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List of works by Ross Overbeek

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Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

scientific article
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

scientific article
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article
The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

scientific article published on March 26, 1998
PATRIC, the bacterial bioinformatics database and analysis resource

scientific article
The winds of (evolutionary) change: breathing new life into microbiology

scientific article
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

scientific article
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis

scientific article
The genome sequence of the facultative intracellular pathogen Brucella melitensis

scientific article
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

scientific article
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus

scientific article
Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586

scientific article
The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea

scientific article (publication date: July 2002)
Missing genes in metabolic pathways: a comparative genomics approach

scientific article published on April 1, 2003
Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover

scientific article
The ERGO genome analysis and discovery system

scientific article
Accessing the SEED genome databases via Web services API: tools for programmers

scientific article
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models

scientific article
FIGfams: yet another set of protein families

scientific article published on 17 September 2009
Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter

scientific article
Discovering lactic acid bacteria by genomics

scientific article
Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives

scientific article
Antimicrobial Resistance Prediction in PATRIC and RAST.

scientific article published on 14 June 2016
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

scientific article published on December 2006
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

scientific article
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

scientific article
Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.

scientific article published in January 2013
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

scientific article
Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.

scientific article
Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis

scientific article published in September 2005
Comparative genomics of NAD biosynthesis in cyanobacteria.

scientific article
Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

scientific article published on October 2002
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

scientific article
Annotation of bacterial and archaeal genomes: improving accuracy and consistency

scientific article published on 21 July 2007
Real time metagenomics: using k-mers to annotate metagenomes

scientific article
Bioinformatics classification and functional analysis of PhoH homologs

scientific article published on 30 December 2002
Automatic detection of subsystem/pathway variants in genome analysis

scientific article published in June 2005
Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities

scientific article
PATRIC as a unique resource for studying antimicrobial resistance

scientific article published on 31 July 2017
Connecting genotype to phenotype in the era of high-throughput sequencing.

scientific article published on 21 March 2011
Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method

scientific article
Synergistic use of plant-prokaryote comparative genomics for functional annotations

scientific article
Building the blueprint of life

scientific article published on July 1, 2010
Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

scientific article
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

scientific article published on July 1, 2014
Phage Genome Annotation Using the RAST Pipeline.

scientific article published in January 2018
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

scientific article published on 01 January 2020
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

scientific article published on 17 June 2016
Modeling central metabolism and energy biosynthesis across microbial life

scientific article

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