Robert A. Edwards

According to our database, Robert A. Edwards authored at least 31 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes.

Katelyn McNair, Peter Salamon, Robert A. Edwards, Anca M. Segall

BMC Bioinform., December, 2024

2023

Phables: from fragmented assemblies to high-quality bacteriophage genomes.

Vijini Mallawaarachchi, Michael J. Roach, Przemyslaw Decewicz, Bhavya Nalagampalli Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L. K. Hutton, Elizabeth A. Dinsdale, Robert A. Edwards

Bioinform., October, 2023

Classification Confidence in Exploratory Learning: A User's Guide.

Peter Salamon, David Salamon, Vito Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall

Mach. Learn. Knowl. Extr., June, 2023

2022

Ten simple rules and a template for creating workflows-as-applications.

Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Nalagampalli Papudeshi, Scott A. Handley, C. Titus Brown, Nathan S. Watson-Haigh, Robert A. Edwards

PLoS Comput. Biol., December, 2022

Organizing the bacterial annotation space with amino acid sequence embeddings.

Susanna R. Grigson, Jody C. McKerral, James G. Mitchell, Robert A. Edwards

BMC Bioinform., December, 2022

Estimating Classification Confidence Using Kernel Densities.

Peter Salamon, David Salamon, Vito Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall

CoRR, 2022

2021

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Felipe Hernandes Coutinho, Asier Zaragoza-Solas, Mario López-Pérez, Jakub Barylski, Andrzej Zielezinski, Bas E. Dutilh, Robert A. Edwards, Francisco Rodríguez-Valera

Patterns, 2021

2020

PhANNs, a fast and accurate tool and web server to classify phage structural proteins.

Vito Adrian Cantu, Peter Salamon, Victor Seguritan, Jackson Redfield, David Salamon, Robert A. Edwards, Anca M. Segall

PLoS Comput. Biol., November, 2020

2019

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.

Carol L. Ecale Zhou, Stephanie Malfatti, Jeffrey A. Kimbrel, Casandra Philipson, Katelyn McNair, Theron Hamilton, Robert A. Edwards, Brian Souza

Bioinform., 2019

PHANOTATE: a novel approach to gene identification in phage genomes.

Katelyn McNair, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, Robert A. Edwards

Bioinform., 2019

2018

Searching the Sequence Read Archive using Jetstream and Wrangler.

Kyle Levi, Mats Rynge, Eroma Abeysinghe, Robert A. Edwards

Proceedings of the Practice and Experience on Advanced Research Computing, 2018

2017

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive.

Pedro J. Torres, Robert A. Edwards, Katelyn McNair

Bioinform., 2017

PMAnalyzer: a new web interface for bacterial growth curve analysis.

Daniel Cuevas, Robert A. Edwards

Bioinform., 2017

2016

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards

Bioinform., 2016

2014

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

Ross A. Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce D. Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens

Nucleic Acids Res., 2014

2013

Combining de novo and reference-guided assembly with scaffold_builder.

Genivaldo Gueiros Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, Robert A. Edwards

Source Code Biol. Medicine, 2013

2012

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.

Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, Mya Breitbart

BMC Bioinform., 2012

Identification and removal of ribosomal RNA sequences from metatranscriptomes.

Robert Schmieder, Yan Wei Lim, Robert A. Edwards

Bioinform., 2012

PHACTS, a computational approach to classifying the lifestyle of phages.

Katelyn McNair, Barbara A. Bailey, Robert A. Edwards

Bioinform., 2012

Real Time Metagenomics: Using <i>k</i>-mers to annotate metagenomes.

Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek

Bioinform., 2012

Reference-independent comparative metagenomics using cross-assembly: crAss.

Bas E. Dutilh, Robert Schmieder, James Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John Mokili

Bioinform., 2012

2011

Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets.

Ramy K. Aziz, Bhakti Dwivedi, Mya Breitbart, Robert A. Edwards

BMC Bioinform., 2011

Quality control and preprocessing of metagenomic datasets.

Robert Schmieder, Robert A. Edwards

Bioinform., 2011

2010

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.

Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robert A. Edwards

BMC Bioinform., 2010

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

Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards

BMC Bioinform., 2010

2009

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes.

Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer

PLoS Comput. Biol., 2009

Deviations from Ultrametricity in Phage Protein Distances.

Chad Wagner, Anna Salamon, Robert A. Edwards, Forest Rohwer, Peter Salamon

Open Syst. Inf. Dyn., 2009

2008

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Folker Meyer, Daniel Paarmann, Mark D'Souza, Robert Olson, Elizabeth M. Glass, Michael Kubal, Tobias Paczian, Alexis A. Rodriguez, Rick Stevens, Andreas Wilke, Jared Wilkening, Robert A. Edwards

BMC Bioinform., 2008

2007

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, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens

Nucleic Acids Res., 2007

2006

An application of statistics to comparative metagenomics.

Beltran Rodriguez-Brito, Forest Rohwer, Robert A. Edwards

BMC Bioinform., 2006

Finding novel genes in bacterial communities isolated from the environment.

Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006