Robert A. Edwards

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 16

Top Topics

Functional Analysis

Escherichia Coli

Genomic Sequences

Generating High Quality

Top Venues

PLoS Comput. Biol.

Publications

Michael J. Roach, Bradley J. Hart, Sarah J. Beecroft, Bhavya Nalagampalli Papudeshi, Laura K. Inglis, Susanna R. Grigson, Vijini Mallawaarachchi, George Bouras, Robert A. Edwards
Koverage: Read-coverage analysis for massive (meta)genomics datasets. J. Open Source Softw. 9 (96) (2024)
Katelyn McNair, Peter Salamon, Robert A. Edwards, Anca M. Segall
PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes. BMC Bioinform. 25 (1) (2024)
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Hansheng Xue, Bhavya Nalagampalli Papudeshi, Susanna R. Grigson, George Bouras, Rosa E. Prahl, Anubhav Kaphle, Andrey Verich, Berenice Talamantes-Becerra, Elizabeth A. Dinsdale, Robert A. Edwards
Solving genomic puzzles: computational methods for metagenomic binning. Briefings Bioinform. 25 (5) (2024)
Peter Salamon, David Salamon, Vito Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall
Classification Confidence in Exploratory Learning: A User's Guide. Mach. Learn. Knowl. Extr. 5 (3) (2023)
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
Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinform. 39 (10) (2023)
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
Ten simple rules and a template for creating workflows-as-applications. PLoS Comput. Biol. 18 (12) (2022)
Peter Salamon, David Salamon, V. Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall
Estimating Classification Confidence Using Kernel Densities. CoRR (2022)
Susanna R. Grigson, Jody C. McKerral, James G. Mitchell, Robert A. Edwards
Organizing the bacterial annotation space with amino acid sequence embeddings. BMC Bioinform. 23 (1) (2022)
Felipe Hernandes Coutinho, Asier Zaragoza-Solas, Mario López-Pérez, Jakub Barylski, Andrzej Zielezinski, Bas E. Dutilh, Robert A. Edwards, Francisco Rodríguez-Valera
RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. Patterns 2 (7) (2021)
Vito Adrian Cantu, Peter Salamon, Victor Seguritan, Jackson Redfield, David Salamon, Robert A. Edwards, Anca M. Segall
PhANNs, a fast and accurate tool and web server to classify phage structural proteins. PLoS Comput. Biol. 16 (11) (2020)
Katelyn McNair, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, Robert A. Edwards
PHANOTATE: a novel approach to gene identification in phage genomes. Bioinform. 35 (22) (2019)
Carol L. Ecale Zhou, Stephanie Malfatti, Jeffrey A. Kimbrel, Casandra Philipson, Katelyn McNair, Theron Hamilton, Robert A. Edwards, Brian Souza
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates. Bioinform. 35 (21) (2019)
Kyle Levi, Mats Rynge, Eroma Abeysinghe, Robert A. Edwards
Searching the Sequence Read Archive using Jetstream and Wrangler. PEARC (2018)
Daniel Cuevas, Robert A. Edwards
PMAnalyzer: a new web interface for bacterial growth curve analysis. Bioinform. 33 (12) (2017)
Pedro J. Torres, Robert A. Edwards, Katelyn McNair
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive. Bioinform. 33 (15) (2017)
Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. Bioinform. 32 (3) (2016)
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
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42 (Database-Issue) (2014)
Genivaldo Gueiros Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, Robert A. Edwards
Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol. Medicine 8 (2013)
Katelyn McNair, Barbara A. Bailey, Robert A. Edwards
PHACTS, a computational approach to classifying the lifestyle of phages. Bioinform. 28 (5) (2012)
Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek
-mers to annotate metagenomes. Bioinform. 28 (24) (2012)
Robert Schmieder, Yan Wei Lim, Robert A. Edwards
Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinform. 28 (3) (2012)
Bas E. Dutilh, Robert Schmieder, James Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John Mokili
Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinform. 28 (24) (2012)
Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, Mya Breitbart
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. BMC Bioinform. 13 (2012)
Robert Schmieder, Robert A. Edwards
Quality control and preprocessing of metagenomic datasets. Bioinform. 27 (6) (2011)
Ramy K. Aziz, Bhakti Dwivedi, Mya Breitbart, Robert A. Edwards
Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets. BMC Bioinform. 12 (S-7) (2011)
Robert Schmieder, Yan Wei Lim, Forest Rohwer, Robert A. Edwards
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinform. 11 (2010)
Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards
Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinform. 11 (2010)
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
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. PLoS Comput. Biol. 5 (12) (2009)
Chad Wagner, Anna Salamon, Robert A. Edwards, Forest Rohwer, Peter Salamon
Deviations from Ultrametricity in Phage Protein Distances. Open Syst. Inf. Dyn. 16 (1) (2009)
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
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 9 (2008)
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
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35 (Database-Issue) (2007)
Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye
Finding novel genes in bacterial communities isolated from the environment. ISMB (Supplement of Bioinformatics) (2006)
Beltran Rodriguez-Brito, Forest Rohwer, Robert A. Edwards
An application of statistics to comparative metagenomics. BMC Bioinform. 7 (2006)