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

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D206-D214

2014

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

Scientific reports, 2015-02, Vol.5 (1), p.8365-8365, Article 8365

2015

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

Nucleic acids research, 2017-01, Vol.45 (D1), p.D535-D542

2017

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

PloS one, 2012-10, Vol.7 (10), p.e48053-e48053

2012

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PATRIC, the bacterial bioinformatics database and analysis resource

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D581-D591

2014

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PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

Frontiers in microbiology, 2016-02, Vol.7, p.118-118

2016

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

PloS one, 2021-04, Vol.16 (4), p.e0250092-e0250092

2021

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The RAST Server: rapid annotations using subsystems technology

BMC genomics, 2008-02, Vol.9 (1), p.75-75, Article 75

2008

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

BMC bioinformatics, 2019-10, Vol.20 (1), p.486-486, Article 486

2019

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PATRIC as a unique resource for studying antimicrobial resistance

Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1094-1102

2019

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

Nature biotechnology, 2004-12, Vol.22 (12), p.1554-1558

2004

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The Use of Gene Clusters to Infer Functional Coupling

Proceedings of the National Academy of Sciences - PNAS, 1999-03, Vol.96 (6), p.2896-2901

1999

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Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model

BMC genomics, 2011-04, Vol.12 (1), p.187-187, Article 187

2011

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Phage Genome Annotation Using the RAST Pipeline

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1681, p.231

2018

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Genome of Non-O1 Vibrio cholerae NRT36S Demonstrates the Presence of Pathogenic Mechanisms That Are Distinct from Those of O1 Vibrio cholerae

Infection and Immunity, 2007-05, Vol.75 (5), p.2645-2647

2007

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A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

Briefings in bioinformatics, 2021-11, Vol.22 (6)

2021

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Real Time Metagenomics: Using k-mers to annotate metagenomes

Bioinformatics, 2012-12, Vol.28 (24), p.3316-3317

2012

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WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

Nucleic acids research, 2000-01, Vol.28 (1), p.123-125

2000

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Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance

Methods in molecular biology (Clifton, N.J.), 2024, Vol.2802, p.547

2024

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Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method

Journal of molecular evolution, 2004-05, Vol.58 (5), p.615-631

2004

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

Nucleic acids research, 2007-01, Vol.35 (Database issue), p.D347-D353

2007

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Enabling comparative modeling of closely related genomes: Example genus Brucella

3 Biotech, 2015-02, Vol.5 (1), p.101-105

2015

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

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

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

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

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

PATRIC, the bacterial bioinformatics database and analysis resource

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

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

The RAST Server: rapid annotations using subsystems technology

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

PATRIC as a unique resource for studying antimicrobial resistance

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

The Use of Gene Clusters to Infer Functional Coupling

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model

Phage Genome Annotation Using the RAST Pipeline

Genome of Non-O1 Vibrio cholerae NRT36S Demonstrates the Presence of Pathogenic Mechanisms That Are Distinct from Those of O1 Vibrio cholerae

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

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

Real Time Metagenomics: Using k-mers to annotate metagenomes

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance

Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method

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

Enabling comparative modeling of closely related genomes: Example genus Brucella

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