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Robert A. Edwards

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2020 – today

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2024
[j30]
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  - journals/bib/MallawaarachchiWXPGBPKV24
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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)
[j29]
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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): 82 (2024)
[j28]
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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): 6235 (2024)
2023
[j27]
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  - journals/bioinformatics/MallawaarachchiRDPGGBHIH23
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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)
[j26]
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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): 803-829 (2023)
2022
[j25]
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  - journals/bmcbi/GrigsonMME22
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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): 385 (2022)
[j24]
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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): 1010705 (2022)
[i1]
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  - journals/corr/abs-2207-06529
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Peter Salamon, David Salamon, Vito Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall:
Estimating Classification Confidence Using Kernel Densities. CoRR abs/2207.06529 (2022)
2021
[j23]
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  - journals/patterns/CoutinhoZLBZDER21
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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): 100274 (2021)
2020
[j22]
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  - journals/ploscb/CantuSSRSES20
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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): 1007845 (2020)

2010 – 2019

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2019
[j21]
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  - journals/bioinformatics/ZhouMKPMHES19
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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): 4402-4404 (2019)
[j20]
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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): 4537-4542 (2019)
2018
[c2]
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  - conf/xsede/LeviRAE18
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Kyle Levi, Mats Rynge, Eroma Abeysinghe, Robert A. Edwards:
Searching the Sequence Read Archive using Jetstream and Wrangler. PEARC 2018: 50:1-50:7
2017
[j19]
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  - journals/bioinformatics/CuevasE17
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Daniel Cuevas, Robert A. Edwards:
PMAnalyzer: a new web interface for bacterial growth curve analysis. Bioinform. 33(12): 1905-1906 (2017)
[j18]
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  - journals/bioinformatics/TorresEM17
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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): 2389-2391 (2017)
2016
[j17]
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  - journals/bioinformatics/SilvaGDE16
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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): 354-361 (2016)
2014
[j16]
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  - journals/nar/OverbeekOPODDEGPSVWXS14
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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): 206-214 (2014)
2013
[j15]
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  - journals/scfbm/SilvaDMESDE13
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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: 23 (2013)
2012
[j14]
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  - journals/bioinformatics/SchmiederLE12
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Robert Schmieder, Yan Wei Lim, Robert A. Edwards:
Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinform. 28(3): 433-435 (2012)
[j13]
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Katelyn McNair, Barbara A. Bailey, Robert A. Edwards:
PHACTS, a computational approach to classifying the lifestyle of phages. Bioinform. 28(5): 614-618 (2012)
[j12]
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  - journals/bioinformatics/DutilhSNFSEM12
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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): 3225-3231 (2012)
[j11]
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  - journals/bioinformatics/EdwardsODPVSO12
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Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek:
Real Time Metagenomics: Using k-mers to annotate metagenomes. Bioinform. 28(24): 3316-3317 (2012)
[j10]
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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: 37 (2012)
2011
[j9]
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Robert Schmieder, Robert A. Edwards:
Quality control and preprocessing of metagenomic datasets. Bioinform. 27(6): 863-864 (2011)
[j8]
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  - journals/bmcbi/AzizDBE11
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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): A9 (2011)
2010
[j7]
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  - journals/bmcbi/DiszACOOVSE10
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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: 319 (2010)
[j6]
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  - journals/bmcbi/SchmiederLRE10
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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: 341 (2010)

2000 – 2009

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2009
[j5]
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  - journals/osid/WagnerSERS09
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Chad Wagner, Anna Salamon, Robert A. Edwards, Forest Rohwer, Peter Salamon:
Deviations from Ultrametricity in Phage Protein Distances. Open Syst. Inf. Dyn. 16(1): 75-84 (2009)
[j4]
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  - journals/ploscb/AnglyWPESVABCDDFHHHKMMMMMNRSWZZR09
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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)
2008
[j3]
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  - journals/bmcbi/MeyerPDOGKPRSWWE08
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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)
2007
[j2]
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  - journals/nar/McNeilRABCDEGHKMMMOOOPPPPRSVVZXZOS07
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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): 347-353 (2007)
2006
[j1]
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  - journals/bmcbi/Rodriguez-BritoRE06
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Beltran Rodriguez-Brito, Forest Rohwer, Robert A. Edwards:
An application of statistics to comparative metagenomics. BMC Bioinform. 7: 162 (2006)
[c1]
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  - conf/ismb/KrauseDBEPRMS06
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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: 281-289

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