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 (ISMB (Supplement of Bioinformatics), 2006)

An application of statistics to comparative metagenomics. - Beltran Rodriguez-Brito; Forest Rohwer; Robert A. Edwards (BMC Bioinform., 2006)

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; et al. (Nucleic Acids Res., 2007)

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)

Deviations from Ultrametricity in Phage Protein Distances. - Chad Wagner; Anna Salamon; Robert A. Edwards; Forest Rohwer; Peter Salamon (Open Syst. Inf. Dyn., 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; et al. (PLoS Comput. Biol., 2009)

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)

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)

Quality control and preprocessing of metagenomic datasets. - Robert Schmieder; Robert A. Edwards (Bioinform., 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)

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)

Real Time Metagenomics: Using k-mers to annotate metagenomes. - Robert A. Edwards; Robert Olson; Terry Disz; Gordon D. Pusch; Veronika Vonstein; Rick Stevens; Ross A. Overbeek (Bioinform., 2012)

PHACTS, a computational approach to classifying the lifestyle of phages. - Katelyn McNair; Barbara A. Bailey; Robert A. Edwards (Bioinform., 2012)

Identification and removal of ribosomal RNA sequences from metatranscriptomes. - Robert Schmieder; Yan Wei Lim; Robert A. Edwards (Bioinform., 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)

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)

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 002; Terry Disz; Robert A. Edwards; Svetlana Gerdes; Bruce D. Parrello; Maulik Shukla; Veronika Vonstein; Alice R. Wattam; et al. (Nucleic Acids Res., 2014)

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)

PMAnalyzer: a new web interface for bacterial growth curve analysis. - Daniel Cuevas; Robert A. Edwards (Bioinform., 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)

Searching the Sequence Read Archive using Jetstream and Wrangler. - Kyle Levi; Mats Rynge; Eroma Abeysinghe; Robert A. Edwards (PEARC, 2018)

PHANOTATE: a novel approach to gene identification in phage genomes. - Katelyn McNair; Carol Zhou; Elizabeth A. Dinsdale; Brian Souza; Robert A. Edwards (Bioinform., 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)

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., 2020)

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)

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)

Organizing the bacterial annotation space with amino acid sequence embeddings. - Susanna R. Grigson; Jody C. McKerral; James G. Mitchell; Robert A. Edwards (BMC Bioinform., 2022)

Ten simple rules and a template for creating workflows-as-applications. - Michael J. Roach 001; 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., 2022)

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., 2023)

Phables: from fragmented assemblies to high-quality bacteriophage genomes. - Vijini Mallawaarachchi; Michael J. Roach 001; 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., 2023)

Solving genomic puzzles: computational methods for metagenomic binning. - 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 (Briefings Bioinform., 2024)

Koverage: Read-coverage analysis for massive (meta)genomics datasets. - Michael J. Roach 001; Bradley J. Hart; Sarah J. Beecroft; Bhavya Nalagampalli Papudeshi; Laura K. Inglis; Susanna R. Grigson; Vijini Mallawaarachchi; George Bouras; Robert A. Edwards (J. Open Source Softw., 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., 2024)