Publications by authors named "Robert Beiko"

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The case for microbiome stewardship: what it is and how to get there.
Mallory J Choudoir, Suzanne L Ishaq, Robert G Beiko, Diego S Silva, Emma Allen-Vercoe

mSystems· May 2025

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ParallelEvolCCM: Quantifying Coevolutionary Patterns Among Genomic Features.
Robert G Beiko, Chaoyue Liu, João Vitor Cavalcante, Ryan C Fink

Genome Biol Evol· May 2025

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Profiling lateral gene transfer events in the human microbiome using WAAFLE.
Tiffany Y Hsu, Etienne Nzabarushimana, Dennis Wong, Chengwei Luo, Robert G Beiko

Nat Microbiol· January 2025

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Plaseval: a framework for comparing and evaluating plasmid detection tools.
Aniket Mane, Haley Sanderson, Aaron P White, Rahat Zaheer, Robert Beiko

BMC Bioinformatics· November 2024

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Identification of key drivers of antimicrobial resistance in using machine learning.
Jee In Kim, Alexander Manuele, Finlay Maguire, Rahat Zaheer, Tim A McAllister, Robert G Beiko

Can J Microbiol· October 2024

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Mock microbial community meta-analysis using different trimming of amplicon read lengths.
Diana Haider, Michael W Hall, Julie LaRoche, Robert G Beiko

Environ Microbiol· January 2024

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Profiling novel lateral gene transfer events in the human microbiome.
Tiffany Y Hsu, Etienne Nzabarushimana, Dennis Wong, Chengwei Luo, Robert G Beiko

bioRxiv· August 2023

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The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.
Chaoyue Liu, Toby Kenney, Robert G Beiko, Hong Gu

Syst Biol· June 2023

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Correction: Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution.
Michael William Hall, Nimali Chandhema Wellappuli, Ruo Chen Huang, Kay Wu, David King Lam, Robert Gerald Beiko

ISME Commun· May 2023

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Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution.
Michael William Hall, Nimali Chandhema Wellappuli, Ruo Chen Huang, Kay Wu, David King Lam, Robert Gerald Beiko

ISME Commun· March 2023

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Compact and automated eDNA sampler for in situ monitoring of marine environments.
Andre Hendricks, Connor M Mackie, Edward Luy, Colin Sonnichsen, James Smith, Robert G Beiko

Sci Rep· March 2023

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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
Brian P Alcock, William Huynh, Romeo Chalil, Keaton W Smith, Amogelang R Raphenya, Robert G Beiko

Nucleic Acids Res· January 2023

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Genome-scale prediction of bacterial promoters.
Miria Bernardino, Robert Beiko

Biosystems· November 2022

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Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study.
Edgar Gulavi, Fridah Mwendwa, David O Atandi, Patricia O Okiro, Michael Hall, Robert G Beiko

BMC Microbiol· November 2022

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Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective.
Jee In Kim, Finlay Maguire, Kara K Tsang, Theodore Gouliouris, Sharon J Peacock, Robert G Beiko

Clin Microbiol Rev· September 2022

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Exploring the mobilome and resistome of in a One Health context across two continents.
Haley Sanderson, Kristen L Gray, Alexander Manuele, Finlay Maguire, Amjad Khan, Robert G Beiko

Microb Genom· September 2022

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deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes.
Ahmad Pesaranghader, Stan Matwin, Marina Sokolova, Jean-Christophe Grenier, Robert G Beiko

Bioinformatics· May 2022

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Identifying novel β-lactamase substrate activity through prediction of antimicrobial resistance.
Kara K Tsang, Finlay Maguire, Haley L Zubyk, Sommer Chou, Arman Edalatmand, Robert G Beiko

Microb Genom· January 2021

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Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.
Finlay Maguire, Baofeng Jia, Kristen L Gray, Wing Yin Venus Lau, Robert G Beiko

Microb Genom· October 2020

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PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.
Michael A Peabody, Wing Yin Venus Lau, Gemma R Hoad, Baofeng Jia, Finlay Maguire, Robert G Beiko

Bioinformatics· May 2020

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CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
Brian P Alcock, Amogelang R Raphenya, Tammy T Y Lau, Kara K Tsang, Mégane Bouchard, Robert G Beiko

Nucleic Acids Res· January 2020

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Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning.
Finlay Maguire, Muhammad Attiq Rehman, Catherine Carrillo, Moussa S Diarra, Robert G Beiko

mSystems· August 2019

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16S rRNA Gene Analysis with QIIME2.
Michael Hall, Robert G Beiko

Methods Mol Biol· July 2019

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Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt.
Gavin M Douglas, Robert G Beiko, Morgan G I Langille

Methods Mol Biol· July 2019

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RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data.
Praveen Nadukkalam Ravindran, Paul Bentzen, Ian R Bradbury, Robert G Beiko

Mol Ecol Resour· January 2019

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