Publications by authors named "Gordon Pusch"

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BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.
Maulik Shukla, Alice R Wattam, Antonio Aleman, Roshni Bhattacharya, Nicole Bowers, Gordon D Pusch

Nucleic Acids Res· November 2025

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Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.
Alice R Wattam, Nicole Bowers, Thomas Brettin, Neal Conrad, Clark Cucinell, Gordon D Pusch

Methods Mol Biol· May 2024

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Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.
Robert D Olson, Rida Assaf, Thomas Brettin, Neal Conrad, Clark Cucinell, Gordon D Pusch

Nucleic Acids Res· January 2023

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A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.
Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas Brettin, Emily M Dietrich, Gordon D Pusch

Brief Bioinform· November 2021

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Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC.
Bruce Parrello, Rory Butler, Philippe Chlenski, Gordon D Pusch, Ross Overbeek

PLoS One· September 2021

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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
James J Davis, Alice R Wattam, Ramy K Aziz, Thomas Brettin, Ralph Butler, Gordon D Pusch

Nucleic Acids Res· January 2020

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A machine learning-based service for estimating quality of genomes using PATRIC.
Bruce Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie Overbeek, Gordon D Pusch

BMC Bioinformatics· October 2019

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PATRIC as a unique resource for studying antimicrobial resistance.
Dionysios A Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas Brettin, Christopher Bun, Gordon D Pusch

Brief Bioinform· July 2019

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Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
Alice R Wattam, Thomas Brettin, James J Davis, Svetlana Gerdes, Ronald Kenyon, Gordon D Pusch

Methods Mol Biol· November 2018

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Phage Genome Annotation Using the RAST Pipeline.
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh

Methods Mol Biol· June 2018

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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Gordon D Pusch

Nucleic Acids Res· January 2017

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PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.
James J Davis, Svetlana Gerdes, Gary J Olsen, Robert Olson, Gordon D Pusch

Front Microbiol· February 2016

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Enabling comparative modeling of closely related genomes: example genus Brucella.
José P Faria, Janaka N Edirisinghe, James J Davis, Terrence Disz, Anna Hausmann, Gordon D Pusch

3 Biotech· February 2015

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RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
Thomas Brettin, James J Davis, Terry Disz, Robert A Edwards, Svetlana Gerdes, Gordon D Pusch

Sci Rep· February 2015

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High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
Samuel M D Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M T Bradbury, Gordon Pusch

Proc Natl Acad Sci U S A· July 2014

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PATRIC, the bacterial bioinformatics database and analysis resource.
Alice R Wattam, David Abraham, Oral Dalay, Terry L Disz, Timothy Driscoll, Gordon D Pusch

Nucleic Acids Res· January 2014

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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Ross Overbeek, Robert Olson, Gordon D Pusch, Gary J Olsen, James J Davis

Nucleic Acids Res· January 2014

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SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.
Ramy K Aziz, Scott Devoid, Terrence Disz, Robert A Edwards, Christopher S Henry, Gordon D Pusch

PLoS One· April 2013

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Phylogenetic conservatism of functional traits in microorganisms.
Adam C Martiny, Kathleen Treseder, Gordon Pusch

ISME J· April 2013

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Real time metagenomics: using k-mers to annotate metagenomes.
Robert A Edwards, Robert Olson, Terry Disz, Gordon D Pusch, Veronika Vonstein

Bioinformatics· December 2012

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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.
Robert Boissy, Azad Ahmed, Benjamin Janto, Josh Earl, Barry G Hall, Gordon D Pusch

BMC Genomics· April 2011

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The RAST Server: rapid annotations using subsystems technology.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Gordon D Pusch

BMC Genomics· February 2008

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The genome of non-O1 Vibrio cholerae NRT36S demonstrates the presence of pathogenic mechanisms that are distinct from those of O1 Vibrio cholerae.
Yuansha Chen, Judith A Johnson, Gordon D Pusch, J Glenn Morris, O Colin Stine

Infect Immun· May 2007

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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
Leslie Klis McNeil, Claudia Reich, Ramy K Aziz, Daniela Bartels, Matthew Cohoon, Gordon D Pusch

Nucleic Acids Res· January 2007

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The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Ross Overbeek, Tadhg Begley, Ralph M Butler, Jomuna V Choudhuri, Han-Yu Chuang, Gordon D Pusch

Nucleic Acids Res· October 2005

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