List of works by Ross Overbeek

A high-performance parallel theorem prover

A machine learning-based service for estimating quality of genomes using PATRIC

scientific article published on 03 October 2019

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

scientific article

Aligning Multiple RNA Sequences

Annotation of bacterial and archaeal genomes: improving accuracy and consistency

scientific article published on 21 July 2007

Antimicrobial Resistance Prediction in PATRIC and RAST.

scientific article published on 14 June 2016

Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

scientific article

Automated Reasoning. Introduction and Applications.

scientific article published in 1986

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

scientific article published in January 2013

Automatic detection of subsystem/pathway variants in genome analysis

scientific article published in June 2005

Bioinformatics classification and functional analysis of PhoH homologs

scientific article published on 30 December 2002

Building the blueprint of life ⬇️

scientific article published on July 1, 2010

Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover

scientific article

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

scientific article

Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities

scientific article

Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis

scientific article published in September 2005

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

scientific article

Comparative genomics of NAD biosynthesis in cyanobacteria.

scientific article

Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii

scientific article

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

scientific article

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

scientific article

Connecting Sequence Data to Virulence Factors in Streptococcus Genomes

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

Discovering lactic acid bacteria by genomics

scientific article

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

scientific article published on October 2002

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article published in Nature

FIGfams: yet another set of protein families

scientific article published on 17 September 2009

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

scientific article published on 17 June 2016

Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter.

scientific article

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

scientific article

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

scientific article

Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis

scientific article

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

scientific article published on July 2014

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

scientific article

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

scientific article

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

scientific article

In search of genome annotation consistency: solid gene clusters and how to use them

article

Missing genes in metabolic pathways: a comparative genomics approach ⬇️

scientific article published on April 1, 2003

Modeling central metabolism and energy biosynthesis across microbial life

scientific article

Moving to a higher level of abstraction

scientific article published on 01 January 2007

PATRIC as a unique resource for studying antimicrobial resistance.

scientific article published on 31 July 2017

PATRIC, the bacterial bioinformatics database and analysis resource

scientific article

Phage Genome Annotation Using the RAST Pipeline.

scientific article published in January 2018

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

scientific article

Real time metagenomics: using k-mers to annotate metagenomes

scientific article

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data

scientific article

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

scientific article

Searching for genomic organizational motifs: Explorations of the Escherichia coli chromosome

scientific article published in 1993

Set theory in first-order logic: Clauses for Gödel's axioms

scientific article published in 1986

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

scientific article published on 15 April 2021

Synergistic use of plant-prokaryote comparative genomics for functional annotations

scientific article

The ERGO genome analysis and discovery system

scientific article

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

scientific article published on December 2006

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

scientific article published on 01 January 2020

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

scientific article

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

scientific article

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

scientific article

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

scientific article (publication date: July 2002)

The genome sequence of the facultative intracellular pathogen Brucella melitensis

scientific article

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

scientific article

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

scientific article

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

scientific article

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