
D. Rodionov, C. Yang, Xiaoqing Li, I. Rodionova +9 more
2010BMC Genomics95 citations Open access
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The SEED: a peer-to-peer environment for genome annotation
R. Overbeek, T. Disz, Rick L. Stevens
2004CACM94 citations
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Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
A. Wattam, T. Brettin, James J. Davis, S. Gerdes +12 more
2018Methods in molecular biology93 citations
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Synergistic use of plant-prokaryote comparative genomics for functional annotations
S. Gerdes, B. El-Yacoubi, M. Bailly, I. Blaby +9 more
2011BMC Genomics87 citations Open access
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Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.
I. Anderson, A. Sorokin, V. Kapatral, G. Reznik +19 more
2005FEMS Microbiology Letters87 citations Open access
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Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.
V. Kapatral, Natalia N. Ivanova, I. Anderson, G. Reznik +10 more
2003Genome Research85 citations Open access
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Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights.
A. Bhattacharyya, S. Stilwagen, G. Reznik, Helene Feil +18 more
2002Genome Research84 citations Open access
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Phage Genome Annotation Using the RAST Pipeline.
K. McNair, R. Aziz, G. Pusch, R. Overbeek +2 more
2018Methods in molecular biology78 citations Open access
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Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus
D. Rodionov, P. Novichkov, E. Stavrovskaya, I. Rodionova +15 more
2011BMC Genomics78 citations Open access
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High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Samuel M. D. Seaver, S. Gerdes, Océane Frelin, Claudia Lerma-Ortiz +14 more
2014Proceedings of the National Academy of Sciences of the United States of America76 citations Open access
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Real Time Metagenomics: Using k-mers to annotate metagenomes
R. Edwards, Robert Olson, T. Disz, G. Pusch +3 more
2012Bioinform.69 citations Open access
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Comparative Genomics of NAD Biosynthesis in Cyanobacteria
S. Gerdes, O. Kurnasov, K. Shatalin, Boris M. Polanuyer +4 more
2006Journal of Bacteriology55 citations Open access
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